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Relevant bibliographies by topics / Brownian dynamics simulations (BDS)

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Journal articles

Academic literature on the topic 'Brownian dynamics simulations (BDS)'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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

1

GUPTA, V. K. "BROWNIAN DYNAMICS SIMULATION OF CATCH TO SLIP TRANSITION OVER A MODEL ENERGY LANDSCAPE." Journal of Biological Systems 24, no. 02n03 (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 (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 (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 (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 (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 (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 (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 (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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