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Items: 1 to 20 of 99

1.

Microcanonical coarse-graining of the kinetic Ising model.

Sigg D, Voelz VA, Carnevale V.

J Chem Phys. 2020 Feb 28;152(8):084104. doi: 10.1063/1.5139228.

PMID:
32113343
2.

A general method for spatially coarse-graining Metropolis Monte Carlo simulations onto a lattice.

Liu X, Seider WD, Sinno T.

J Chem Phys. 2013 Mar 21;138(11):114104. doi: 10.1063/1.4794686.

PMID:
23534624
3.

Mesoscale model of polymer melt structure: self-consistent mapping of molecular correlations to coarse-grained potentials.

Ashbaugh HS, Patel HA, Kumar SK, Garde S.

J Chem Phys. 2005 Mar 8;122(10):104908.

PMID:
15836359
4.

First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids.

Lyubimov I, Guenza MG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 1):031801. Epub 2011 Sep 13.

PMID:
22060394
5.

Coarse-grained lattice kinetic Monte Carlo simulation of systems of strongly interacting particles.

Dai J, Seider WD, Sinno T.

J Chem Phys. 2008 May 21;128(19):194705. doi: 10.1063/1.2913241.

PMID:
18500884
6.

Isomerization kinetics of flexible molecules in the gas phase: Atomistic versus coarse-grained sampling.

Falvo C, Gamboa-Suárez A, Cazayus-Claverie S, Parneix P, Calvo F.

J Chem Phys. 2018 Aug 21;149(7):072334. doi: 10.1063/1.5026688.

PMID:
30134728
7.

Numerical tests of nucleation theories for the Ising models.

Ryu S, Cai W.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jul;82(1 Pt 1):011603. Epub 2010 Jul 15.

PMID:
20866625
8.

The multiscale coarse-graining method. V. Isothermal-isobaric ensemble.

Das A, Andersen HC.

J Chem Phys. 2010 Apr 28;132(16):164106. doi: 10.1063/1.3394862.

PMID:
20441257
9.

Hybrid multiscale coarse-graining for dynamics on complex networks.

Shen C, Chen H, Hou Z, Kurths J.

Chaos. 2018 Dec;28(12):123122. doi: 10.1063/1.5048962.

PMID:
30599515
10.

Coarse-graining errors and numerical optimization using a relative entropy framework.

Chaimovich A, Shell MS.

J Chem Phys. 2011 Mar 7;134(9):094112. doi: 10.1063/1.3557038.

PMID:
21384955
11.

Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes.

Matsuoka T, Tanaka S, Ebina K.

Biosystems. 2014 Mar;117:15-29. doi: 10.1016/j.biosystems.2013.12.008. Epub 2014 Jan 10.

PMID:
24418347
12.

Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems.

Katsoulakis MA, Plechác P.

J Chem Phys. 2013 Aug 21;139(7):074115. doi: 10.1063/1.4818534.

PMID:
23968080
13.

The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems.

Kalligiannaki E, Harmandaris V, Katsoulakis MA, Plecháč P.

J Chem Phys. 2015 Aug 28;143(8):084105. doi: 10.1063/1.4928857.

PMID:
26328816
14.

Energy-conserving coarse-graining of complex molecules.

Español P, Serrano M, Pagonabarraga I, Zúñiga I.

Soft Matter. 2016 May 25;12(21):4821-37. doi: 10.1039/c5sm03038b.

PMID:
27127809
15.

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth.

de la Cruz R, Guerrero P, Calvo J, Alarcón T.

J Comput Phys. 2017 Dec 1;350:974-991. doi: 10.1016/j.jcp.2017.09.019.

16.

Numerical coarse-graining of fluid field theories.

Villet MC, Fredrickson GH.

J Chem Phys. 2010 Jan 21;132(3):034109. doi: 10.1063/1.3289723.

PMID:
20095730
17.

Coarse-graining protein structures with local multivariate features from molecular dynamics.

Zhang Z, Wriggers W.

J Phys Chem B. 2008 Nov 6;112(44):14026-35. doi: 10.1021/jp806291p. Epub 2008 Oct 15.

18.

An automatic coarse-graining and fine-graining simulation method: application on polyethylene.

Chen LJ, Qian HJ, Lu ZY, Li ZS, Sun CC.

J Phys Chem B. 2006 Nov 30;110(47):24093-100.

PMID:
17125381
19.

A test of systematic coarse-graining of molecular dynamics simulations: Transport properties.

Fu CC, Kulkarni PM, Shell MS, Leal LG.

J Chem Phys. 2013 Sep 7;139(9):094107. doi: 10.1063/1.4819472.

PMID:
24028102
20.

Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations.

Qvist J, Schober H, Halle B.

J Chem Phys. 2011 Apr 14;134(14):144508. doi: 10.1063/1.3578472.

PMID:
21495765

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