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Journal articles on the topic 'Brownian dynamics simulations (BDS)'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

GUPTA, V. K. "BROWNIAN DYNAMICS SIMULATION OF CATCH TO SLIP TRANSITION OVER A MODEL ENERGY LANDSCAPE." Journal of Biological Systems 24, no. 02n03 (June 2016): 275–93. http://dx.doi.org/10.1142/s0218339016500145.

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We perform Brownian dynamics simulation (BDS) of catch to slip transition over a model energy landscape. Through our BDS we demonstrate that for forces below the critical force the bond rupture occurs mostly through the catch pathway while for forces above the critical force the bond rupture occurs mostly through the slip pathway. We also demonstrate that the shoulder in the bond rupture force distribution switches to peak as the loading rate increases progressively and the bond lifetime is maximized at the model dependent critical force. The force dependent bond lifetime obtained via transforming the bond rupture force distribution at a given loading rate is in excellent agreement with that obtained from our BDS at constant forces. An alternative to the current mechanism of catch to slip transition is presented and validated through BDS.

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2

Geyer, T., C. Gorba, and V. Helms. "Interfacing Brownian dynamics simulations." Journal of Chemical Physics 120, no. 10 (March 8, 2004): 4573–80. http://dx.doi.org/10.1063/1.1647522.

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3

Oettinger, Hans Christian. "Variance Reduced Brownian Dynamics Simulations." Macromolecules 27, no. 12 (June 1994): 3415–23. http://dx.doi.org/10.1021/ma00090a041.

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4

Huber, Gary A., and J. Andrew McCammon. "Brownian Dynamics Simulations of Biological Molecules." Trends in Chemistry 1, no. 8 (November 2019): 727–38. http://dx.doi.org/10.1016/j.trechm.2019.07.008.

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5

He, Siqian, and Harold A. Scheraga. "Brownian dynamics simulations of protein folding." Journal of Chemical Physics 108, no. 1 (January 1998): 287–300. http://dx.doi.org/10.1063/1.475379.

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6

Erban, Radek. "From molecular dynamics to Brownian dynamics." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 470, no. 2167 (July 8, 2014): 20140036. http://dx.doi.org/10.1098/rspa.2014.0036.

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Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.

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7

Wade, R. C. "Brownian dynamics simulations of enzyme-substrate encounter." Biochemical Society Transactions 24, no. 1 (February 1, 1996): 254–59. http://dx.doi.org/10.1042/bst0240254.

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8

Li, Lei, Ronald G. Larson, and Tam Sridhar. "Brownian dynamics simulations of dilute polystyrene solutions." Journal of Rheology 44, no. 2 (March 2000): 291–322. http://dx.doi.org/10.1122/1.551087.

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9

Meng, Xuan-Yu, Yu Xu, Hong-Xing Zhang, Mihaly Mezei, and Meng Cui. "Predicting Protein Interactions by Brownian Dynamics Simulations." Journal of Biomedicine and Biotechnology 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/121034.

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We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions.

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10

BRAŃKA, ARKADIUSZ C. "ON ALGORITHMS FOR BROWNIAN DYNAMICS COMPUTER SIMULATIONS." Computational Methods in Science and Technology 4, no. 1 (1998): 35–42. http://dx.doi.org/10.12921/cmst.1998.04.01.35-42.

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11

Cass, M. J., D. M. Heyes, and R. J. English. "Brownian Dynamics Simulations of Associating Diblock Copolymers." Langmuir 23, no. 12 (June 2007): 6576–87. http://dx.doi.org/10.1021/la063210j.

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12

Huertas de la Torre, Marisa, Riccardo Forni, and Giuseppe Chirico. "Brownian dynamics simulations of fluorescence fluctuation spectroscopy." European Biophysics Journal 30, no. 2 (May 11, 2001): 129–39. http://dx.doi.org/10.1007/s002490000117.

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13

DÜNWEG, BURKHARD, and WOLFGANG PAUL. "BROWNIAN DYNAMICS SIMULATIONS WITHOUT GAUSSIAN RANDOM NUMBERS." International Journal of Modern Physics C 02, no. 03 (September 1991): 817–27. http://dx.doi.org/10.1142/s0129183191001037.

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We point out that in a Brownian dynamics simulation it is justified to use arbitrary distribution functions of random numbers if the moments exhibit the correct limiting behavior prescribed by the Fokker-Planck equation. Our argument is supported by a simple analytical consideration and some numerical examples: We simulate the Wiener process, the Ornstein-Uhlenbeck process and the diffusion in a Φ4 potential, using both Gaussian and uniform random numbers. In these examples, the rate of convergence of the mean first exit time is found to be nearly identical for both types of random numbers.

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14

Suman, Balram, and Satish Kumar. "Brownian dynamics simulations of hydrophobic dendrimer adsorption." Molecular Simulation 35, no. 1-2 (January 2009): 38–49. http://dx.doi.org/10.1080/08927020802191966.

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15

Podtelezhnikov, Alexei, and Alexander Vologodskii. "Simulations of Polymer Cyclization by Brownian Dynamics." Macromolecules 30, no. 21 (October 1997): 6668–73. http://dx.doi.org/10.1021/ma970391a.

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16

Wijmans, Christopher M., and Eric Dickinson. "Brownian dynamics simulations of filled particle gels." Journal of the Chemical Society, Faraday Transactions 94, no. 1 (1998): 129–37. http://dx.doi.org/10.1039/a706632e.

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17

Berger, Jeffrey W., and Jane M. Vanderkooi. "Brownian dynamics simulations of intramolecular energy transfer." Biophysical Chemistry 30, no. 3 (July 1988): 257–69. http://dx.doi.org/10.1016/0301-4622(88)85021-x.

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18

Sanyal, Subrata, and Ajay K. Sood. "Relaxation dynamics in dense binary colloidal mixtures: Brownian dynamics simulations." Physical Review E 57, no. 1 (January 1, 1998): 908–23. http://dx.doi.org/10.1103/physreve.57.908.

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19

van den Noort, A., and W. J. Briels. "Brownian dynamics simulations of concentration coupled shear banding." Journal of Non-Newtonian Fluid Mechanics 152, no. 1-3 (June 2008): 148–55. http://dx.doi.org/10.1016/j.jnnfm.2007.11.001.

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20

Adolf, David B., and Mark D. Ediger. "Brownian dynamics simulations of local motions in polyisoprene." Macromolecules 24, no. 21 (October 1991): 5834–42. http://dx.doi.org/10.1021/ma00021a018.

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21

Azevedo, T. N., and L. G. Rizzi. "Microrheology of filament networks from Brownian dynamics simulations." Journal of Physics: Conference Series 1483 (February 2020): 012001. http://dx.doi.org/10.1088/1742-6596/1483/1/012001.

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22

Chang, Rakwoo, and Arun Yethiraj. "Brownian dynamics simulations of salt-free polyelectrolyte solutions." Journal of Chemical Physics 116, no. 12 (2002): 5284. http://dx.doi.org/10.1063/1.1453396.

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23

Guo, Kunkun, Julian Shillcock, and Reinhard Lipowsky. "Treadmilling of actin filaments via Brownian dynamics simulations." Journal of Chemical Physics 133, no. 15 (October 21, 2010): 155105. http://dx.doi.org/10.1063/1.3497001.

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24

Lyulin, Alexey V., Geoffrey R. Davies, and David B. Adolf. "Brownian Dynamics Simulations of Dendrimers under Shear Flow." Macromolecules 33, no. 9 (May 2000): 3294–304. http://dx.doi.org/10.1021/ma992128a.

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25

Brańka, A. C., and D. M. Heyes. "Algorithms for Brownian dynamics computer simulations: Multivariable case." Physical Review E 60, no. 2 (August 1, 1999): 2381–87. http://dx.doi.org/10.1103/physreve.60.2381.

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26

Xu, Yueyi, and Micah J. Green. "Brownian dynamics simulations of nanosheet solutions under shear." Journal of Chemical Physics 141, no. 2 (July 14, 2014): 024905. http://dx.doi.org/10.1063/1.4884821.

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27

Zakharov, P. N., N. A. Abrashitova, A. V. Shmatok, V. O. Ryzhikh, N. B. Gudimchuk, and F. I. Ataullakhanov. "PGA HPC Implementation of Microtubule Brownian Dynamics Simulations." Proceedings of the Institute for System Programming of the RAS 28, no. 3 (2016): 241–66. http://dx.doi.org/10.15514/ispras-2016-28(3)-15.

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28

Ilie, Ioana M., Wouter K. den Otter, and Wim J. Briels. "Rotational Brownian Dynamics simulations of clathrin cage formation." Journal of Chemical Physics 141, no. 6 (August 14, 2014): 065101. http://dx.doi.org/10.1063/1.4891306.

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29

Potter, Michael J., Brock Luty, Huan-Xiang Zhou, and J. Andrew McCammon. "Time-Dependent Rate Coefficients from Brownian Dynamics Simulations." Journal of Physical Chemistry 100, no. 12 (January 1996): 5149–54. http://dx.doi.org/10.1021/jp953229n.

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30

Yu, Wenbin, Chung F. Wong, and John Zhang. "Brownian Dynamics Simulations of Polyalanine in Salt Solutions." Journal of Physical Chemistry 100, no. 37 (January 1996): 15280–89. http://dx.doi.org/10.1021/jp960124r.

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31

Xiao, C., and D. M. Heyes. "Brownian dynamics simulations of attractive polymers in solution." Journal of Chemical Physics 117, no. 5 (August 2002): 2377–88. http://dx.doi.org/10.1063/1.1488928.

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32

Carpen, Ileana C., and John F. Brady. "Microrheology of colloidal dispersions by Brownian dynamics simulations." Journal of Rheology 49, no. 6 (November 2005): 1483–502. http://dx.doi.org/10.1122/1.2085174.

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33

Kenward, Martin, and Kevin D. Dorfman. "Brownian dynamics simulations of single-stranded DNA hairpins." Journal of Chemical Physics 130, no. 9 (March 7, 2009): 095101. http://dx.doi.org/10.1063/1.3078795.

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34

Heyes, D. M., and J. R. Melrose. "Brownian Dynamics Simulations of Electro-Rheological Fluids, II." Molecular Simulation 5, no. 5 (December 1990): 293–306. http://dx.doi.org/10.1080/08927029008022415.

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35

Torres-Díaz, I., and C. Rinaldi. "Brownian dynamics simulations of ellipsoidal magnetizable particle suspensions." Journal of Physics D: Applied Physics 47, no. 23 (May 13, 2014): 235003. http://dx.doi.org/10.1088/0022-3727/47/23/235003.

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36

Heyes, D. M., and J. R. Melrose. "Brownian dynamics simulations of model hard-sphere suspensions." Journal of Non-Newtonian Fluid Mechanics 46, no. 1 (January 1993): 1–28. http://dx.doi.org/10.1016/0377-0257(93)80001-r.

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37

Perlmutter, Jason D., and Michael F. Hagan. "Brownian Dynamics Simulations of Polymer Mediated Capsid Assembly." Biophysical Journal 104, no. 2 (January 2013): 413a—414a. http://dx.doi.org/10.1016/j.bpj.2012.11.2305.

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38

Erban, Radek. "Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472, no. 2186 (February 2016): 20150556. http://dx.doi.org/10.1098/rspa.2015.0556.

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Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl − ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

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39

Corry, Ben, Matthew Hoyles, Toby W. Allen, Michael Walker, Serdar Kuyucak, and Shin-Ho Chung. "Reservoir Boundaries in Brownian Dynamics Simulations of Ion Channels." Biophysical Journal 82, no. 4 (April 2002): 1975–84. http://dx.doi.org/10.1016/s0006-3495(02)75546-x.

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40

Chirico, G., and J. Langowski. "Brownian dynamics simulations of supercoiled DNA with bent sequences." Biophysical Journal 71, no. 2 (August 1996): 955–71. http://dx.doi.org/10.1016/s0006-3495(96)79299-8.

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41

Huber, G. A., and S. Kim. "Weighted-ensemble Brownian dynamics simulations for protein association reactions." Biophysical Journal 70, no. 1 (January 1996): 97–110. http://dx.doi.org/10.1016/s0006-3495(96)79552-8.

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42

Nissfolk, Jarl, Tobias Ekholm, and Christer Elvingson. "Brownian dynamics simulations on a hypersphere in 4-space." Journal of Chemical Physics 119, no. 13 (October 2003): 6423–32. http://dx.doi.org/10.1063/1.1603729.

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43

Jardat, M., O. Bernard, C. Treiner, G. R. Kneller, and P. Turq. "Dynamical properties of electrolyte solutions from Brownian dynamics simulations." Le Journal de Physique IV 10, PR5 (March 2000): Pr5–113—Pr5–116. http://dx.doi.org/10.1051/jp4:2000514.

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44

Heyes, D. M., and A. C. Branka. "Brownian Dynamics Simulations of Model Near-Hard-Sphere Suspensions." Physics and Chemistry of Liquids 26, no. 3 (October 1993): 153–60. http://dx.doi.org/10.1080/00319109308030658.

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45

Lipková, Jana, Konstantinos C. Zygalakis, S. Jonathan Chapman, and Radek Erban. "Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions." SIAM Journal on Applied Mathematics 71, no. 3 (January 2011): 714–30. http://dx.doi.org/10.1137/100794213.

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46

Fiore, Andrew M., Florencio Balboa Usabiaga, Aleksandar Donev, and James W. Swan. "Rapid sampling of stochastic displacements in Brownian dynamics simulations." Journal of Chemical Physics 146, no. 12 (March 28, 2017): 124116. http://dx.doi.org/10.1063/1.4978242.

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47

Mielke, Steven P., Craig J. Benham, and Niels Grønbech-Jensen. "Persistence Lengths of DNA Obtained from Brownian Dynamics Simulations†." Journal of Physical Chemistry A 113, no. 16 (April 23, 2009): 4213–16. http://dx.doi.org/10.1021/jp8107599.

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48

Vigilante, Wyatt, Oscar Lopez, and Jerome Fung. "Brownian dynamics simulations of sphere clusters in optical tweezers." Optics Express 28, no. 24 (November 13, 2020): 36131. http://dx.doi.org/10.1364/oe.409078.

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49

Lyulin, Alexey V., David B. Adolf, and Geoffrey R. Davies. "Brownian dynamics simulations of linear polymers under shear flow." Journal of Chemical Physics 111, no. 2 (July 8, 1999): 758–71. http://dx.doi.org/10.1063/1.479355.

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50

Segovia-Gutiérrez, Juan Pablo, Juan de Vicente, Roque Hidalgo-Álvarez, and Antonio M. Puertas. "Brownian dynamics simulations in magnetorheology and comparison with experiments." Soft Matter 9, no. 29 (2013): 6970. http://dx.doi.org/10.1039/c3sm00137g.

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