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Literature DB >> 12496076

Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.

Miguel X Fernandes¹, José García de la Torre.

Abstract

We have developed a Brownian dynamics simulation algorithm to generate Brownian trajectories of an isolated, rigid particle of arbitrary shape in the presence of electric fields or any other external agents. Starting from the generalized diffusion tensor, which can be calculated with the existing HYDRO software, the new program BROWNRIG (including a case-specific subprogram for the external agent) carries out a simulation that is analyzed later to extract the observable dynamic properties. We provide a variety of examples of utilization of this method, which serve as tests of its performance, and also illustrate its applicability. Examples include free diffusion, transport in an electric field, and diffusion in a restricting environment.

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Year: 2002 PMID： 12496076 PMCID： PMC1302384 DOI： 10.1016/S0006-3495(02)75309-5

Source DB: PubMed Journal: Biophys J ISSN： 0006-3495 Impact factor: 4.033

21 in total

1. HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

Authors: J García de la Torre; M L Huertas; B Carrasco
Journal: J Magn Reson Date: 2000-11 Impact factor: 2.229

2. HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images.

Authors: J García de la Torre; O Llorca; J L Carrascosa; J M Valpuesta
Journal: Eur Biophys J Date: 2001-10 Impact factor: 1.733

3. Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins.

Authors: J García de la Torre
Journal: Biophys Chem Date: 2001-11-28 Impact factor: 2.352

4. Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape.

Authors: J Garcia de la Torre
Journal: Biophys Chem Date: 2001-12-25 Impact factor: 2.352

5. An analytical solution to the problem of the orientation of rigid particles by planar obstacles. Application to membrane systems and to the calculation of dipolar couplings in protein NMR spectroscopy.

Authors: M X Fernandes; P Bernadó; M Pons; J García de la Torre
Journal: J Am Chem Soc Date: 2001-12-05 Impact factor: 15.419

Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.

1. HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

2. HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images.

3. Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins.

4. Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape.

5. An analytical solution to the problem of the orientation of rigid particles by planar obstacles. Application to membrane systems and to the calculation of dipolar couplings in protein NMR spectroscopy.

6. Boundary element modeling of biomolecular transport.

7. Frictional coefficients of multisubunit structures. I. Theory.

8. Dynamics of fluorescence polarization in macromolecules.

9. Multistep Brownian dynamics: application to short wormlike chains.

Review 10. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications.

1. Unbiased rotational moves for rigid-body dynamics.

2. Diffusional encounter of barnase and barstar.

3. Electrostatic rate enhancement and transient complex of protein-protein association.

4. Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics.

5. Brownian dynamics of subunit addition-loss kinetics and thermodynamics in linear polymer self-assembly.

6. Effects of macromolecular crowding on intracellular diffusion from a single particle perspective.

7. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

8. Neutron spin-echo studies of hemoglobin and myoglobin: multiscale internal dynamics.

9. Browndye: A Software Package for Brownian Dynamics.

10. Diffusion in crowded biological environments: applications of Brownian dynamics.