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Items: 1 to 50 of 60

1.

tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules.

Griffiths MZ, Shinoda W.

J Chem Inf Model. 2019 Aug 20. doi: 10.1021/acs.jcim.9b00480. [Epub ahead of print]

PMID:
31398283
2.

Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation.

Takeda K, Andoh Y, Shinoda W, Okazaki S.

Langmuir. 2019 Aug 20;35(33):10877-10884. doi: 10.1021/acs.langmuir.9b01607. Epub 2019 Aug 7.

PMID:
31355646
3.

Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers.

Fujimoto K, Payal RS, Hattori T, Shinoda W, Nakagaki M, Sakaki S, Okazaki S.

J Comput Chem. 2019 Jul 19. doi: 10.1002/jcc.26034. [Epub ahead of print]

PMID:
31322762
4.

Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup.

Hanashima S, Murakami K, Yura M, Yano Y, Umegawa Y, Tsuchikawa H, Matsumori N, Seo S, Shinoda W, Murata M.

Biophys J. 2019 Jul 23;117(2):307-318. doi: 10.1016/j.bpj.2019.06.019. Epub 2019 Jun 25.

PMID:
31303249
5.

A coarse-grain model for entangled polyethylene melts and polyethylene crystallization.

Hall KW, Sirk TW, Klein ML, Shinoda W.

J Chem Phys. 2019 Jun 28;150(24):244901. doi: 10.1063/1.5092229.

PMID:
31255065
6.

Structure of Hydrated Crystal (Lc), Tilted Gel (Lβ'), and Liquid Crystal (Lα) Phases of Linear Alkylbenzene Sulfonate (LAS) Studied by X-ray Diffraction and Molecular Dynamics Simulation.

Takeda K, Andoh Y, Shinoda W, Okazaki S.

Langmuir. 2019 Jul 9;35(27):9011-9019. doi: 10.1021/acs.langmuir.9b01199. Epub 2019 Jun 24.

PMID:
31180227
7.

Free energy analysis of membrane pore formation process in the presence of multiple melittin peptides.

Miyazaki Y, Okazaki S, Shinoda W.

Biochim Biophys Acta Biomembr. 2019 Jul 1;1861(7):1409-1419. doi: 10.1016/j.bbamem.2019.03.002. Epub 2019 Mar 15.

PMID:
30885804
8.

SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol.

Seo S, Shinoda W.

J Chem Theory Comput. 2019 Jan 8;15(1):762-774. doi: 10.1021/acs.jctc.8b00987. Epub 2018 Dec 18.

PMID:
30514078
9.

Direct Evidence for Li Ion Hopping Conduction in Highly Concentrated Sulfolane-Based Liquid Electrolytes.

Dokko K, Watanabe D, Ugata Y, Thomas ML, Tsuzuki S, Shinoda W, Hashimoto K, Ueno K, Umebayashi Y, Watanabe M.

J Phys Chem B. 2018 Nov 29;122(47):10736-10745. doi: 10.1021/acs.jpcb.8b09439. Epub 2018 Nov 16.

PMID:
30403858
10.

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids.

Shinoda W, Hatanaka Y, Hirakawa M, Okazaki S, Tsuzuki S, Ueno K, Watanabe M.

J Chem Phys. 2018 May 21;148(19):193809. doi: 10.1063/1.5009814.

PMID:
30307251
11.

Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals.

Rath SL, Liu H, Okazaki S, Shinoda W.

J Chem Inf Model. 2018 Feb 26;58(2):328-337. doi: 10.1021/acs.jcim.7b00471. Epub 2018 Jan 24.

PMID:
29309148
12.

Transferable coarse-grained model for perfluorosulfonic acid polymer membranes.

Kuo AT, Okazaki S, Shinoda W.

J Chem Phys. 2017 Sep 7;147(9):094904. doi: 10.1063/1.4986287.

PMID:
28886657
13.

Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission.

Xiao Q, Sherman SE, Wilner SE, Zhou X, Dazen C, Baumgart T, Reed EH, Hammer DA, Shinoda W, Klein ML, Percec V.

Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):E7045-E7053. doi: 10.1073/pnas.1708380114. Epub 2017 Aug 7.

14.

Effect of the cation on the stability of cation-glyme complexes and their interactions with the [TFSA]- anion.

Tsuzuki S, Mandai T, Suzuki S, Shinoda W, Nakamura T, Morishita T, Ueno K, Seki S, Umebayashi Y, Dokko K, Watanabe M.

Phys Chem Chem Phys. 2017 Jul 19;19(28):18262-18272. doi: 10.1039/c7cp02779f.

PMID:
28696458
15.

Permeability across lipid membranes.

Shinoda W.

Biochim Biophys Acta. 2016 Oct;1858(10):2254-2265. doi: 10.1016/j.bbamem.2016.03.032. Epub 2016 Apr 14. Review.

16.

Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes.

MacDermaid CM, Kashyap HK, DeVane RH, Shinoda W, Klauda JB, Klein ML, Fiorin G.

J Chem Phys. 2015 Dec 28;143(24):243144. doi: 10.1063/1.4937153.

PMID:
26723629
17.

Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism.

Kawamoto S, Klein ML, Shinoda W.

J Chem Phys. 2015 Dec 28;143(24):243112. doi: 10.1063/1.4933087.

PMID:
26723597
18.

Structures of [Li(glyme)](+) complexes and their interactions with anions in equimolar mixtures of glymes and Li[TFSA]: analysis by molecular dynamics simulations.

Tsuzuki S, Shinoda W, Matsugami M, Umebayashi Y, Ueno K, Mandai T, Seki S, Dokko K, Watanabe M.

Phys Chem Chem Phys. 2015 Jan 7;17(1):126-9. doi: 10.1039/c4cp04718d.

PMID:
25407234
19.

[70]Fullerenes assist the formation of phospholipid bicelles at low lipid concentrations.

Ikeda A, Kiguchi K, Hida T, Yasuhara K, Nobusawa K, Akiyama M, Shinoda W.

Langmuir. 2014 Oct 21;30(41):12315-20. doi: 10.1021/la503732q. Epub 2014 Oct 10.

PMID:
25275703
20.

Free energy analysis along the stalk mechanism of membrane fusion.

Kawamoto S, Shinoda W.

Soft Matter. 2014 May 7;10(17):3048-54. doi: 10.1039/c3sm52344f.

PMID:
24695575
21.

Interactions in ion pairs of protic ionic liquids: comparison with aprotic ionic liquids.

Tsuzuki S, Shinoda W, Miran MS, Kinoshita H, Yasuda T, Watanabe M.

J Chem Phys. 2013 Nov 7;139(17):174504. doi: 10.1063/1.4827519.

PMID:
24206313
22.

Effect of different substituents on the water-solubility and stability properties of 1 : 2 [60]fullerene derivative·gamma-cyclodextrin complexes.

Ikeda A, Hirata A, Ishikawa M, Kikuchi J, Mieda S, Shinoda W.

Org Biomol Chem. 2013 Dec 7;11(45):7843-51. doi: 10.1039/c3ob41513a. Epub 2013 Sep 24.

PMID:
24061283
23.

Human RGM249-derived small RNAs potentially regulate tumor malignancy.

Miura N, Shimizu M, Shinoda W, Tsuno S, Sato R, Wang X, Jo J, Tabata Y, Hasegawa J.

Nucleic Acid Ther. 2013 Oct;23(5):332-43. doi: 10.1089/nat.2013.0424.

24.

A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation.

Kawamoto S, Nakamura T, Nielsen SO, Shinoda W.

J Chem Phys. 2013 Jul 21;139(3):034108. doi: 10.1063/1.4811677.

PMID:
23883011
25.

Intermolecular interactions in Li+-glyme and Li+-glyme-TFSA- complexes: relationship with physicochemical properties of [Li(glyme)][TFSA] ionic liquids.

Tsuzuki S, Shinoda W, Seki S, Umebayashi Y, Yoshida K, Dokko K, Watanabe M.

Chemphyschem. 2013 Jun 24;14(9):1993-2001. doi: 10.1002/cphc.201200843. Epub 2013 Apr 17.

PMID:
23595866
26.

Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory.

Nakamura T, Shinoda W.

J Chem Phys. 2013 Mar 28;138(12):124903. doi: 10.1063/1.4795579.

PMID:
23556747
27.

Regioselective recognition of a [60]fullerene-bisadduct by cyclodextrin.

Ikeda A, Ishikawa M, Aono R, Kikuchi J, Akiyama M, Shinoda W.

J Org Chem. 2013 Mar 15;78(6):2534-41. doi: 10.1021/jo3027609. Epub 2013 Feb 20.

PMID:
23391002
28.

Molecular dynamics study of catanionic bilayers composed of ion pair amphiphile with double-tailed cationic surfactant.

Kuo AT, Chang CH, Shinoda W.

Langmuir. 2012 May 29;28(21):8156-64. doi: 10.1021/la300651u. Epub 2012 May 15.

PMID:
22564043
29.

Computer simulation studies of self-assembling macromolecules.

Shinoda W, DeVane R, Klein ML.

Curr Opin Struct Biol. 2012 Apr;22(2):175-86. doi: 10.1016/j.sbi.2012.01.011. Epub 2012 Mar 6. Review.

PMID:
22402497
30.

Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics.

Levine BG, LeBard DN, DeVane R, Shinoda W, Kohlmeyer A, Klein ML.

J Chem Theory Comput. 2011 Dec 13;7(12):4135-45. doi: 10.1021/ct2005193. Epub 2011 Nov 22.

PMID:
26598358
31.

Cholesterol effect on water permeability through DPPC and PSM lipid bilayers: a molecular dynamics study.

Saito H, Shinoda W.

J Phys Chem B. 2011 Dec 29;115(51):15241-50. doi: 10.1021/jp201611p. Epub 2011 Dec 1.

PMID:
22081997
32.

Effects of hesperidin on the progression of hypercholesterolemia and fatty liver induced by high-cholesterol diet in rats.

Wang X, Hasegawa J, Kitamura Y, Wang Z, Matsuda A, Shinoda W, Miura N, Kimura K.

J Pharmacol Sci. 2011;117(3):129-38. Epub 2011 Oct 7.

33.

Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems.

Nakamura T, Shinoda W, Ikeshoji T.

J Chem Phys. 2011 Sep 7;135(9):094106. doi: 10.1063/1.3626410.

PMID:
21913752
34.

Effects of conformational flexibility of alkyl chains of cations on diffusion of ions in ionic liquids.

Tsuzuki S, Matsumoto H, Shinoda W, Mikami M.

Phys Chem Chem Phys. 2011 Apr 7;13(13):5987-93. doi: 10.1039/c0cp02087g. Epub 2011 Feb 21.

PMID:
21336402
35.

Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids.

DeVane R, Jusufi A, Shinoda W, Chiu CC, Nielsen SO, Moore PB, Klein ML.

J Phys Chem B. 2010 Dec 16;114(49):16364-72. doi: 10.1021/jp1070264. Epub 2010 Nov 19.

PMID:
21090655
36.

Interactions of perfluoroalkyltrifluoroborate anions with li ion and imidazolium cation: effects of perfluoroalkyl chain on motion of ions in ionic liquids.

Tsuzuki S, Umecky T, Matsumoto H, Shinoda W, Mikami M.

J Phys Chem B. 2010 Sep 9;114(35):11390-6. doi: 10.1021/jp104380s.

PMID:
20707368
37.

Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field.

Shinoda W, DeVane R, Klein ML.

J Phys Chem B. 2010 May 27;114(20):6836-49. doi: 10.1021/jp9107206.

38.

Coarse-grained potential models for phenyl-based molecules: II. Application to fullerenes.

Chiu CC, DeVane R, Klein ML, Shinoda W, Moore PB, Nielsen SO.

J Phys Chem B. 2010 May 20;114(19):6394-400. doi: 10.1021/jp9117375.

PMID:
20426450
39.

Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data.

DeVane R, Klein ML, Chiu CC, Nielsen SO, Shinoda W, Moore PB.

J Phys Chem B. 2010 May 20;114(19):6386-93. doi: 10.1021/jp9117369.

PMID:
20426449
40.

A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.

Devane R, Shinoda W, Moore PB, Klein ML.

J Chem Theory Comput. 2009 Aug 11;5(8):2115-2124.

41.

A mean field approach for computing solid-liquid surface tension for nanoscale interfaces.

Chiu CC, Ranatunga RJ, Torres Flores D, Pérez DV, Moore PB, Shinoda W, Nielsen SO.

J Chem Phys. 2010 Feb 7;132(5):054706. doi: 10.1063/1.3308625.

PMID:
20136332
42.

Size-dependent hydrophobic to hydrophilic transition for nanoparticles: a molecular dynamics study.

Chiu CC, Moore PB, Shinoda W, Nielsen SO.

J Chem Phys. 2009 Dec 28;131(24):244706. doi: 10.1063/1.3276915.

PMID:
20059098
43.

Molecular dynamics simulations of ionic liquids: cation and anion dependence of self-diffusion coefficients of ions.

Tsuzuki S, Shinoda W, Saito H, Mikami M, Tokuda H, Watanabe M.

J Phys Chem B. 2009 Aug 6;113(31):10641-9. doi: 10.1021/jp811128b.

PMID:
19591511
44.

Models for phosphatidylglycerol lipids put to a structural test.

Hénin J, Shinoda W, Klein ML.

J Phys Chem B. 2009 May 14;113(19):6958-63. doi: 10.1021/jp900645z.

45.

Area per ligand as a function of nanoparticle radius: a theoretical and computer simulation approach.

Kalescky RJ, Shinoda W, Moore PB, Nielsen SO.

Langmuir. 2009 Feb 3;25(3):1352-9. doi: 10.1021/la8032918.

46.

Enhanced hydrophobicity of fluorinated lipid bilayer: a molecular dynamics study.

Saito H, Shinoda W, Mikami M.

J Phys Chem B. 2008 Sep 11;112(36):11305-9. doi: 10.1021/jp801057k. Epub 2008 Aug 19.

PMID:
18710280
47.

Large-scale molecular dynamics simulations of self-assembling systems.

Klein ML, Shinoda W.

Science. 2008 Aug 8;321(5890):798-800. doi: 10.1126/science.1157834.

PMID:
18687954
48.

Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation.

Matubayasi N, Shinoda W, Nakahara M.

J Chem Phys. 2008 May 21;128(19):195107. doi: 10.1063/1.2919117.

PMID:
18500905
49.

United-atom acyl chains for CHARMM phospholipids.

Hénin J, Shinoda W, Klein ML.

J Phys Chem B. 2008 Jun 12;112(23):7008-15. doi: 10.1021/jp800687p. Epub 2008 May 16.

PMID:
18481889
50.

Efficient free energy calculation of water across lipid membranes.

Shinoda K, Shinoda W, Mikami M.

J Comput Chem. 2008 Sep;29(12):1912-8. doi: 10.1002/jcc.20956.

PMID:
18366020

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