Results 241 to 250 of about 6,841,171 (281)

Brownian dynamics simulation of protein association

Journal of Computer-Aided Molecular Design, 1988
The Brownian Dynamics (BD) method is applied to study the diffusive dynamics and interaction of two proteins, cytochrome c (CYTC) and cytochrome c peroxidase (CYP). We examine the role of protein electrostatic charge distribution in the facilitation of protein-protein docking prior to the electron transfer step, assessing the influence of individual ...
Scott H. Northrup, J. Alan Luton, Jeffrey O. Boles, John C. L. Reynolds   +3 more
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Brownian dynamics simulations of Laponite colloid suspensions

Physical Review E, 2004
Colloidal suspensions of Laponite clay platelets are studied by means of Brownian dynamics simulations. The platelets carry discrete charged sites which interact via a Yukawa potential. As in the paper by S. Kutter et al. [J. Chem. Phys. 112, 311 (2000)], two models are considered.
G, Odriozola, M, Romero-Bastida, F de J, Guevara-Rodríguez   +2 more
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Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program

2014
This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum ...
Tongye, Shen, Chung F, Wong
openaire   +2 more sources

Lysozyme dimerization: brownian dynamics simulation

Journal of Molecular Modeling, 2005
The lysozyme dimerization reaction has been studied within the framework of encounter-complex (EC) formation theory using the MacroDox software package. Two types of energetically favorite ECs were determined. In the first of them, active-center amino acids of lysozyme take part in the complex formation or the second molecule blocks accessibility to ...
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Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation

Journal of the American Chemical Society, 2001
We report the implementation of an all-atom Brownian dynamics simulation model of peptides using the constraint algorithm LINCS. The algorithm has been added as a part of UHBD. It uses adaptive time steps to achieve a balance between computational speed and stability.
T, Shen, C F, Wong, J A, McCammon
openaire   +2 more sources

Brownian Dynamics Simulations of Associating Diblock Copolymers

Langmuir, 2007
A novel coarse-grained computational model for associating polymers is proposed that is based on a Gaussian "blob" representation of the polymer chains. The model allows a large number of model polymers to be simulated at moderate computational cost over a wide packing fraction range using the Brownian dynamics, BD, technique.
M J, Cass, D M, Heyes, R J, English
openaire   +2 more sources

Brownian dynamics simulations of fluorescence fluctuation spectroscopy

European Biophysics Journal, 2001
We have developed a program for the simulation of the fluorescence fluctuations as detected from highly diluted samples of (bio)molecules. The model is applied to translational diffusion and takes into account the hydrodynamic interactions. The solution concentration is kept constant by assuming periodic boundary conditions and spans here the range 0.5<
de la Torre, MH, Forni, R, CHIRICO, GIUSEPPE   +2 more
openaire   +3 more sources

An efficient algorithm for the brownian dynamics simulation of aggregation

Computer Physics Communications, 1986
Computer simulation techniques have proven to be quite useful for studying the structure of particulates produced by the process of growth through the aggregation of smaller particles. In this paper we introduce an efficient algorithm for use in the computer simulation of the kinetics of the growth of particulates. The new algorithm is based on sorting
Sullivan, Francis, Mountain, Raymond D.
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Brownian dynamics simulation of helix‐capping motifs

Biopolymers, 2003
AbstractHelix ‐capping motifs are believed to play an important role in stabilizing α‐helices and defining helix start and stop signals. We performed microsecond scale Brownian dynamics simulations to study ten XAAD sequences, with X = (A,E,I,L,N,Q,S,T,V,Y), to examine their propensity to form helix capping motifs and correlate these results with those
Tongye, Shen, Chung F, Wong, J Andrew, McCammon   +2 more
openaire   +2 more sources

Brownian Dynamics Simulation of the Dynamics of Stretched DNA

Volume 6: 10th International Conference on Multibody Systems, Nonlinear Dynamics, and Control, 2014
DNA is a long flexible polymer and is involved in several fundamental cellular processes such as transcription, replication and chromosome packaging. These processes induce forces and torques in the DNA which deform it. These deformations in turn affect the structure and function of DNA.
Ikenna D. Ivenso, Todd D. Lillian
openaire   +1 more source