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Items: 1 to 20 of 92

1.

Assessing the two-body diffusion tensor calculated by the bead models.

Wang N, Huber GA, McCammon JA.

J Chem Phys. 2013 May 28;138(20):204117. doi: 10.1063/1.4807590.

2.

Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres.

Carrasco B, García de la Torre J, Zipper P.

Eur Biophys J. 1999;28(6):510-5.

PMID:
10460344
3.
4.

BROWNIAN DYNAMICS SIMULATION OF MACROMOLECULE DIFFUSION IN A PROTOCELL.

Ando T, Skolnick J.

Quantum Bioinform IV (2010). 2011;28:413-426.

5.

Bead-model calculation of scattering diagrams: Brownian dynamics study of flexibility in immunoglobulin IgG1.

Díaz FG, López Cascales JJ, García de la Torre J.

J Biochem Biophys Methods. 1993 Jul;26(4):261-71.

PMID:
8409198
6.

Matrix-free Brownian dynamics simulation technique for semidilute polymeric solutions.

Saadat A, Khomami B.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Sep;92(3):033307. doi: 10.1103/PhysRevE.92.033307. Epub 2015 Sep 29.

PMID:
26465586
7.

Hydrodynamic radii and diffusion coefficients of particle aggregates derived from the bead model.

Adamczyk Z, Sadlej K, Wajnryb E, Ekiel-Jezewska ML, Warszyński P.

J Colloid Interface Sci. 2010 Jul 15;347(2):192-201. doi: 10.1016/j.jcis.2010.03.066. Epub 2010 Apr 3.

PMID:
20430400
8.

Microscopic theory of topologically entangled fluids of rigid macromolecules.

Sussman DM, Schweizer KS.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jun;83(6 Pt 1):061501. Epub 2011 Jun 7.

PMID:
21797366
9.

Translational diffusion of macromolecules and nanoparticles modeled as non-overlapping bead arrays in an effective medium.

Allison S, Pei H, Haynes M, Xin Y, Law L, Labrum J, Augustin D.

J Phys Chem B. 2008 May 8;112(18):5858-66. doi: 10.1021/jp710700n. Epub 2008 Apr 17.

PMID:
18416571
10.

Toward an Accurate Modeling of Hydrodynamic Effects on the Translational and Rotational Dynamics of Biomolecules in Many-Body Systems.

Długosz M, Antosiewicz JM.

J Phys Chem B. 2015 Jul 2;119(26):8425-39. doi: 10.1021/acs.jpcb.5b04675. Epub 2015 Jun 23.

PMID:
26068580
11.

An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations.

Geyer T, Winter U.

J Chem Phys. 2009 Mar 21;130(11):114905. doi: 10.1063/1.3089668.

PMID:
19317564
12.

Friction of -bead macromolecules in solution: effects of the bead-solvent interaction.

Uvarov A, Fritzsche S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jan;73(1 Pt 1):011111. Epub 2006 Jan 31.

PMID:
16486126
13.

Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs.

Rocco M, Byron O.

Eur Biophys J. 2015 Sep;44(6):417-31. doi: 10.1007/s00249-015-1042-9. Epub 2015 Jun 12. Erratum in: Eur Biophys J. 2015 Sep;44(6):433-6.

PMID:
26066679
14.

Intrinsic viscosity of bead models for macromolecules and nanoparticles.

García de la Torre J, Amorós D, Ortega A.

Eur Biophys J. 2010 Feb;39(3):381-8. doi: 10.1007/s00249-009-0405-5. Epub 2009 Feb 6.

PMID:
19198827
15.

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion.

Ando T, Skolnick J.

Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18457-62. doi: 10.1073/pnas.1011354107. Epub 2010 Oct 11.

16.

N log N method for hydrodynamic interactions of confined polymer systems: Brownian dynamics.

Hernández-Ortiz JP, de Pablo JJ, Graham MD.

J Chem Phys. 2006 Oct 28;125(16):164906.

PMID:
17092138
17.

Hydrodynamic multibead modeling: problems, pitfalls, and solutions. 1. Ellipsoid models.

Zipper P, Durchschlag H.

Eur Biophys J. 2010 Feb;39(3):437-47. doi: 10.1007/s00249-009-0424-2. Epub 2009 Mar 12.

PMID:
19280183
18.
19.

Gold bead-strings in silica nanowires: a simple diffusion model.

Fletcher NH, Elliman RG, Kim TH.

Nanotechnology. 2009 Feb 25;20(8):085613. doi: 10.1088/0957-4484/20/8/085613. Epub 2009 Feb 3.

PMID:
19417461
20.

Dynamic electro-optic properties of macromolecules and nanoparticles in solution: a review of computational and simulation methodologies.

García de la Torre J.

Colloids Surf B Biointerfaces. 2007 Apr 15;56(1-2):4-15. Epub 2006 Oct 12. Review.

PMID:
17125977

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