Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.device.2024.100363

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Language：English   Publishing type：Research paper (scientific journal)  

Highly polar and charged molecules, such as oligonucleotides, face significant barriers in crossing the cell membrane to access the cytoplasm. To address this problem, we developed a light-triggered twistable tetraphenylethene (TPE) derivative, TPE-C-N, to facilitate the intracellular delivery of charged molecules through an endocytosis-independent pathway. The central double bond of TPE in TPE-C-N is planar in the ground state but becomes twisted in the excited state. Under light irradiation, this planar-to-twisted structural change induces continuous cell membrane disturbances. Such disturbance does not lead to permanent damage to the cell membrane. TPE-C-N significantly enhanced the intracellular delivery of negatively charged molecules under light irradiation when endocytosis was inhibited through low-temperature treatment, confirming the endocytosis-independent nature of this delivery method. We have successfully demonstrated that the TPE-C-N-mediated light-controllable method can efficiently promote the intracellular delivery of charged molecules, such as peptides and oligonucleotides, with molecular weights ranging from 1000 to 5000 Da.

DOI： 10.1039/d3tb02956e

PubMed

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Language：English   Publishing type：Research paper (scientific journal)  

Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.

DOI： 10.1016/j.bpc.2024.107204

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jcim.3c01611

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

We investigated ethanol-induced structural changes in liposomes on a time scale from microseconds to tens of seconds using a microfluidic-based small-angle X-ray scattering (SAXS) measurement system coupled with molecular dynamics (MD) simulations.

DOI： 10.1039/d3na01073b

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jpcb.3c05864

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.3c01016

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Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jctc.3c00733

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Language：English   Publishing type：Research paper (scientific journal)  

Boron neutron capture therapy (BNCT) is a promising modality for cancer treatment because of its minimal invasiveness. To maximize the therapeutic benefits of BNCT, the development of efficient platforms for the delivery of boron agents is indispensable. Here, we prepared carborane-integrated immunoliposomes via an exchanging reaction to achieve HER-2-targeted BNCT. The conjugation of an anti-HER-2 antibody to carborane-integrated liposomes successfully endowed these liposome with targeting properties toward HER-2-overexpressing human ovarian cancer cells (SK-OV3); the resulting BNCT activity toward SK-OV3 cells obtained using the current immunoliposomal system was 14-fold that of the l-BPA/fructose complex, which is a clinically available boron agent. Moreover, the growth of spheroids treated with our system followed by thermal neutron irradiation was significantly suppressed compared with treatment with the l-BPA/fructose complex.

DOI： 10.1002/chem.202302486

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Publishing type：Research paper (scientific journal)   Publisher：Japan Society for Bioscience, Biotechnology, and Agrochemistry  

DOI： 10.1271/kagakutoseibutsu.61.419

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.3c04285

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Here,we report the use of molecular dynamics simulationswitha polarizable force field to investigate Li-ion dynamics in sulfolane(SL)-based electrolytes. In SL-based highly concentrated electrolytes(HCEs) (e.g., SL/Li = 2:1), Li displays faster translational motionthan other components, which should be related to the structural anddynamical properties of SL. In HCEs, a transient conduction networkthat penetrated the simulation system was always observed. Rapid (<1ns) Li-ion hopping between adjacent coordination sites was observedthroughout the network. Additionally, SLs rotated in the same timeframewithout disrupting the conduction network. This rotation is believedto promote the hopping diffusion in the network. This was followedby a rotational relaxation of the SL dipole axis around the non-polarcyclohydrocarbon segment of SL (& SIM;3.3 ns), which involves areorganization of the network structure and an enhancement of thetranslational motion of the coordinating Li ions. The observed lifetimeof Li-SL coordination was longer (>11 ns). Hence, it wasconcludedthat the faster Li translational motion was obtained due to the fasterrotational relaxation time of SL rather than the lifetime of Li-SLbinding. The faster rotation of SL is related to its amphiphilic molecularstructure with compact non-polar segments. Transport properties, suchas the Onsager transport coefficients, ionic conductivity, and transferencenumber under anion-blocking conditions, were also analyzed to characterizethe features of the SL-based electrolyte.

DOI： 10.1021/acs.jpcc.3c02155

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The parameters of the polarizableforce field used formoleculardynamics simulations of Li diffusion in high-concentration lithiumbis(trifluoro-methanesulfonyl)-amide (Li[TFSA]) sulfone(sulfolane, dimethylsulfone, ethylmethylsulfone, and ethyl-i-propylsulfone) solutions were refined. The densities ofthe solutions obtained by molecular dynamics simulations reproducedwell the experimental values. The calculated concentration, temperature,and solvent dependencies of self-diffusion coefficients of ions andsolvents in the mixtures well reproduce the experimentally observeddependencies. Ab initio calculations show that theintermolecular interactions between Li ions and four sulfones arenot largely different. Conformational analyses show that sulfolanecan change the conformation more easily owing to lower barrier heightfor pseudorotation compared to the rotational barrier heights of diethylsulfoneand ethylmethylsulfone. Molecular dynamics simulations indicate thatthe easy conformation change of solvent affects the rotational relaxationof the solvent and the diffusion of Li ion in the mixture. The easyconformation change of sulfolane is one of the causes of faster diffusionof Li ion in the mixture of Li[TFSA] and sulfolane compared to themixtures of smaller dimethylsulfone and ethylmethylsulfone.

DOI： 10.1021/acs.jpcb.3c02009

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Publisher：American Chemical Society (ACS)  

Lipid nanoparticles (LNPs) are essential carrier particles in drug delivery systems, particularly in ribonucleic acid delivery. In preparing lipid-based nanoparticles, microfluidic-based ethanol injection may produce precisely size-controlled nanoparticles. Ethanol is critical in LNP formation and post-treatment processes and affects liposome size, structure, lamellarity, and drug-loading efficiency. However, the effects of time-dependent changes in the ethanol concentration on the structural dynamics of liposomes are not clearly understood. Herein, we investigated ethanol-induced structural changes in liposomes on a time scale from microseconds to tens of seconds using a microfluidic-based small-angle X-ray scattering (SAXS) measurement system coupled with molecular dynamics (MD) simulations. The time-resolved SAXS measurement system revealed that single unilamellar liposomes converted to multilamellar liposomes within 0.8 s of contact with ethanol, and the d-spacing was decreased from 6.1 (w/o ethanol) to 4.4 nm (80% ethanol) with increasing ethanol concentration. We conducted 1 µs MD simulations to understand the molecular-level structural changes in the liposomes. The MD simulations revealed that the changes in the lamellar structure caused by ethanol at the molecular level could explain the structural changes in the liposomes observed via time-resolved SAXS. Therefore, the post-treatment process to remove residual ethanol is critical in liposome formation.

DOI： 10.26434/chemrxiv-2023-6ldv7

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Localized high-concentration electrolytes (LHCEs), whichare mixturesof highly concentrated electrolytes (HCEs) and non-coordinating diluents,have attracted significant interest as promising liquid electrolytesfor next-generation Li secondary batteries, owing to their variousbeneficial properties both in the bulk and at the electrode/electrolyteinterface. We previously reported that the large Li+-iontransference number in sulfolane (SL)-based HCEs, attributed to theunique exchange/hopping-like Li+-ion conduction, decreasedupon dilution with the non-coordinating hydrofluoroether (HFE) despitethe retention of the local Li+-ion coordination structure.Therefore, in this study, we investigated the effects of HFE dilutionon the Li+ transference number and the solution structureof SL-based LHCEs via the analysis of dynamic ion correlations andmolecular dynamics simulations. The addition of HFE caused nano-segregationin the SL-based LHCEs to afford polar and nonpolar domains and fragmentationof the polar ion-conducting pathway into smaller clusters with increasingHFE content. Analysis of the dynamic ion correlations revealed thatthe anti-correlated Li+-Li+ motions weremore pronounced upon HFE addition, suggesting that the Li+ exchange/hopping conduction is obstructed by the non-ion-conductingHFE-rich domains. Thus, the HFE addition affects the entire solutionstructure and ion transport without significantly affecting the localLi(+)-ion coordination structure. Further studies on iontransport in LHCEs would help obtain a design principle for liquidelectrolytes with high ionic conductivity and large Li+-ion transference numbers.

DOI： 10.1021/acs.jpcc.3c02112

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.bios.2023.115318

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/chem.202203071

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.3c00389

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

The elucidation of the factors determining liquid structures and transport properties of ionic liquids is important for the design and development of ionic liquid electrolytes. This personal account introduces the importance of computational methods for studying ionic liquids. Molecular dynamics simulations provide detailed information on liquid structures of ionic liquid such as the structures of solvated cation complexes in equimolar mixtures of glymes and Li[TFSA] and the effects of the charges of electrode on liquid structure near the electrode. Ab initio calculations reveal that the magnitude of the attraction between ions and conformational flexibility ions play important roles in determining transport properties of ionic liquids. First principle molecular dynamics simulations elucidate why solvated cation complex is stable in the equimolar mixtures, although the Li+-[TFSA](-) interaction is greater than Li+-glyme interaction.

DOI： 10.1002/tcr.202200272

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Language：English   Publishing type：Research paper (scientific journal)  

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1002/chem.202203071

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulations with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. An elastic network model was adopted to maintain the secondary structure within a single chain. The side-chain analogues reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable association free energy (potential of mean force) in water compared to those from AA MD. A series of peptides/proteins adsorbed onto or penetrated into the membrane simulated by the CG MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins as comparable to those in the orientations of proteins in membranes (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated the good performance of the SPICA FF.

DOI： 10.1021/acs.jctc.1c01207

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.

DOI： 10.1016/j.bbamem.2022.183955

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry ({RSC})  

DOI： 10.1039/D2CP01348G

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.macromol.1c00762

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Informa {UK} Limited  

DOI： 10.1080/00268976.2021.1910355

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Publishing type：Research paper (scientific journal)  

DOI： 10.1063/5.0065765

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcb.1c01148

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.macromol.0c02398

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry ({RSC})  

DOI： 10.1039/D0CP04898D

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Publishing type：Research paper (international conference proceedings)  

Driven by the importance of urinary cell-free DNA (cfDNA) as cancer biomarkers, the effectiveness of cfDNA isolation from body fluids can impact clinical usability, especially for molecular diagnostic. However, cfDNA isolations are currently hampered by the dilution of small fragmented cfDNA in body fluids. In this work, we report the unique properties of nanowires assisting the isolation of urinary cfDNA based on specific chemical interactions, maximizing the effectiveness of the platform that could never be achieved with the conventional methods.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

The authors propose a novel method to evaluate the position-dependent diffusion constant by analyzing unperturbed segments of a trajectory determined by the additional flat-bottom potential. The accuracy of this novel method is first established by studying homogeneous systems, where the reference value can be obtained by the Einstein relation. The applicability of this new method to heterogeneous systems is then demonstrated by studying a hydrophobic solute near a hydrophobic wall. The proposed method is also comprehensively compared with popular conventional methods, whereby the significance of the present method is illustrated. The novel method is powerful and useful for studying kinetics in heterogeneous systems based on molecular dynamics calculations.

DOI： 10.1021/acs.jctc.0c00448

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Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

DOI： 10.1101/2020.10.27.357079

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

Diphytanoylphosphatidylcholine (DPhPC) is a synthetic phospholipid in which two methyl-branched acyl chains are introduced into the glycerol moiety, mimicking phospholipids of eukaryotic and eubacterial origins. The lipid bilayers of DPhPC reproduce the outstanding physical properties of methyl-branched lipids that occur in archaeal membranes. DPhPC is commonly used as the base lipid in biophysical experiments, particularly for recording ion-channel currents. However, the dynamics of lipid molecules that induces their useful physical properties is still unclear. In this study, we examined the conformation and orientation of the methyl-branched acyl chain of DPhPC in a membrane using 2H nuclear magnetic resonance (NMR) measurements of the synthetic lipid with a high stereochemical purity and molecular dynamics (MD) simulations. Deuterium-labeled 3',3'-CD3,D-DPhPC (2) and 7',7'-CD3,D-DPhPC (3) showed the characteristic quadrupole splitting width in the 2H NMR spectra, which corresponded to the bent orientation reported for the archaeal lipid PGP-Me [Yamagami, M., et al. (2019) Biochemistry58, 3869-3879]. However, MD simulations, which reproduced the 2H NMR results well, unveiled the unknown features of DPhPC in the membrane; DPhPC has a chain-specific average orientation, where two bent orientations with upward and downward methyl groups occur at positions C3 and C7 of the sn-1 and sn-2 chains of DPhPC, respectively. These MD and NMR results reveal that these two bent orientations define the average orientation of DPhPC for the shallow part of the acyl chains, which is considered to be an important factor in the stability of DPhPC membranes.

DOI： 10.1021/acs.biochem.0c00589

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcc.0c03485

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

The asymmetric lipid composition in plasma membranes within the inner leaflet is not typically suitable for domain formation. Thus elucidation of the likelihood of the formation or stability of a raft-like domain in the inner leaflet is necessary. Herein we investigated the phase behavior of asymmetric membranes using coarse-grained molecular dynamics simulations. The lipid leaflet comprising dioleoylphosphatidylcholine (DOPC) and cholesterol (Chol) does not typically show well-developed domains in symmetric bilayer membranes; however, it does separate into liquid ordered (Lo) and liquid disordered (Ld) phases when the opposing leaflet containing sphingomyelin (SM), DOPC, and Chol demonstrates domain formation. We determine that interdigitated acyl chains modulated the partitioning of Chol in the opposing leaflet, resulting in phase separation. Similarly, the acyl chain length of SM within the opposing leaflet affected the phase behavior of the leaflet. Our results reveal the crucial role of interdigitation in determining the phase status in asymmetric membranes.

DOI： 10.1021/acs.jpclett.0c01317

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/batt.201900197

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/batt.201900197

Publishing type：Research paper (scientific journal)  

DOI： 10.1063/5.0007957

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcb.0c01972

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Publishing type：Research paper (scientific journal)  

DOI： 10.3390/polym12020447

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jctc.9b00946

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Publishing type：Research paper (scientific journal)  

©2020 IUPAC & De Gruyter. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. For more information, please visit: http://creativecommons.org/licenses/by-nc-nd/4.0/ 2020. Entecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two-and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-Atomistic molecular dynamic (MD) calculations. A free energy minimum of-19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum,-4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.

DOI： 10.1515/pac-2020-0109

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry ({RSC})  

DOI： 10.1039/C9SM02165E

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.biochem.9b00835

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jcim.9b01010

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.langmuir.9b02656

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Language：English   Publishing type：Research paper (scientific journal)  

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Publishing type：Research paper (scientific journal)  

DOI： 10.1063/1.5123983

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.polymer.2019.121766

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jcim.9b00480

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.biochem.9b00469

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.polymer.2019.121570

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcc.9b05502

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.langmuir.9b01607

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.langmuir.9b01199

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Understanding the molecular mechanism underlying pore formation in lipid membranes by antimicrobial peptides is of great importance in biological sciences as well as in drug design applications. Melittin has been widely studied as a pore forming peptide, though the molecular mechanism for pore formation is still illusive. We examined the free energy barrier for the creation of a pore in lipid membranes with and without multiple melittin peptides. It was found that six melittin peptides significantly stabilized a pore, though a small barrier (a few kBT) for the formation still existed. With five melittin peptides or fewer, the pore formation barrier was much higher, though the established pore was in a local energy minimum. Although seven melittins effectively reduced the free energy barrier, a single melittin peptide left the pore after a long time MD simulation probably because of the overcrowded environment around the bilayer pore. Thus, it is highly selective for the number of melittin peptides to stabilize the membrane pore, as was also suggested by the line tension evaluations. The free energy cost required to insert a single melittin into the membrane is too high to explain the one-by-one insertion mechanism for pore formation, which also supports the collective melittin mechanism for pore formation.

DOI： 10.1016/j.bbamem.2019.03.002

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.bpj.2019.06.019

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Publishing type：Research paper (scientific journal)   Publisher：{AIP} Publishing  

DOI： 10.1063/1.5092229

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.polymer.2019.03.006

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jctc.8b00987

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcb.8b09439

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Publishing type：Research paper (scientific journal)   Publisher：{AIP} Publishing  

DOI： 10.1063/1.5009814

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society  

Around 270 million individuals currently live with hepatitis B virus (HBV) infection. Heteroaryldihydropyrimidines (HAPs) are a family of antivirals that target the HBV capsid protein and induce aberrant self-assembly. The capsids formed resemble the native capsid structure but are unable to propagate the virus progeny because of a lack of RNA/DNA. Under normal conditions, self-assembly is initiated by the viral genome. The mode of action of HAPs, however, remains largely unknown. In this work, using molecular dynamics simulations, we attempted to understand the action of HAP by comparing the dynamics of capsid proteins with and without HAPs. We found that the inhibitor is more stable in higher oligomers. It retains its stability in the hexamer throughout 1 μs of simulation. Our results also show that the inhibitor might help in stabilizing the C-terminus, the HBc 149-183 arginine-rich domain of the capsid protein. The C-termini of dimers interact with each other, assisted by the HAP inhibitor. During capsid assembly, the termini are supposed to directly interact with the viral genome, thereby suggesting that the viral genome might work in a similar way to stabilize the capsid protein. Our results may help in understanding the underlying molecular mechanism of HBV capsid self-assembly, which should be crucial for exploring new drug targets and structure-based drug design.

DOI： 10.1021/acs.jcim.7b00471

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society  

We describe here the electrochemical properties and battery performance of polymer electrolytes composed of ABA-triblock copolymers and Li-glyme solvate ionic liquids (SILs), which consist of the [Li(glyme)]+ complex cation and bis(trifluoromethanesulfoly)amide ([TFSA]-) anion, to simultaneously achieve high ionic conductivity, thermal stability, and a wide potential window. Three different block copolymers, consisting of a SIL-incompatible A segment (polystyrene, PSt) and SIL-compatible B segments (poly(methyl methacrylate) (PMMA), poly(ethylene oxide) (PEO), and poly(butyl acrylate) (PBA)) were synthesized. The SILs were solidified with the copolymers through physical cross-linking by the self-assembly of the PSt segment. The thermal and electrochemical properties of the polymer electrolytes were significantly affected by the stability of the [Li(glyme)]+ complex in the block copolymer B segments, and the preservation of the SILs contributed to their thermal stabilities and oxidation stabilities greater than 4 V vs Li/Li+. Pulsed-field gradient spin-echo nuclear magnetic resonance measurements of the polymer electrolytes and molecular dynamics simulation indicate that the [Li(glyme)]+ complex cation is unstable in the PEO matrix because of the competitive coordination of the PEO chain and glyme with Li+. On the other hand, the complex structure of [Li(glyme)]+ is stable in the PMMA- and PBA-based polymer electrolytes because of the weak interaction between Li+ and the polymer chains. By use of the PMMA- and PBA-based polymer electrolytes, 4-V class Li batteries with a LiCoO2 cathode and a Li metal anode could be operated stably at 60 °C
in contrast, this was not possible using the PEO-based electrolyte.

DOI： 10.1021/acs.chemmater.7b04274

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DOI： 10.1016/j.cplett.2018.07.011

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Other Link： http://orcid.org/0000-0002-3388-9227

Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.polymer.2018.05.033

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Mechanical deformation has been proposed to influence the proton conduction of perfluorosulfonic acid (PFSA) polymer membranes. We conducted a series of all-atom molecular dynamics simulations to understand how stretching affects the structural and dynamic properties of hydrated membranes composed of different equivalent weights (EWs) of PFSA at different water contents. The simulations reveal that the Young's modulus and yield stress of the membrane decreases with increasing water content, which is qualitatively in good agreement with experimental observations. When the PFSA membrane was stretched along a particular axis, the ionomer backbone chains became extended along the stretching direction and were aligned parallel to each other. The elongation of the ionomer backbone enhances hydronium ion diffusivity in the stretching direction at low water content. However, at high water content, the side chains orient themselves perpendicularly to the stretching direction in order to associate with free hydronium ions; this results in lower hydronium ion mobility. Furthermore, the higher EW PFSA is better aligned along the direction of stretching than the lower EW PFSA. The effect of stretching on proton transport is more pronounced in the higher EW PFSA membrane.

DOI： 10.1021/acs.jpcc.7b05719

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes. (C) 2017 Author(s).

DOI： 10.1063/1.4986287

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybrid hydrogenated-fluorinated JDs are reported to coassemble by film hydration at specific ratios into an unprecedented class of supramolecular Janus particles (JPs) denoted Janus dendrimersomes (JDSs). They consist of a dumbbell-shaped structure composed of an onion-like hydrogenated vesicle and an onion-like fluorinated vesicle tethered together. The synthesis of dye-tagged analogs of each JD component enabled characterization of JDS architectures with confocal fluorescence microscopy. Additionally, a simple injection method was used to prepare sub-micron JDSs, which were imaged with cryogenic transmission electron microscopy (cryo-TEM). As reported previously, different ratios of the same three-component system yielded a variety of structures including homogenous onion-like vesicles, core-shell structures, and completely self-sorted hydrogenated and fluorinated vesicles. Taken together with the JDSs reported herein, a self-sorting pathway is revealed as a function of the relative concentration of the hybrid JD, which may serve to stabilize the interface between hydrogenated and fluorinated bilayers. The fission-like pathway suggests the possibility of fusion and fission processes in biological systems that do not require the assistance of proteins but instead may result from alterations in the ratios of membrane composition.

DOI： 10.1073/pnas.1708380114

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

The interactions of glymes with alkali or alkaline earth metal cations depend strongly on the metal cations. For example, the stabilization energies (E-form) calculated for the formation of cation-triglyme (G3) complexes with Li+, Na+, K+, Mg2+, and Ca2+ at the MP2/6-311G** level were -95.6, -66.4, -52.5, -255.0, and -185.0 kcal mol(-1), respectively, and those for the cation-tetraglyme (G4) complexes were -107.7, -76.3, -60.9, -288.3 and -215.0 kcal mol(-1), respectively. The electrostatic and induction interactions are the major source of the attraction in the complexes; the contribution of the induction interactions to the attraction is especially significant in the divalent cationglyme complexes. The binding energies of the cation-G3 complexes with Li+, Na+, K+, Mg2+, and Ca2+ and the bis(trifluoromethylsulfonyl)amide anion ([TFSA](-)) were -83.9, -86.6, -80.0, -196.1, and -189.5 kcal mol(-1), respectively, and they are larger than the binding energies of the corresponding cation-G4 complexes (-73.6, -75.0, -77.4, -172.1, and -177.2 kcal mol(-1), respectively). The binding energies and conformational flexibility of the cation-glyme complexes also affect the melting points of equimolar mixtures of glyme and TFSA salts. Furthermore, the interactions of the metal cations with the oxygen atoms of glymes significantly decrease the HOMO energy levels of glymes. The HOMO energy levels of glymes in the cation-glyme-TFSA complexes are lower than those of isolated glymes, although they are higher than those of the cation-glyme complexes.

DOI： 10.1039/c7cp02779f

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Many morphological models have been proposed to describe the water swelling behavior and proton transport mechanism of perfluorosulfonic acid (PFSA) polymer membranes through experimental and modeling studies. However, the ongoing structural debate has not been completely resolved yet. We here conducted a series of all-atom molecular dynamics simulations of hydrated PFSA membranes to evaluate changes in the membrane morphology at different water contents. We found a similar dependence of the morphology on the water content between PFSA membranes with equivalent weight (EW) of 844 and 1144 g/equiv. That is, the morphology of the aqueous domain changes with increasing water content from a channel-network structure to a tortuous layered structure, and once attaining the tortuous layered structure, the water layer just thickened gradually by further increasing water content. Furthermore, we found more heterogeneous water domains in the higher-EW PFSA membrane, demonstrating the stronger aggregation behavior of the aqueous domains in the high-EW membranes. The variation of the PFSA membrane morphology observed here is useful to understand the proton transport mechanism and design new materials suitable for polymer electrolyte fuel cells in the near future.

DOI： 10.1021/acs.jpcc.6b08015

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Rog. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbamem.2016.03.032

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The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion. (C) 2015 AIP Publishing LLC.

DOI： 10.1063/1.4933087

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The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

DOI： 10.1063/1.4937153

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An accurate and efficient algorithm for calculating the 3D pressure field has been developed and implemented in the open-source molecular dynamics package, LAMMPS. Additionally, an algorithm to compute the pressure profile along the radial direction in spherical coordinates has also been implemented. The latter is particularly useful for systems showing a spherical symmetry such as micelles and vesicles. These methods yield precise pressure fields based on the Irving-Kirkwood contour integration and are particularly useful for biomolecular force fields. The present methods are applied to several systems including a buckled membrane and a vesicle.
Program summary
Program title: Compute stress spatial
Catalogue identifier: AEVH_v1_0
Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEVH_v1_0.html
Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 7799
No. of bytes in distributed program, including test data, etc.: 149739
Distribution format: tar.gz
Programming language: C++.
Computer: All.
Operating system: All.
Supplementary material: The input and expected output for the examples given in the manuscript can be downloaded here.
Classification: 7.7.
Nature of problem:
A precise calculation of the pressure (stress) field requires the implementation of the contour integration [2] for each pair in the cluster potentials.
Solution method:
We have implemented the method for calculating the local-volume average of the pressure field expressed by a contour integration with a delta function for the given molecular configuration obtained by molecular dynamics simulation [3].
Restrictions:
Because the definition of pressure field is based on the contour integration, the long-range interactions represented as Ewald summation are not included. In addition, the potential represented as a combination of pair and angle potential, such as Tersoff and Stillinger-Weber potential, and the interaction as a geometric constraint (shake, rigid body, etc.) are not available for current version.
Running time:
The examples provided take between 3 and 6 min each to run.
References:
[1] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys. 117 (1995) 1-19.
[2] P. Schofield and J.R. Henderson, Proc. R. Soc. Loud. A. 379 (1982) 231.
[3] T. Nakamura, W. Shinoda, and T. Ikeshoji, J. Chem. Phys. 135 (2011) 094106. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cpc.2014.11.017

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

Molecular dynamics simulations of equimolar mixtures of glymes (triglyme and tetraglyme) and Li[TFSA] (lithium bis(trifluoromethylsulfonyl) amide) show that the glyme chain length affects the coordination geometries of Li+, which induces the changes in interactions between the [Li(glyme)](+) complex and [TFSA](-) anions and diffusion of ions in the equimolar mixtures.

DOI： 10.1039/c4cp04718d

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The incorporation of neutral [70]fullerenes (C-70) led to bicelle formation in a relatively low lipid concentration range from neutral lipid mixtures (DMPC/DHPC). Furthermore, C70 addition resulted in the formation of large bicelles with a radius of ca. 100 nm, in contrast to C70-free bicelles that were formed from anionic lipid mixtures (DMPC/DHPC/DMPG). The stabilization of these bicelles was attributed to C-70 incorporation into the membranes.

DOI： 10.1021/la503732q

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Using a supramolecular approach, water-soluble fullerenes were developed to increase the applicability of fullerenes in aqueous environments. gamma-Cyclodextrin bicapped fullerene (C-60 center dot gamma-CD) complex was proposed as one of the strong candidates to show high solubility and stability in aqueous solution. In this work, a series of free energy simulations of C-60 center dot gamma-CD complex in both water and aqueous DMSO solution has been carried out to understand the effect of solvents on the thermodynamic stability of the complex. A high stability of the complex was observed in these solvents, although the stability was slightly reduced by the addition of DMSO to aqueous solution. The reduced stability in DMSO was illuminated by the change of complex structure, as well as solvation structure. The two-dimensional free energy map for the dissociation of the C-60 center dot gamma-CD complex elucidated a possible pathway for a dissociation of single gamma-CD from the C-60 center dot gamma-CD complex. The information obtained on the molecular viewpoint might be useful to design a new stable water-soluble complex based on fullerene derivatives.

DOI： 10.1021/jp5029905

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WALTER DE GRUYTER GMBH  

A series of molecular dynamics (MD) simulations has been undertaken to investigate the effective interaction between vesicles including PC (phosphatidylcholine) and PE (phosphatidylethanolamine) lipids using the Shinoda-DeVane-Klein coarse-grained force field. No signatures of fusion were detected during MD simulations employing two apposed unilamellar vesicles, each composed of 1512 lipid molecules. Association free energy of the two stable vesicles depends on the lipid composition. The two PC vesicles exhibit a purely repulsive interaction with each other, whereas two PE vesicles show a free energy gain at the contact. A mixed PC/PE (1: 1) vesicle shows a higher flexibility having a lower energy barrier on the deformation, which is caused by lipid sorting within each leaflet of the membranes. With a preformed channel or stalk between proximal membranes, PE molecules contribute to stabilize the stalk. The results suggest that the lipid components forming the membrane with a negative spontaneous curvature contribute to stabilize the stalk between two vesicles in contact.

DOI： 10.1515/pac-2014-5023

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The free energy profile of the stalk model of membrane fusion has been calculated using coarse-grained molecular dynamics simulations. The proposed method guides the lipid configuration using a guiding wall potential to make the transition from two apposed membranes to a stalk and a fusion pore. The free energy profile is obtained with a thermodynamic integration scheme using the mean force working on the guiding wall as a response of the system. We applied the method to two apposed flat bilayers composed of dioleoyl phosphatidylethanolamine/dioleoyl phosphatidylcholine expanding over the simulation box under the periodic boundary conditions. The two transition states are identified as pre-stalk and pre-pore states. The free energy barrier for the latter is confirmed to be in good agreement with that estimated by the pulling method. The present method provides a practical way to calculate the free energy profile along the stalk mechanism.

DOI： 10.1039/c3sm52344f

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We have demonstrated that C60 derivatives bearing a pyrrolidine moiety as well as a variety of other substituents can form 1:2 complexes with γ-cyclodextrin (γ-CDx) using a mechanochemical high-speed vibration milling apparatus. When the influence of the steric hindrance of the substituents on the formation of the complexes was negligible, the water-solubilities of the complexes were shown experimentally to be completely dependent on the hydrophobic properties of the substituent. Furthermore, the stabilities of the γ-CDx-complexes of several different C60 derivatives were found to be similar to or slightly higher than that of the C60·γ-CDx complex, with the solubilities of the complexes showing no correlation to the stabilities. Based on the results of a series of theoretical investigations, we have shown that the stabilities of the γ-CDx-complexes can be affected not only by steric effects but also by the polarities of the substituent groups, which exist in the vicinity of the upper rim of γ-CDx, because the water bound to the polar group can assist in the stabilisation of the complexes. © 2013 The Royal Society of Chemistry.

DOI： 10.1039/c3ob41513a

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The stabilization energies for the formation (Eform) of 11 ion pairs of protic and aprotic ionic liquids were studied by MP2/6-311G ** level ab initio calculations to elucidate the difference between the interactions of ions in protic ionic liquids and those in aprotic ionic liquids. The interactions in the ion pairs of protic ionic liquids (diethylmethylammonium dema and dimethylpropylammonium dmpa based ionic liquids) are stronger than those of aprotic ionic liquids (ethyltrimethylammonium etma based ionic liquids). The Eform for the demaCF3SO3 and dmpaCF3SO3 complexes (-95.6 and -96.4 kcal/mol, respectively) are significantly larger (more negative) than that for the etmaCF3SO3 complex (-81.0 kcal/mol). The same trend was observed for the calculations of ion pairs of the three cations with the Cl-, BF4-, TFSA - anions. The anion has contact with the N-H bond of the dema + or dmpa+ cations in the most stable geometries of the dema+ and dmpa+ complexes. The optimized geometries, in which the anions locate on the counter side of the cations, are 11.0-18.0 kcal/mol less stable, which shows that the interactions in the ions pairs of protic ionic liquids have strong directionality. The Eform for the less stable geometries for the dema+ and dmpa+ complexes are close to those for the most stable etma+ complexes. The electrostatic interaction, which is the major source of the attraction in the ion pairs, is responsible for the directionality of the interactions and determining the magnitude of the interaction energy. Molecular dynamic simulations of the demaTFSA and dmpaTFSA ionic liquids show that the N-H bonds of the cations have contact with the negatively charged (oxygen and nitrogen) atoms of TFSA- anion, while the strong directionality of the interactions was not suggested from the simulation of the etma CF 3SO3 ionic liquid. © 2013 AIP Publishing LLC.

DOI： 10.1063/1.4827519

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The stabilization energies (ΔEform) calculated for the formation of the Li+ complexes with mono-, di- tri- and tetra-glyme (G1, G2, G3 and G4) at the MP2/6-311G* level were -61.0, -79.5, -95.6 and -107.7 kcal mol-1, respectively. The electrostatic and induction interactions are the major sources of the attraction in the complexes. Although the ΔEform increases by the increase of the number of the O⋯Li contact, the ΔEform per oxygen atom decreases. The negative charge on the oxygen atom that has contact with the Li+ weakens the attractive electrostatic and induction interactions of other oxygen atoms with the Li+. The binding energies calculated for the [Li(glyme)]+ complexes with TFSA- anion (glyme=G1, G2, G3, and G4) were -106.5, -93.7, -82.8, and -70.0 kcal mol-1, respectively. The binding energies for the complexes are significantly smaller than that for the Li+ with the TFSA- anion. The binding energy decreases by the increase of the glyme chain length. The weak attraction between the [Li(glyme)]+ complex (glyme=G3 and G4) and TFSA - anion is one of the causes of the fast diffusion of the [Li(glyme)]+ complex in the mixture of the glyme and the Li salt in spite of the large size of the [Li(glyme)]+ complex. The HOMO energy level of glyme in the [Li(glyme)]+ complex is significantly lower than that of isolated glyme, which shows that the interaction of the Li + with the oxygen atoms of glyme increases the oxidative stability of the glyme. The interactions in Li+-glymes-TFSA- complexes: The interactions of Li+ with glymes (tri- and tetra-glyme) are strong (-96 and -108 kcal mol-1), while the interactions of the [Li(glyme)]+ complexes with TFSA- (-82 and -70 kcal mol-1) are weaker than that between Li+ and TFSA - (-137 kcal mol-1). Copyright © 2013 WILEY-VCH Verlag GmbH &amp
Co. KGaA, Weinheim.

DOI： 10.1002/cphc.201200843

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The three different regioisomers of bis-N-methylfulleropyrrolidines have been separated by controlling the relative amounts of γ-cyclodextrin and dimethyl sulfoxide (DMSO) contained in solutions of these compounds. When a small amount of γ-CDx was used in a mechanochemical high-speed vibration milling apparatus, the trans-1 and trans-2•γ-CDx complexes were separated from the trans-3•γ-CDx complex. In contrast, trans-3 was extracted in a relatively high ratio with an excess of γ-CDx. The addition of DMSO to aqueous solutions of the fullerene derivative•γ-CDx complexes allowed for the three regioisomers to be obtained in high purity (&gt
95%). The basis for the observed regioselective separation was a competition between the relative stabilities and solubilities of the complexes in the water and water-DMSO solvents. The stabilities of the complexes in water were assessed by the number of hydrogen bonding interactions between the two γ-CDx units using molecular dynamics simulations. To the best of our knowledge, this is the first reported example of the isolation of the different regioisomers of fullerene derivatives using host-guest complexes. © 2013 American Chemical Society.

DOI： 10.1021/jo3027609

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A numerical method is proposed for evaluating the curvature dependency of elastic parameters of a spherical vesicle based on a calculation of the pressure profile across the membrane. The proposed method is particularly useful for small unilamellar vesicles (SUVs), in which the internal structure of the membrane is asymmetric owing to the high curvature. In this case, the elastic energy is insufficiently described as a perturbation from a planar membrane. The calculated saddle-splay curvature modulus of SUVs, which is about 16 nm in diameter, is found to be much higher than that of a planar membrane. A comparison of the free energy change in the initial stage of vesicle-to-bicelle transformation with the Fromherz theory demonstrates that the elastic parameters estimated for SUVs provide better estimation of the free energy than those estimated for a planar membrane. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4795579]

DOI： 10.1063/1.4795579

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

Poly(ethylene glycol) (PEG) and various zwitterionic species are now used routinely as components in soft biomaterials. The study of mixtures composed of PEGylated-lipids with zwitterionic lipids provides an excellent opportunity to understand molecular interactions in such systems. To this end, we examine the liposome/bicelle/micelle phase behavior of such mixtures in bulk solution and as monolayers at the air-water interface, utilizing a coarse-grained molecular-dynamics (CG-MD) approach rooted in experimental parameters that inform the nature of the short-range interactions. Specifically, we examine mixtures of PEGylated lipid and dimyristoylphosphatidylcholine (DMPC) lipid monolayers and find the standard force fields yield calculated surface tensions in agreement with experiment. Long-time CG-MD simulations (similar to 0.5 microsecond) of the self-assembly for different concentrations of PEG indicate the critical micellar size for the aggregate to form a bicelle from a spherical micellar nucleus. At lower PEG concentrations we find self-assembly of the PEGylated lipid into a liposome coexisting with a mixture of smaller bicelles. Examination of large individual bicelles (1000 lipids) at increasing concentrations of PEG indicates that the degree of PEG de-mixing towards the outer radius of the bicelle is correlated with the overall concentration of PEG in the bicelle. The CG-MD approach used herein should be a useful complement to experimental studies designed to probe solute (drug) interactions with such membrane systems.

DOI： 10.1039/c3sm52290c

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A new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that accounts for thermal fluctuations of the membrane surface. The method has been successfully applied to a dimyristoyl phosphatidylcholine bilayer simulated with a coarse-grained model. A well-converged bending rigidity was obtained for the tension-free membrane and showed reasonable agreement with that obtained from the height fluctuation spectrum. © 2013 AIP Publishing LLC.

DOI： 10.1063/1.4811677

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Language：English   Publishing type：Part of collection (book)   Publisher：SPRINGER INT PUBLISHING AG  

Amphiphilic polymers have the ability to self-assemble into supramolecular structures of great complexity and utility. Nowadays, molecular dynamics simulations can be employed to investigate the self-assembly of modestly sized natural and synthetic macromolecules into structures, such as micelles, worms ( cylindrical micelles), or vesicles composed of membrane bilayers organized as single or multilamellar structures. This article presents a perspective on the use of large-scale computer simulation studies that have been used to understand the formation of such structures and their interaction with nanoscale solutes. Advances in this domain of research have been possible due to relentless progress in computer power plus the development of so-called coarse-grained intermolecular interaction models that encode the basic architecture of the amphiphilic macromolecules of interest.

DOI： 10.1007/12_2013_262

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Functionalized single-walled carbon nanotubes (SWNTs) are widely applied in biomedical science. To understand the interaction between SWNTs and biological systems, various studies have attempted to use coarsegrained molecular dynamics (CGMD). However, there is limited validation of the existing CG models of SWNTs. Here, we present CG models for both pristine and carboxylated SVVNTs which are validated against experimental dispersion data. In addition, we present the first ever DLVO analysis of the colloidal stability of parallel SWNTs and establish that the solvent-induced repulsion between fullerenes, which is not considered in DLVO theory, is crucial to obtain a correct physical picture of SWNT dispersibility. The results presented here provide physical insight into the colloidal stability of SWNTs and can be applied to large-scale MD studies of biological systems.

DOI： 10.1021/jp307545m

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The physical stability of catanionic vesicles is important for the development of novel drug or DNA carriers. For investigating the mechanism by which catanionic vesicles are stabilized, molecular dynamics (MD) simulation is an attractive approach that provides microscopic structural information on the vesicular bilayer. In this study, MD simulation was applied to investigate the bilayer properties of catanionic vesicles composed of an ion pair amphiphile (IPA), hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS), and a double-tailed cationic surfactant, ditetradecyldimethylammonium chloride (DTDAC). Structural information regarding membrane elasticity and the organization and conformation of surfactant molecules was obtained based on the resulting trajectory. Simulation results showed that a proper amount of DTDAC could be used to complement the asymmetric structure between HTMA and DS, resulting in an ordered hydrocarbon chain packing within the rigid membrane observed in the mixed HTMA-DS/DTDAC system. The coexistence of gel and fluid phases was also observed in the presence of excess DTDAC. MD simulation results agreed well with results obtained from experimental studies examining mixed HTMA-DS/DTDAB vesicles.

DOI： 10.1021/la300651u

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CURRENT BIOLOGY LTD  

Coarse-grained (CG) molecular models are now widely used to understand the structure and functionality of macromolecular self-assembling systems. In the last few years, significant efforts have been devoted to construct quantitative CG models based on data from molecular dynamics (MD) simulations with more detailed all-atom (AA) intermolecular force fields as well as experimental thermodynamic data. We review some of the recent progress pertaining to the MD simulation of self-assembling macromolecular systems, using as illustrations the application of CG models to probe surfactant and lipid self-assembly including liposome and dendrimersome formation as well as the interaction of biomembranes with nanoparticles.

DOI： 10.1016/j.sbi.2012.01.011

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Many unusual phenomena in surfactant solutions below the critical micelle concentration have been attributed to the existence of premicelles. Here we investigate the properties of premicelles in aqueous solutions of non-ionic surfactants surrounding the critical micelle concentration (CMC) using advanced computer simulations. The concentration of premicelles increases with total concentration up to the CMC, above which the concentrations of free monomers and premicelles remain nearly constant. Analysis shows premicellar structures ranging from spherical to chain-like. Monomer exchange kinetics are observed to depend strongly on the aggregate size, with premicelles exhibiting extremely short (1.3 ns) relaxation times relative to full sized micelles (72 ns). (C) 2011 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2011.11.075

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The effect of carbon-based nanoparticles (CNPs) on biological systems is currently of great concern. Yet, few experimental techniques are capable of directly imaging and probing the energetics of such nano-bio systems. Here, we use coarse grain molecular dynamics simulations to study spherical fullerene molecules interacting with dipalmitoyl phosphatidylcholine (DPPC) lipid membranes. Using free energy calculations we show that all the tested fullerene molecules can spontaneously diffuse into both a lipid bilayer and a lipid monolayer. In addition, we establish that large fullerene molecules tend to partition preferentially into bilayers, which affects the lipid monolayer-to-bilayer transition during the respiration cycle. Our results identify a possible CNP perturbation to the function of the pulmonary monolayer membrane and suggest a potential pathway for CNP entry into the body through lung inhalation.

DOI： 10.1039/c2sm26357b

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The computational design of advanced materials based on surfactant self-assembly without ever stepping foot in the laboratory is an important goal, but there are significant barriers to this approach, because of the limited spatial and temporal scales accessible by computer simulations. In this paper, we report our work to bridge the gap between laboratory and computational time scales by implementing the coarse-grained (CG) force field previously reported by Shinoda et al. [Shinoda, W.; DeVane, R.; Klein, M. L. Mol. Simul. 2007, 33, 27-36] into the HOOMD-Blue graphical processing unit (GPU)-accelerated molecular dynamics (MD) software package previously reported by Anderson et al. [Anderson, J. A.; Lorenz, C. D.; Travesset, A. J. Comput. Phys. 2008, 227, 5342-5359]. For a system of 25 750 particles, this implementation provides performance on a single GPU, which is superior to that of a widely used parallel MD simulation code running on an optimally sized CPU-based cluster. Using our GPU setup, we have collected 0.6 ms of MD trajectory data for aqueous solutions of 7 different nonionic polyethylene glycol (PEG) surfactants, with most of the systems studied representing similar to 1 000 000 atoms. From this data, we calculated various properties as a function of the length of the hydrophobic tails and PEG head groups. Specifically, we determined critical micelle concentrations (CMCs), which are in good agreement with experimental data, and characterized the size and shape of micelles. However, even with the microsecond trajectories employed in this study, we observed that the micelles composed of relatively hydrophobic surfactants are continuing to grow at the end of our simulations. This suggests that the final micelle size distributions of these systems are strongly dependent on initial conditions and that either longer simulations or advanced sampling techniques are needed to properly sample their equilibrium distributions. Nonetheless, the combination of coarse-grained modeling and GPU acceleration marks a significant step toward the computational prediction of the thermodynamic properties of slowly evolving surfactant systems.

DOI： 10.1021/ct2005193

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Water permeability of two different lipid bilayers of dipalmitoylphosphatidylcholine (DPPC) and palmitoylsphingomyelin (PSM) in the absence and presence of cholesterol (0-50 mol %) have been studied by molecular dynamics simulations to elucidate the molecular mechanism of the reduction in water leakage across the membranes by the addition of cholesterol. An enhanced free energy barrier was observed in these membranes with increased cholesterol concentration, and this was explained by the reduced cavity density around the cholesterol in the hydrophobic membrane core. There was an increase of trans conformers in the hydrophobic lipid chains adjacent to the cholesterol, which reduced the cavity density. The enhanced free energy barrier was found to be the main reason to reduce the water permeability with increased cholesterol concentration. At low cholesterol concentrations the PSM bilayer exhibited a higher free energy barrier than the DPPC bilayer for water permeation, while at greater than 30 mol % of cholesterol the difference became minor. This tendency for the PSM and DPPC bilayers to resemble each other at higher cholesterol concentrations was similar to commonly observed trends in several structural properties, such as order parameters, cross-sectional area per molecule, and cavity density profiles in the hydrophobic regions of bilayer membranes. These results demonstrate that DPPC and PSM bilayers with high cholesterol contents possess similar physical properties, which suggests that the solubility of cholesterol in these lipid bilayers has importance for an understanding of multicomponent lipid membranes with cholesterol.

DOI： 10.1021/jp201611p

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We propose a novel method for computing the pressure tensor along the radial axis of a molecular system with spherical symmetry. The proposed method uses the slice averaged pressure to improve the numerical stability and precision significantly. Simplified expressions of the local pressure are derived for a conventional molecular force field including non-bond, bond stretching, angle bending, and torsion interactions; these expressions are advantageous in terms of the computational cost. We also discuss an algorithm to avoid numerical singularity. Finally, the method is successfully applied to three different molecular systems, i.e., a water droplet in oil, a spherical micelle, and a liposome. (C) 2011 American Institute of Physics. [doi:10.1063/1.3626410]

DOI： 10.1063/1.3626410

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Language：Japanese   Publisher：THE MEMBRANE SOCIETY OF JAPAN  

We developed a coarse-grained (CG) molecular model, which is useful to investigate a self-assembling process of lipids and surfactants in an aqueous solution or a phase transition process at the molecular resolution. The CG model is designed to reproduce the interfacial properties, solvation free energy, as well as molecular distribution functions obtained from simulations with the all-atomic detail. The systematic CG modeling enabled us to investigate large molecular assemblies such as liposomes with chemical characterization of molecule, which is not accessible by previous phenomenological models. Several application studies given in this paper will elucidate the power of CG molecular dynamics simulation to shed light on molecular processes in lipid membranes happening on the scale of ‹ 100 nm.

DOI： 10.5360/membrane.36.31

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

Molecular dynamics simulations of ionic liquids [1-alkyl-3-methylimidazolium (alkyl = ethyl, butyl and hexyl), N-butylpyridinium, N-butyl-N,N,N-trimethylammonium and N-butyl-N-methylpyrrolidinium cations combined with the (CF3SO2)N-2 (TFSA) anion] show that the conformational flexibility of the alkyl chains in the cations is one of the important factors determining the diffusion of ions. Artificial constraint imposed on the internal rotation of alkyl chains significantly decreases the self-diffusion coefficients of cations and anions. The internal rotation of the C-N bond connecting the alkyl chain and the aromatic ring has large effects on the diffusion of ions in imidazolium and pyridinium based ionic liquids. The calculated self-diffusion coefficients of cations and anions decrease 20-40% by imposing the torsional constraint of the C-N bond. On the other hand the torsional constraint of the C-N bond does not largely change the diffusion of ions in the quaternary alkyl ammonium based ionic liquids. The conformational flexibility of the terminal C-C-C-C bond of the alkyl chains has large effects on the diffusion of ions in the quaternary alkyl ammonium based ionic liquids. The influence of the electrostatic interactions and the high density of ionic liquids on the diffusion of ions were studied. The electrostatic interactions have the paramount importance on the slow diffusion of ions in ionic liquids, while the high density of ionic liquids is also responsible for the slow diffusion. The electrostatic interactions and the high density of ionic liquids enhance the effects of the torsional constraint on the diffusion of ions, which suggests that the charge-ordering structure and small free volume originated in the strong electrostatic interactions are the causes of the significant effects of the conformational flexibility on the diffusion of ions in ionic liquids.

DOI： 10.1039/c0cp02087g

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Nanoparticles (NPs) and molecular surfactants are two classes of compounds which spontaneously localize at oil/water interfaces. Industrial and commercial applications of these systems often require precise two-dimensional organization of the localized NPs. An impediment to the realization of such systems is our under-developed understanding of the physics which governs the behavior of NPs in the presence of surfactants. Here we present a range of molecular dynamics simulation studies on non-ionic NP/surfactant systems. Analysis of the results allows us to relate the dispersive interactions of the NPs and surfactants to their physical behavior at oil/water interfaces.

DOI： 10.1021/bk-2011-1070.ch018

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The transfer of various nano-scale fullerenes into lipid bilayers has been studied using all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations. The free energy change, when C-60, C-180, and C-540 fullerenes are transferred from water to the interior of a lipid [dioleoylphosphatidylcholine (DOPC)] bilayer, has been calculated. Upon entering the lipid bilayer, the largest (2.4 nm diameter) fullerene causes local distortions in the bilayer surface, which were previously observed in carbon nanotube simulations. These local distortions, however, do not lead to any free energy barriers to bilayer entry. The free energy profiles confirm spontaneous absorption of all three fullerenes. Qualitative agreement was observed when comparing fullerene partitioning in water/bilayer systems to water-hexane systems. In contrast to these nonspecific single fullerene properties, extensive CG-MD simulations of fullerene rich lipid bilayers reveal substantial impact of fullerene-size on the bilayer stability. While previous CG-MD simulations indicated that bilayer bound C-60 aggregates have little effect on the bilayer structure, the present MD simulations indicate that C-540 aggregation has drastic effects. Specifically, the observed destabilization likely has implications for understanding the cytotoxic mechanisms of nano-carbon particles upon uptake by biological cells.

DOI： 10.1039/c0sm00963f

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We present a new coarse-grained (CG) molecular model for ionic surfactants, which is compatible with previously developed CG models for nonionic surfactants and lipids. The CG force field is described by rather simple interaction functions including a separate non-truncated Coulomb interaction term between charged segments. The CG surfactant model reproduces experimental surface tension and density as well as distribution functions from all-atomic molecular models. A CG molecular dynamics simulation of sodium dodecyl sulfate (SDS) micellar solution produces a reasonable distribution of monomers between micelles and the bulk solution. The SDS model is used to investigate the effect of salt on micelle size and adsorption on a carbon nanotube; studies which help elucidate the applicability and transferability of the present CG model. Trial computations on a Langmuir monolayer of ionic surfactants illustrate how truncation of the Coulomb interaction can significantly influence the counter ion distribution.

DOI： 10.1039/c1sm05173c

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Nanoparticles (NPs) and surfactants can spontaneously concentrate at the interface between two immiscible liquids, such as oil and water. Systems of high oil-water interfacial area, such as emulsions, are the basis of many industries and consumer products. Although NPs and surfactants are currently incorporated into many of these applications, their mutual interfacial behavior is not completely understood. Here we present molecular dynamics simulations of NPs and non-ionic surfactant in the vicinity of an oil-water interface. It was found that in low concentration the surfactants and NPs show cooperative behavior in lowering the oil-water interfacial tension, while at higher surfactant concentration this synergy is attenuated. It was also found that binding of surfactants to the NP surface decreases the surfactant efficiency in lowering the interfacial tension, while concurrently creating a barrier to NP aggregation.

DOI： 10.1039/c1sm05145h

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A lipid assembly composed of a finite number of lipid molecules can have multiple metastable structures. Using a series of coarse-grained molecular dynamics simulations, we evaluate the free energy profile for the transformation of a small vesicle to a disk-like structure called a bicelle. This free energy is found to be lower than that predicted from continuum elastic theory. For small unilamellar vesicles, the relaxation of the internal structure of the membrane is suggested to play an important role in lowering the free energy barrier for the vesicle-to-bicelle transformation.

DOI： 10.1039/c1sm05404j

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Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based molecules. Here, we developed the cross parameters necessary to unite those force fields and then applied the model to investigate the nature of benzene and C-60 interactions with lipid bilayers. The interaction parameters between the phenyl and lipid CG sites are based on experimental and all atom (AA) molecular dynamics (MD) data. The resulting force field was tested on benzene rich lipid bilayers and shown to reproduce general behavior expected from experiments. The parameters were then applied to C-60 interactions with lipid bilayers. Overall, the results showed excellent agreement with AA MD and experimental observations. In the C-60 lipid systems, the fullerenes were shown to aggregate even at the lowest concentrations investigated.

DOI： 10.1021/jp1070264

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Language：English   Publishing type：Part of collection (book)   Publisher：Wiley-VCH  

DOI： 10.1002/9783527632633.ch9

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

The recently developed coarse-grained (CG) molecular model enables us to investigate meso-scopic morphologies of self-assembly of amphiphilic molecules at the molecular level. The present CG model is designed to well reproduce the interfacial properties, solvation free energy, as well as molecular distribution obtained from simulations at the all-atomic detail. The transferability and versatility is demonstrated by applying the model to the bulk aqueous solution as well as to the air/water interfacial system.<br>

DOI： 10.2142/biophys.50.232

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The stabilization energies (E(form)) for the formation of the perfluoroalkyltrifluoroborate complexes with Li(+) and 1-ethyl-3-methylimidazolium cation (emim(+)) were calculated at the MP2/6-311G** level. The Eform values calculated for the Li[BF(4)], Li[BF(3)CF(3)], Li[BF(3)C(2)F(5)], Li[BF(3)C(3)F(7)], and Li [BF(3)C(4)F(9)] complexes were -144.1, -139.3, -137.4, -136.3, and -135.4 kcal/mol, respectively. The E(form), values calculated for the [emim][BF(4)], [emim][BF(3)CF(3)], [emim] [BF(3)C(2)F(5)], [emim] [BF(3)C(3)F(7)], and [emim][BF(3)C(4)F(9)] complexes were -85.2, -81.2, -79.7, -79.7, and -79.2 kcal/mol, respectively. The electrostatic interactions are the major source of the attraction in the complexes, whereas the contribution of the induction interactions to the attraction is not negligible. The interactions of the perfluoroalkyltrifluoroborate anions with Li(+) and emim(+) are substantially weaker than those of the BF(4)(-) because of the weaker electrostatic interactions. The analysis of the interactions suggests that the weaker interactions between the BF(3)CF(3)(-) and emim(+) compared with those between the BF(4)(-) and emim(+) are the cause of the lower viscosity of the [emim][BF(3)CF(3)] ionic liquid compared with the [emim][BF(4)] ionic liquid. The order of experimental self-diffusion coefficients of the cations and anions in the ionic liquids is BF(4)(-) &lt; BF(3)CF(3)(-) similar to BF(3)C(2)F(5)(-) &gt; BF(3)C(3)F(7)(-) &gt; BF(3)C(4)F(9)(-), which is well reproduced by the molecular dynamic simulations. The analysis of the rotational relaxation of emim(+) suggests that the translational diffusion of cations and anions is associated with the rotational diffusion of emim(+).

DOI： 10.1021/jp104380s

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A coarse-grained intermolecular potential has been parametrized for phenyl-based molecules. The parametrization was accomplished by fitting to experimental thermodynamic data. Specifically, the intermolecular potentials, which were based on Lennard-Jones functional forms, were parametrized and validated using experimental surface tension, density, and partitioning data. This approach has been used herein to develop parameters for coarse-grained interaction sites that are applicable to a variety of phenyl-based molecules, including analogues of the amino acid side chains of phenylalanine and tyrosine. Comparison of the resulting coarse-grain model to atomistic simulations shows a high level of structural and thermodynamic agreement between the two models, despite the fact that no atomistic simulation data was used in the parametrization of the coarse-grain intermolecular potentials.

DOI： 10.1021/jp9117369

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A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CO lipid bilayers have reasonable molecular areas, chain order parameters, and elastic properties. The computed surface pressure vs area (pi-A) curve for a dipalmitoyl phosphatidylcholine (DPPC) monolayer demonstrates a significant improvement over the previous CO models. The DPPC monolayer has a longer persistence length than a polyethyleneglycol (PEG) lipid monolayer, exhibiting a long-lived curved monolayer surface under negative tension. The bud ejected from an oversaturated DPPC monolayer has a large bicelle-like structure, which is different from the micellar bud formed from an oversaturated PEG lipid monolayer. We have successfully observed vesicle formation during CG-MD simulations, starting from an aggregate of dimyristoyl phosphatidylcholine (DMPC) molecules. Depending on the aggregate size, the lipid assembly spontaneously transforms into a closed vesicle or a bicelle. None of the various intermediate structures between these extremes seem to be stable. An attempt to observe fusion of two vesicles through the application of an external adhesion force was not successful. The present CO force field also supports stable multilamellar DMPC vesicles.

DOI： 10.1021/jp9107206

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The interaction of fullerenes with biological systems and the environment is a topic of current interest. Coarse-grained molecular dynamics (CGMD) simulations are well-suited to investigate some of the factors involved because they provide access to time and length scales that are not accessible using fully atomistic simulation methods. In the case of buckyballs (C-60) and single-walled carbon nanotubes (SWNTs), it is necessary to parametrize a CG force field that accurately captures the balance between fullerene-fullerene and fullerene-solvent interactions. Herein, we derive CG force field parameters for C-60 and SWNTs by using the optimized benzene parameters from part I [DeVane, R.; Chiu, C.-c.; Nielsen, S. O.; Shinoda, W.; Moore, P. B.; Klein, M. L. J. Phys. Chem. B 2010, doi: 10.1021/jp9117369]. Solubility, transfer free energy, and dimerization free-energy data for C-60 and SWNTs obtained using the proposed models show excellent agreement with experimental and fully atomistic MD data. In particular, cluster analysis of C-60 aggregation in a hydrocarbon melt corroborates the force field parameters. The aggregation behavior of the present CG force field differs considerably from that of models currently in widespread use. The combined results provide a strong basis for applying this model for further large-scale MD studies involving C-60 and SWNTs.

DOI： 10.1021/jp9117375

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The physical properties of a liquid in contact with a solid are largely determined by the solid-liquid surface tension. This is especially true for nanoscale systems with high surface area to volume ratios. While experimental techniques can only measure surface tension indirectly for nanoscale systems, computer simulations offer the possibility of a direct evaluation of solid-liquid surface tension although reliable methods are still under development. Here we show that using a mean field approach yields great physical insight into the calculation of surface tension and into the precise relationship between surface tension and excess solvation free energy per unit surface area for nanoscale interfaces. Previous simulation studies of nanoscale interfaces measure either excess solvation free energy or surface tension, but these two quantities are only equal for macroscopic interfaces. We model the solid as a continuum of uniform density in analogy to Hamaker&apos;s treatment of colloidal particles. As a result, the Hamiltonian of the system is imbued with parametric dependence on the size of the solid object through the integration limits for the solid-liquid interaction energy. Since the solid-liquid surface area is a function of the size of the solid, and the surface tension is the derivative of the system free energy with respect to this surface area, we obtain a simple expression for the surface tension of an interface of arbitrary shape. We illustrate our method by modeling a thin nanoribbon and a solid spherical nanoparticle. Although the calculation of solid-liquid surface tension is a demanding task, the method presented herein offers new insight into the problem, and may prove useful in opening new avenues of investigation. c 2010 American Institute of Physics. [doi: 10.1063/1.3308625]

DOI： 10.1063/1.3308625

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A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2010.01.029

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We study the shear effect on the lamellar structure of surfactants in water using dissipative particle dynamics simulations. Starting from a lamellar structure without shear flow, we increase the shear rate and then decrease it stepwisely. A weak shear changes the lamellar plane to be parallel to the shear direction though the lamellar normal has no specific direction on the plane normal to the shear direction. By increasing the shear rate, the lamellar normal eventually flips to the vorticity direction regardless of the initial configuration. Lamellar normal would stay along the vorticity direction on decreasing the shear rate. The hysteresis is also found in shear-stress. By varying the shear rate, the time needed to reach the final unique state is significantly shortened compared with that observed with a constant shear rate. We find a correlation between the excess shear-stress and the tilt angle of surfactant in lamellar. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2009.10.009

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Molecular dynamics simulations have become a standard tool for the investigation of biological and soft matter systems. Water models serve as the basis of force fields used in molecular dynamics simulations of these systems. This article reports on an examination of the utility of a set of coarse-grained (CG) water models, with different resolutions, interaction potentials (Lennard-Jones, Morse), and cut-off distances. The relationships between the parameters under specific choices of the above options and the thermodynamic properties, such as density, surface tension, and compressibility, were found to fit simple mathematical equations. The limits of applicability of these CG water models were explored by checking the melting temperature. If a CG site is mapped to one or two real water molecules, a simple model with appropriate combinations of cut-off distances, functional forms, and parameters can be found to simultaneously match the experimental values of density, surface tension, and compressibility under ambient conditions. If more water molecules are included in a CG site, either the melting temperature approaches or surpasses room temperature, or the surface tension and compressibility cannot both be matched simultaneously. In striving for computational efficiency, it is still possible to find a simple CG water model with three water molecules contained in a CG bead that generates a liquid state of water with realistic values of density, surface tension and compressibility at ambient condition, but coarser models are not recommended.

DOI： 10.1080/00268976.2010.503197

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The physical properties of nanoscale materials often vary with their size, unlike the corresponding bulk material properties, which can only be changed by modifying the material composition. In particular, it is believed that hydration phenomena are length scale dependent. The manifestation of hydrophobicity over multiple length scales plays a crucial role in self-assembly processes such as protein folding and colloidal stability. In the case of particles composed of a bulk hydrophobic material, it is well known that the free energy of hydration monotonically increases with particle size. However, the size-dependent free energy of hydration for particles composed of a bulk hydrophilic material has not been studied. Here we show that the free energy of hydration is not a monotonic function of particle size, but rather, changes sign from positive to negative as the particle size increases. In other words, the particle is hydrophobic at small size and hydrophilic at large size. This behavior arises from a purely geometrical effect caused by the curvature of the particle-water interface. We explore the consequences of this phenomenon on colloidal stability and find that it dictates the shape of colloidal aggregates.

DOI： 10.1063/1.3276915

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Molecular dynamics simulations of a series of ionic liquids [1-alkyl-3-methylimidazolium (alkyl = methyl, ethyl, butyl, hexyl, and octyl), 1-butylpyridinium, N-butyl-N,N,N-trimethylammonium and N-butyl-N-methylpyrrolidinium cations combined with a (CF(3)SO(2))(2)N(-) anion ([mmim][TFSA], [emim][TFSA], [bmim][TFSA], [C(6)mim][TFSA], [C(8)mim][TFSA], [bpy][TFSA], [(n-C(4)H(9))(CH(3))(3)N][TFSA], and [bmpro][TFSA]) and a 1-butyl-3-methylimidazolium combined with BF(4)(-), PF(6)(-), CF(3)CO(2)(-), CF(3)SO(3)(-), and (C(2)F(5)SO(2))(2)N(-) anions ([bmim][BF(4)], [bmim][PF(6)], [bmim][CF(3)CO(2)], [bmim][CF(3)SO(3)], and [bmim][BETA])] were carried out using the OPLS force field for ionic liquids. The force field was refined on the basis of ab initio molecular orbital calculations of isolated ions and experimental densities for four ionic liquids. The densities calculated for the 13 ionic liquids agreed with the experimental values within a 2% error. The self-diffusion coefficients calculated for the ions in the 13 ionic liquids were compared with the experimental values obtained by the NMR measurements. Although the calculated self-diffusion coefficients were about 1 order smaller than the experimental ones, the cation and anion dependence (the effects of alkyl chain length in imidazolium, cation structures, and anion species) of the experimental self-diffusion coefficients was reproduced by the simulations quite well in most cases. The translational motion of the terminal carbon atoms in the alkyl chains of the imidazolium cations oil the time scale of a few nanoseconds is significantly faster than that of the atoms in the imidazolium rings and anions, which suggests that the dynamics of atoms in the polar domains of the ionic liquids is significantly different from that in the nonpolar domains. The factors determining the self-diffusion coefficients of the ions are also discussed.

DOI： 10.1021/jp811128b

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The large quantity of protein sequences being generated from genomic data has greatly outpaced the throughput of experimental protein structure determining methods and consequently brought urgency to the need for accurate protein structure prediction tools. Reduced resolution, or coarse grained (CG) models, have become a mainstay in computational protein structure prediction performing among the best tools available. The quest for high quality generalized CG models presents an extremely challenging yet popular endeavor. To this point, a CG based interaction potential is presented here for the naturally occurring amino acids. In the present approach, three to four heavy atoms and associated hydrogens are condensed into a single CG site. The parametrization of the site-site interaction potential relies on experimental data thus providing a novel approach that is neither based on all-atom (AA) simulations nor experimental protein structural data. Specifically, intermolecular potentials, which are based on Lennard-Jones (LJ) style functional forms, are parametrized using thermodynamic data including surface tension and density. Using this approach, an amino acid potential data set has been developed for use in modeling peptides and proteins. The potential is evaluated here by comparing the solvent accessible surface area (SASA) to AA representations and ranking of protein decoy data sets provided by Decoys &apos;R&apos; Us. The model is shown to perform very well compared to other existing prediction models for these properties.

DOI： 10.1021/ct800441u

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Three atomistic empirical models for phosphatidylglycerol (PG) lipids are tested against structural data in the crystal and liquid crystal states. Simulations of the anhydrous crystal of dimyristoyl-phosphatidylglycerol (DMPG) show that only the CHARMM force field describes the conformation and interactions of PG head groups accurately. The other two models do not reproduce the native network of hydrogen bonds, suggesting the presence of biases in their conformational and nonbonded interaction properties. The CHARMM model is further validated in the biologically relevant liquid crystal phase by comparing experimental small-angle X-ray scattering spectra from DMPG unilamellar vesicles with data calculated from fluid bilayer simulations. The good agreement found in this model-free comparison implies that liquid crystal PG bilayers as described by CHARMM exhibit realistic bilayer thickness and lateral packing. Last, this model is used to simulate a fluid bilayer of palmitoyl-oleoyl-phosphatidylclycerol (POPG). The resulting view of the POPG bilayer structure is at variance with that proposed previously based on simulations, in particular, with respect to lateral packing of head groups and the role of counterions.

DOI： 10.1021/jp900645z

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Inorganic nanoparticles (NPs) display unique size-dependent properties and have applications in many different areas such as medicine and the semiconductor industry. In order to take advantage of these properties, the organization of the NPs must be controlled, either to promote crystallization or to prevent agglomeration. This control is typically acheived by using covalently bound amphiphilic ligands. While the properties of the NPs themselves have been well-characterized, much less is known about the organic ligand coating. Here, we present a theoretical and computer simulation approach to compute the surface area occupied per ligand molecule as a function of the NP radius and of the ligand hydrophilic to lipophilic balance. We employ a self-consistent method which takes into account the full free energy of the NP/ligand/solvent system, which for this study is composed of hydrophobic NPs, alkyl poly(oxyethylene) ligands, and water. We find an order of magnitude higher ligand coverage on NPs compared to flat surfaces, in agreement with some experimental reports. Our approach is fundamentally different from existing computational methods in the literature and builds a foundation for studies of the organization of colloidal NPs in solvents or at interfaces.

DOI： 10.1021/la8032918

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

We discuss three topologically different methods for calculating the surface tension between a flat solid and a liquid from theoretical and computer simulation viewpoints. The first method, commonly used in experiments, measures the contact angle at which a static droplet of liquid rests on a solid surface. We present a new analysis algorithm for this method and explore the effects of line tension on the contact angle. The second method, commonly used computer simulations, uses the pressure tensor through the virial in a system where a thick, infinitely extended slab of liquid rests on a solid surface. The third method, which is original to this paper and is closest to the thermodynamic definition of surface tension, applies to a spherical solid in contact with liquid in which the flat solid is recovered by extrapolating the sphere radius to infinity. We find that the second and third methods agree with each other, while the first method systematically underestimates surface tension values.

DOI： 10.1007/s10910-008-9374-7

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Comparative molecular dynamics calculations of the fluorinated and the non-fluorinated phospholipid bilayers have been carried out to examine the fluorination effects on hydration structure and lipid dynamics. The fluorination of hydrophobic chain causes an increase of hydration in the headgroup, which reorients toward the bilayer normal. Largely restricted wobbling and lateral diffusional motions were observed in the fluorinated lipid bilayer, which would be attributed to the chain stiffness of fluorinated lipids and the tight chain packing in the membrane core. The lateral diffusion coefficients obtained from these calculations show a good agreement with the experimental results. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2008.12.001

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：IEEE  

Discovery of novel Si nanostructures would open up a new avenue for science and technology as the discoveries of C-60 and carbon nanotubes did. With this expectation, we have explored novel Si nanostructures by combining empirical molecular-dynamics simulations and structure optimizations with the density functional theory(1,2,3,4). Our molecular-dynamics simulations demonstrate (1) an icosahedral Si nanodot forms by freezing a droplet in vacuum(1), (2) Si-fullerene-linked nanowires, such as Si-16- and Si-20-linked nanowires, form by freezing liquid Si inside carbon nanotubes(2), and (3) a polyicosahedral Si nanowire forms by freezing liquid Si inside a cylindrical nanopore(3). The unique cage structure of the polyicosahedral Si nanowire allows us to tune the electronic properties by encapsulating guest atoms into its cages. Our density functional theory calculations reveal that a semiconducting hydrogen-terminated polyicosahedral Si nanowire becomes metallic by the sodium and iodine doping(4).

DOI： 10.1109/ULIS.2009.4897539

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Nat. Inst. of Adv. Industrial Science and Technology (AIST)  

We have investigated the processes of invention of PAN (Polyacrylonitrile) carbon fiber and its technology transfer to private companies. From this investigation and analysis, we have found a new R&amp
D management model, named "excited-oscillation model". This model suggests that both the top-down management and the personal motivation should be in phase and synergetic with each other. In this paper, the results and concept of the above model are described in detail.

DOI： 10.5571/syntheng.2.154

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

A molecular dynamics simulation of a partially fluorinated phospholipid bilayer has been carried Out to understand the effects of fluorination of the hydrophobic chains on the structure and water permeability across the membrane. Fluorocarbon chains typically have an all-trans conformation, showing a highly ordered structure in the membrane core compared to ordinary hydrocarbon chains. The free energy profiles of water across the bilayers were successfully estimated by a revised cavity insertion Widom method. The fluorinated bilayer showed a higher free energy barrier than an ordinary nonfluorinated lipid bilayer by about 1.2 kcal/mol, suggesting a lower water permeability of the fluorinated bilayer membrane. A cavity distribution analysis elucidated the reduced free volume in the fluorinated membrane due to the neatly packed chains, which should account for the higher free energy barrier.

DOI： 10.1021/jp801057k

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JOHN WILEY & SONS INC  

An efficient free energy (FE) calculation of a water molecule to go across lipid membranes is presented. Both overlapping distribution and cavity insertion Widom methods are complementarily used. The former is useful for a dense region where water molecules are found, i.e., from the interfacial to bulk water region, while the latter works well in the low density region, i.e., the hydrocarbon region. Since both methods evaluate the excess chemical potential of water, the obtained FE profile is free from the fitting problem usually arisen when a FE difference method is used. A diphytanyl phosphatidylcholine bilayer is used for our test calculations. An excellent and fast convergence of the chemical potential is obtained when each method is applied for the appropriate region. The estimated FE barrier using the Ewald method for the electrostatic interaction is similar to 7.2 kcal/mol, which is higher than that using the interaction cutoff of 20 angstrom by about 0.9 kcal/mol. (C) 2008 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.20956

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Language：English   Publisher：AMER ASSOC ADVANCEMENT SCIENCE  

DOI： 10.1126/science.1157834

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

In all-atom simulations of lipid membranes, explicit hydrogen atoms contained in the hydrocarbon region are described by a large number of degrees of freedom, although they convey only limited physical information. We propose an implicit-hydrogen model for saturated and monounsaturated acyl chains, aimed at complementing the all-atom CHARMM27 model for phospholipid headgroups. Torsional potentials and nonbonded parameters were fitted to reproduce experimental data and free energy surfaces of all-atom model systems. Comparative simulations of fluid-phase POPC bilayers were performed using the all-hydrogen force field and the present model. The hybrid model accelerates a typical bilayer simulation by about 50% while sacrificing a minimal amount of detail with respect to the fully atomistic description. In addition, the united-atom description is energetically compatible with all-atom CHARMM models, making it suitable for simulations of complex membrane systems.

DOI： 10.1021/jp800687p

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

A statistical-mechanical treatment of the molecular binding into lipid membrane is presented in combination with molecular simulation. The membrane solution is viewed as an inhomogeneous, mixed solvent system, and the free energy of solvation of a solute in membrane is computed with a realistic set of potential functions by the method of energy representation. Carbon monoxide, carbon dioxide, benzene, and ethylbenzene are adopted as model solutes to analyze the binding into 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) membrane. It is shown that the membrane inside is more favorable than bulk water and that the solute distribution is diffuse throughout the membrane inside. The membrane-water partition coefficient is then constructed with the help of the Kirkwood-Buff theory from the solvation free energy obtained separately in the hydrophobic, glycerol, headgroup, and aqueous regions. To discuss the role of repulsive and attractive interactions, the solvation free energy is partitioned into the DMPC and water contributions and the effect of water to stabilize the benzene and ethylbenzene solutes within the membrane is pointed out. (c) 2008 American Institute of Physics.

DOI： 10.1063/1.2919117

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

In a previous molecular dynamics study, we predicted a polyicosahedral Si nanostructure which has a Si-20 fullerene cage per icosahedral Si-100 nanodot. The unique cage structure is distinct from the crystalline diamond Si nanostructure. Encapsulating a guest atom into the Si-20 cage allows us to tune the electronic and optical properties. Here, we report on a systematic first-principles study of the effect of the sodium and iodine doping on the physical properties of the hydrogen-terminated polyicosahedral Si nanostructures. Our calculations reveal the strongly guest-dependent and size-dependent physical properties of the polyicosahedral Si nanostructures: (1) the semiconducting guest-free polyicosahedral nanowire becomes metallic by the sodium and iodine doping, (2) the quantum confinement effect is observed in the icosahedral and polyicosahedral nanodots, and (3) the radiative recombination rate comparable to the luminescent amorphous Si nanostructures is expected from some of the Na- and I-doped polyicosahedral nanostructures. From these results, we assert that the polyicosahedral Si nanostructures are promising candidates for the building blocks of the future nanoscale optoelectronic devices.

DOI： 10.1103/PhysRevB.77.075431

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

A coarse-grained (CG) molecular model for nonionic surfactants is presented. The transferability and versatility are demonstrated by applying the model to the bulk aqueous solution as well as to the air-water and oil-water interfacial systems. The model is designed to reproduce several key properties including surface/interfacial tension, bulk density, compressibility, hydration/transfer free energy as well as distribution functions obtained by all-atom molecular dynamics simulations. The CG surfactants are demonstrated to spontaneously organize into micelles, and either hexagonal or lamellar bulk structures, respectively, at the corresponding concentration and thermodynamic conditions for those phases. Moreover, even a hexagonal-to-lamellar phase transformation is attainable using the present CG model. The experimental surface pressure-area (pi-A) curve for a representative surfactant monolayer at the air-water interface is well reproduced. Micelle budding is observed from an overly compressed monolayer; a phenomenon that is likely to be a reasonable finding because the hydration/transfer free energy is a fitted parameter in the model. The correct molecular partitioning together with a relatively rapid relaxation of the CG model system towards equilibrium enables the computation of self-assembled surfactant behavior at the mesoscale regime.

DOI： 10.1039/b808701f

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

A new systematic approach to build coarse-grained (CG) molecular models for surfactants/water systems is proposed. A step-by-step approach using several molecular systems for the parameterization makes the CG model versatile and transferable. The intramolecular bond potentials are determined to reproduce the bond and angle distributions obtained from all-atom (AA) molecular dynamics (MD) simulations. A careful choice of the potential function for nonbonded interactions is essential for better structural properties. Density and surface/interfacial tension data are used for parameter fitting, because these thermodynamic properties are of key importance in characterizing the self-organized surfactant structure. Solvation (hydration) and transfer free energies, which play an essential role in determining the partition of solute molecules, are also taken into account in the model.

DOI： 10.1080/08927020601054050

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

We have performed molecular dynamics simulations of a bilayer formed by the synthetic archaeal lipid, diphytanyl phosphatidylcholine, in NaCl electrolyte solution at four different concentrations (0-4 M) to investigate how structural and dynamic properties of the model archaeal membrane are changed due to the ionic strength of the solution. The archaeal lipid bilayer shows minor changes in their physical properties, indicating the unusual high stability of the membrane against salt, though small reductions of molecular area and lateral diffusion of the lipid are detected at the highest electrolyte concentration of 4 M. Sodium ions penetrate to the ether-rich region, where the ions are likely bound to the ether oxygen in the sn-1 chain rather than to that in the sn-2 chain. The observed salt bridges among two or three neighboring lipids account for the small reduction in the molecular area. The bound ions together with the counter ( chloride) ions give rise to a diffusive electric double layer; as a result, the membrane dipole potential is slightly increased with increasing NaCl concentration.

DOI： 10.1039/b611543h

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BIOPHYSICAL SOCIETY  

Membranes composed of bipolar tetraether lipids have been studied by a series of 25-ns molecular dynamics simulations to understand the microscopic structure and dynamics as well as membrane area elasticity. By comparing macrocyclic and acyclic tetraether and diether archaeal lipids, the effect of tail linkage of the two phytanyl-chained lipids on the membrane properties is elucidated. Tetraether lipids show smaller molecular area and lateral mobility. For the latter, calculated diffusion coefficients are indeed one order-of-magnitude smaller than that of the diether lipid. These two tetraether membranes are alike in many physical properties except for membrane area elasticity. The macrocyclic tetraether membrane shows a higher elastic area expansion modulus than its acyclic counterpart by a factor of three. Free energy profiles of a water molecule crossing the membranes show no major difference in barrier height; however, a significant difference is observed near the membrane center due to the lack of the slip-plane in tetraether membranes.

DOI： 10.1529/biophysj.105.060962

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As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2 O at 300 K, 6.9 in the liquid H2 O at 300 K, and 4.1 in the ice Ih H2 O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2 O has been calculated to be 10% higher than that of H2 O, while it is 13% higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions. © 2005 American Institute of Physics.

DOI： 10.1063/1.2035078

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Path integral molecular dynamics simulations have been carried out to evaluate heat capacities of water in gas, liquid, and solid phases. For convergence, a 100-ps simulation run with a large path integral variable (P ∼ 128) was required even by using the double-centroid virial heat capacity estimator. For all states, the quantum corrections to the heat capacities are significantly large. The calculated heat capacities for vapor and ice I h agreed excellently with experimental data, while that for liquid was less than the experimental value by ∼20% due to the limit of the SPC/F potential model. © 2005 The American Physical Society.

DOI： 10.1103/PhysRevE.71.041204

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Molecules confined in nanopores show unusual behavior not seen in bulk systems. The present paper reports on molecular dynamics simulations of unusual freezing behavior in confined Ar. Similar to bulk Ar, liquid Ar confined in pores with a diameter D&gt;15 sigma (5.1 nm), where sigma is the diameter of the Ar atom, crystallizes when the cooling rate is lower than a critical value (Q(c)). We also find that the spatial confinement does not have significant influence on Q(c) when D&gt;15 sigma (5.1 nm). In the pore of 10 sigma (3.4 nm) in diameter, on the other hand, the behavior is dramatically changed. Crystalline Ar does not appear inside the pore even when the system is cooled at a rate lower than the Q(c) in the bulk system by over two orders of magnitude. Instead, amorphous Ar characterized by local icosahedral configurations is formed in the pore. We further find that, even when crystalline Ar is formed outside the pore, it does not grow deeply into the pore. This supports that the amorphous Ar is actually the most stable phase in the pore. It is well known that Ar is a poor glass former. Our finding that even such an amorphous Ar is the most stable in the pore suggests that, in any system, it is possible to prepare amorphous structure selectively by using nano-molds.

DOI： 10.1063/1.1878693

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Commonly used time steps in dissipative particle dynamics (DPD) simulations are too large and lead to systematic errors in the computed properties. The main source of errors is the inaccurate integration of the conservative force. This error can be reduced to some extent by constructing a smoother force without any abrupt change at the cut-off distance, but the improvement is marginal. Alternatively, we tried smooth forces that also lead to the same conclusion. It is possible to find combinations of parameters for the random and dissipative forces that make errors cancel, but the combinations will depend on the system's thermodynamic state and on the particular force model. The only safe procedure is to use small time steps, i.e. comparable with those used in MD simulations. Alternatively, an improved integration algorithm should be used for the conservative force.

DOI： 10.1080/08927020410001709370

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The lipid membranes found in archaea have high bilayer stability and low permeability. The molecular structure of their constituent lipids is characterized by ether-linked, branched hydrophobic chains, whereas the conventional lipids obtained from eukaryotic or eubacterial sources have ester linked straight chains. In order to elucidate the influence of the ether linkage, instead of an ester one, on the physical properties of the lipid bilayers, we have carried out comparative 10 ns molecular dynamics simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers in water, respectively. We analyze bilayer structures, hydration of the lipids, membrane dipole potentials, and free energy profiles of water and oxygen across the bilayers. We observe that the membrane dipole potential for the ether-DPhPC bilayer, which arises mainly from the ether linkage, is about half of that of the ester-DPhPC. The calculated free energy barrier for a water molecule in the ether-DPhPC bilayer system is slightly higher than that in the ester-DPhPC counterpart, which is in accord with experimental data. (C) 2004 American Institute of Physics.

DOI： 10.1063/1.1806791

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The sliding in a Ni symmetrical tilt grain boundary, Sigma5 (012) [100], is investigated by modified Parrinello-Rahman molecular dynamics which deals with the thermodynamic ensemble characterized by the number of atoms N, temperature T, and the shear stress t. It is found that the grain boundary can slide in the direction perpendicular to the tilt axis [02(1) over bar] with the aid of shear stress in that direction. The sliding is coupled to the migration involving a collective motion of the third layer atoms hopping into the hollow site in between the first (GB) and second layers. Here, the critical stress necessary to move the grain boundary damps almost exponentially as the temperature is increased. At temperatures above about 820 K, random walk of GB migration occurs without the assistance of stress. On the other hand, it is only at much higher shear stress that the grain boundary can slide in the direction parallel to the tilt axis [001]. This may be because this sliding mechanism does not involve the coupling to the migration mode.

DOI： 10.1103/PhysRevB.70.054102

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We studied the effects of chain branching on the water and nonionic (neutral) solute permeability of lipid bilayers in a molecular dynamics simulation comparing two bilayers: dipalmitoylphosphatidylcholine (DPPC) and diphytanoylphosphatidylcholine (DPhPC). The calculated free energy profiles of several neutral solute and water molecules across the lipid membranes showed that chain branching caused no significant changes in the solubility of these molecules inside the membrane core. However, an analysis of the cavity distribution in each of these bilayer systems demonstrated that the branch-chained DPhPC bilayer had, compared with the straight-chained DPPC bilayer, a relatively small and discrete free volume distribution in the hydrophobic part. This suggests that small penetrants have a lower rate of diffusion inside branch-chained lipid bilayers. Actually, water molecules showed lower local diffusion coefficients inside the DPhPC membrane than inside the DPPC membrane. The low penetrant mobility of the former must correlate with the slower dynamics of the branched DPhPC chains. Thus, we conclude that chain branching effects on the permeability are, as far as neutral small penetrants are concerned, attributable mainly to the reduction of chain dynamics. The effects of chain branching on proton permeability are also discussed in the context of the proton-wire hypothesis.

DOI： 10.1021/jp035998+

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Self-assembly of adenine molecules deposited on a Cu(1 1 1) surface shows some characteristic hydrogen-bonding network patterns, such as hexagonal and 'double-chain'. In order to understand the emergence of energetically less favorable 'double-chain' structure, in which adenine molecules form two rows, possible molecular arrangements in the 'double-chain' structure are investigated by potential energy surface (PES) calculations between two single chains. A series of PES calculations elucidates that there are various stable molecular arrangements for the chain pair models: some of the models have both hexagonal and 'double-chain' (I-type) hydrogen-bonding patterns, while the others have only the latter pattern (II-type). Molecular dynamics simulations starting from the obtained 'double-chain' structures are also performed to assess the thermal stability of the structure. It is revealed that some of the II-type 'double-chain' structures remain even at 300 K, while all I-type ones transform into hexagonal arrays. The former result reminds us that the II-type 'double-chain' structures should be observed at room temperature in the STM experiment. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.susc.2004.03.022

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A comparison of branch-chained diphytanoylphosphatidylcholine (DPhPC) and straight-chained dipalmitoylphosphatidylcholine (DPPC) for their dynamics in the bilayers is made using 10 ns molecular dynamics simulations in the microcanonical ensemble. It is demonstrated that DPhPC molecules, compared with DPPC, indeed have slower wobbling, rotational, and translational motions by a factor of 2-3, whereas slightly faster headgroup rotation. The revision of the lipid dynamics due to chain branching is similar to that observed by the addition of cholesterol. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2004.03.145

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Molecular simulations, when they are used to understand properties characterizing the mechanical strength of solid materials, such as stress-strain relation or Born stability criterion, by using elastic constants, are sometimes seriously time consuming. In order to resolve this problem, we propose an efficient simulation approach under constant external stress and temperature, modifying Parrinello-Rahman (PR) method using useful sampling techniques developed recently-massive Nose-Hoover chain method and hybrid Monte Carlo method. Test calculations on the Ni crystal employing the embedded atom method have shown that our method greatly improved the efficiency in sampling the elastic properties compared with the conventional PR method.

DOI： 10.1103/PhysRevB.69.134103

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We studied effects of lipid chain branching on structural and dynamical properties of the lipid bilayers by a comparative molecular dynamics simulation of dipalmitoyl phosphatidylcholine (DPPC) and diphytanoyl phosphatidylcholine (DPhPC) bilayers. Trans-gauche isomerization rate at the dihedrals along the hydrophobic main chain was significantly reduced by chain branching. The slower conformational motion of branched chains lead to slower wobbling of the chain and slower rotational and translational motions of the lipid molecules, compared with straight-chained counterpart. In contrast. headgroup motion was slightly enhanced by the chain branching. The slower dynamics of the branched hydrophobic chains accounts for the high structural bilayer stability and low solute permeability of the branched DPhPC bilayer.

DOI： 10.1063/1.1764171

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.44.S56_4

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In general, bilayers composed of branch-chained lipid molecules are known to have high stability and low ion permeability. To understand how chain branching affects bilayer properties on a molecular level, two molecular dynamics (MD) simulations of lipid bilayers have been undertaken in the isothermal-isobaric ensemble. The first MD simulation was carried out on the straight-chained DPPC bilayer, and the second was carried out on the branch-chained DPhPC bilayer. Chain branching reduced segmental order of the lipid chain. This would be closely related to a high gauche probability at the dihedrals in the vicinity of tert-carbons; these dihedrals brought about the chain bending at the branched segments. Due to the characteristic conformation of the branched chain, some different effects were observed: First, the probability of parallel orientation of the two chains in a lipid was reduced; second, a chain caught between the two chains of the neighboring lipid in the same leaflet of the bilayer was frequently observed. As a consequence, the branched chain showed a much lower overall rate of trans-gauche isomerization than its straight counterpart. In conclusion, the high structural stability of the branched DPhPC bilayer is attributable mainly to the slow conformational motion of the hydrophobic chain, which is clearly correlated with the observed chain "entrapment" between the lateral neighboring lipid molecules.

DOI： 10.1021/jp035493j

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：COMPUTATIONAL PUBLICATIONS  

A bilayer composed of branch-chained lipid molecules is generally believed to have high bilayer stability and low ion leakage. To understand how the chain branching affects the bilayer properties on the molecular level, two molecular dynamics simulations of lipid bilayers have been undertaken in the isothermal-isobaric ensemble. The first simulation was carried out on the straight-chained DPPC bilayer, the second on the branch-chained DPhPC. The detailed analyses on the chain conformation revealed that the segmental order of branched chains was lower than that of straight chains. As for the intermolecular packing order in the bilayer plane, however, a relatively neat lipid arrangement was observed for the branch-chained DPhPC bilayer. A significant lowering in the chain mobility was observed as a result of chain branching. The high bilayer stability of the branch-chained DPhPC bilayer would arise from the low chain mobility and the neat lateral arrangement of the lipid in the bilayer.

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.42.S35_3

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The self-guided molecular dynamics (SGMD) method, which was proposed recently to enhance the efficiency of conformational sampling, has been extended to the isothermal-isobaric ensemble. It was applied to the crystallization of argon fluid in a supercooled state, and verified that crystallization was considerably accelerated with a suitable parameter set for the SGMD method. The algorithm proposed here also works well in the case of pressure-induced crystallization. A series of examinations we have done elucidates the applicable targets that SGMD works effectively. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(01)00054-9

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

In order to obtain a better description for the membrane area of a lipid bilayer, the potential parameter set OPLS, modified with respect to the interaction for the alkyl chain, was adopted for the present molecular dynamics simulation. A long-time and large-scale calculation based upon this modified potential presented a remarkable improvement of the membrane area for the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase, showing a good agreement with experiment. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0167-7322(01)00111-8

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.41.S178_1

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：ELECTROCHEMICAL SOC JAPAN  

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This paper describes a parallel algorithm for Molecular Dynamics simulation of a lipid membrane using the isothermal-isobaric ensemble. A message-passing paradigm is adopted for interprocessor communications using PVM3 (Parallel Virtual Machine). A data decomposition technique is employed for the parallelization of the calculation of intermolecular forces. The algorithm has been tested both on distributed memory architecture (DEC Alpha 500 workstation dusters) and shared memory architecture (SGI Powerchallenge with 20 R10000 processors) for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer consisting of 32 DPPC molecules and 928 water molecules. For each architecture, we measure the execution time with average work load, and the optimal number of processors for the current simulation. Some dynamical quantities are presented for a 2 ns simulation obtained with 5 processors on DEC Alpha 500 workstations. Our results show that the code is extremely efficient on 5-8 processors, and a useful addition to other major computational resources. (C) 1999 Published by Elsevier Science B.V.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Electrostatic properties of the dipalmitoylphosphatidylcholine bilayer in water have been investigated on the basis of molecular dynamics calculations in the isothermal-isobaric ensemble. Analysis of the long-time trajectory of partial charges on the atoms showed that polarization of the total system has an anisotropic fluctuation; the component along the bilayer normal was I order of magnitude smaller than that parallel to the bilayer plane, the polarization of lipid being canceled out mostly by that of water along the bilayer normal. A positive electrostatic potential was observed inside the membrane. The potential was found to vary in two steps across the interface; the first gradient comes from the preferential orientation of the ester group, and the second one is attributed to asymmetrical solvation of water around the phosphate group. Slower reorientation of the dipole projected on the bilayer normal was found than that on the bilayer plane. Dynamics of water near the headgroup was strongly influenced by the hydrogen bonding with the phosphate group.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Membrane area fluctuation of the lipid bilayer has been investigated based upon two-dimensional Voronoi tessellation analysis for the centers of mass of the lipid molecules projected on the bilayer plane. Long-time trajectories of the molecules used in the analysis have been generated by molecular dynamics calculations. The single-molecular area defined by Voronoi polygon showed a broad Gaussian distribution, from which area distribution of the membrane composed of N lipid molecules may satisfactorily be predicted. The fluctuation was found to be caused mainly by thermal motions of the alkyl chains. The number of gauche conformation and alkyl chain length was strongly correlated to the molecular area. Head group motions, however, showed little contribution to the fluctuation. Geometry of Voronoi polygons and the number of nearest neighbor molecules showed rather broad distribution due to the thermal fluctuation. This is in contrast to the structure found in the ripple, gel, and crystal phases. Formation of large pores in the membrane was also investigated. (C) 1998 American Institute of Physics.

DOI： 10.1063/1.476702

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such as atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence to the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in the bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (C) 1997 American Institute of Physics.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

A dipalmitoylphosphatidylcholine (DPPC) bilayer could successfully be simulated in the Nose-Parrinello-Rahman NPT ensemble from an arbitrarily generated crystal-like initial configuration. The initial condition dependence may be small and various artefacts, which were found in molecular dynamics calculations with rectangular cells, could be avoided.

DOI： 10.1016/0009-2614(94)01352-V

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DOI： 10.11436/mssj.11.4_22

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A novel polyicosahedral nanowire is spontaneously formed in a series of annealing molecular dynamics simulations of liquid Si inside a nanopore of 1.36 nm in diameter. The polyicosahedral Si nanowire is stable even in a vacuum up to about 77% of the melting temperature of bulk Si. Our structural energy calculations reveal that the polyicosahedral nanowire is energetically advantageous over the pentagonal one for a wire whose diameter is less than 6.02 nm, though the latter has been recently proposed as the lowest energy wire. These results suggest the possibility of the formation of a new stable polyicosahedral Si nanowire. (c) 2006 American Institute of Physics.

DOI： 10.1063/1.2337291

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The present paper reports on molecular dynamics simulations of the formation process of Si quantum dots (Si QDs). Icosahedral Si QDs are formed spontaneously by freezing 274-, 280-, and 323-atom Si droplets. We find that the initialization of pentagonal channels leads into the overall icosahedral structure. We also study the melting behavior of the 280-atom icosahedral Si QD. We find that the melting point is reduced more than 15% compared with that of bulk Si. A possible approach to synthesize icosahedral Si QDs is discussed. The formation of the icosahedral structure could be expected in other systems characterized by tetrahedral bonding network.

DOI： 10.1103/PhysRevB.72.245321

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Language：English   Publisher：ELSEVIER SCIENCE SA  

A comparison between water and methanol on the interaction with a pendant chain model for perfluorosulfonic ionomers (PFI), CF3OCF2CF2SO3-, was made by using molecular orbital calculation. Intermolecular interaction energy (E-int) of the most stable complex for CF3OCF2CF2SO3- + CH3OH, where methanol associates with sulfonic acid group, is -10.38 kcal/mol at the MP2/aug-cc-pVDZ//B3LYP/631 + G* level, and it is almost the same with that of CF3OCF2CF2SO3- + H2O complex (-10.58 kcal/mol). Since an association of methanol to the sulfonic acid group is quite advantageous in energy, it is expected that, similarly to water, methanol would likely populate around the acidic site. On the contrary, according to a systematic E-int analysis for 500 random configurations, dissimilar distribution of E-int was observed for methanol compared with water. This is because methyl group substitution reduces oxygen surface area and causes more attractive dispersion energy with CF3OCF2CF2SO3- by about 1.0 kcal/mol on average compared with water. To see how the difference in the interaction energy affects the solvation structure of methanol and water to the PFI, molecular dynamics simulations of a CF3OCF2CF2SO3- molecule in methanol solutions have also been carried out at the methanol concentration of 10-90 mol%. Consequently, water probably associates with the sulfonic acid group-pushing methanol close to hydrophobic sites. It was also observed that methanol molecule tends to point its methyl group toward the solute at hydrophobic sites. These results demonstrated that methanol should locate in the vicinity of hydrophobic site compared with water due to methyl group substitution. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.jfluchem.2005.07.004

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Language：English   Publisher：AMER CHEMICAL SOC  

The membranes of a perfluorosulfonic acid polymer swollen in 10-80 wt % methanol solution were investigated to elucidate the methanol effect on their morphologies, such as size of the solvent cluster, solvent location, and polymer structure, by using isothermal-isobaric molecular dynamics simulations. In higher methanol concentrations, we found less-spherical solvent aggregation and a more spread polymer structure because of the ampholytic nature of methanol. The partial radial distribution functions between solvent oxygen and fluorocarbons, which are composed of the main chain, clearly show that methanol is located closer to the polymer matrix than water. On the other hand, water is preferentially located in the vicinity of an acidic headgroup, SO3-, compared with methanol, although both have similar attractive interaction energies to the acidic group. Furthermore, we discussed solvent dynamics and hydrogen bonding between sulfonic oxygen and solvent O-H groups.

DOI： 10.1021/jp052647h

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Molecular dynamics simulations of the swollen membrane of perfluorinated ionomer, which is composed of poly(tetrafluoroethylene) backbones and perfluosulfonic pendant side chains, have been undertaken to analyze the static and dynamic properties of the water and the side chain in the membrane. The calculations were carried out for four different water contents, 5, 10, 20 and 40 wt %, at 358.15 K and 0.1 MPa. The results are summarized as follows: (1) The sulfonic acid is the unique site to which water molecules can bind, and the other sites in the pendant side chain have no bound water even at high water concentration. (2) Sulfonic acids aggregate in the short range within 4.6-7.7 Angstrom despite the electrostatic repulsion between them. In such aggregates, a water molecule bridges two sulfonic acids. (3) Pendant side chains prefer to orient perpendicular to the hydrophilic/hydrophobic interface, and long-range correlation of side chain orientations is observed at 20 and 40 wt % water uptake membranes. (4) In a low water uptake membrane, the dynamics of water is substantially restricted due to strong attractive interactions with acidic sites. In contrast, at high water content, even the water locating near the sulfonic acid is relatively mobile. The short residence time of the bound water reveals that such water can frequently exchange position with relatively free water, which locates in the center of water cluster, in highly swollen membranes.

DOI： 10.1021/jp046434o

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Language：English   Publisher：ROYAL SOC CHEMISTRY  

The intermolecular interaction energies between a water molecule and four models of pendant chains for perfluorinated ionomers, such as CF3OCF2CF2SO3H, CF3OCF2CF2SO3-, CF3CF2CF2COOH, CF3CF2CF2COO-, were analyzed by using a molecular orbital calculation. In order to investigate a variety of configurations.. five hundred random configurations that water and monomer contact at their van der Waals surfaces were generated for each system. We employed an empirical correction method for dispersion energy defined by the equation E-disp = -f(d)(R)C6R-6, so as to reduce the computational costs. The C-6 coefficients of this equation were optimized to reproduce the energies obtained at the MP2/aug-cc-pVDZ level of calculations, and then overall intermolecular interaction energies (E-int = E-HF+E-disp) were evaluated as a summation of E-disp and intermolecular interaction energy at the HF/aug-cc-pVDZ level (E-HF). From these analyses, we obtained the following conclusions. (1) The ether oxygen in the pendant chain cannot bind with water strongly due to fluorination. (2) De-protonations of sulfonic and carboxylic acids extend the region where water molecules sufficiently bind with pendant chains, and this effect would cause rich water absorption when these pendant chains form membranes. Therefore, the degree of proton disassociation would be one of the key factors for the water sorption ratio and membrane morphology. (3) The binding energy of the optimized configuration for CF3CF2CF2COO- + H2O is about 2.5 kcal mol(-1) larger than that for the CF3OCF2CF2SO3-+H2O system because of the larger electron negativities of the oxygen atoms on deprotonated carboxylic acid compared with those on the sulfonic acid.

DOI： 10.1039/b316395d

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We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermalisobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL. (C) 2003 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.10249

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The TACPACK2000 system consists of general purpose molecular dynamics simulators for large scale system of complicated materials such as biopolymer, organic crystal, liquid crystal, polymers, semiconductor, metal and alloy and ceramics and integration system for the simulators. In this presentation, the systematization technologies of the integration system are described. In the database management technology, we have developed the new technology using XML(eXtensible Markup Language) to control uniformly the data composed of molecular structure, crystal structure , potential and pseudopotential function etc. Also in the plug-in function, we have developed the software technologies for program restoration / deletion function to this system, compilation linkage functions of the program and automatic generation function of parameters input screen.

DOI： 10.11547/ciqs2001.tokusi.0.J25.0

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