Results 21 to 30 of about 633,406 (289)

Conformational Changes of Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations

Frontiers in Chemistry, 2021
Glutamine 5′-phosphoribosylpyrophosphate amidotransferase (GPATase) catalyzes the synthesis of phosphoribosylamine, pyrophosphate, and glutamate from phosphoribosylpyrophosphate, as well as glutamine at two sites (i.e., glutaminase and ...
Congcong Li, Siao Chen, Tianci Huang, Fangning Zhang, Jiawei Yuan, Hao Chang, Wannan Li, Weiwei Han   +7 more
doaj   +1 more source

Nonequilibrium Molecular Dynamics Simulations of Coal Ash

Energies, 2020
Both molecular dynamics (MD) and nonequilibrium molecular dynamics (NEMD) simulations were performed to simulate coal ashes using the Guillot-Sator model in this work.
Shi Yu, Ruizhi Chu, Xiao Li, Guoguang Wu, Xianliang Meng   +4 more
doaj   +1 more source

Molecular modelling of cementitious materials: current progress and benefits

RILEM Technical Letters, 2023
Developing new sustainable concrete technology has become an urgent need, requiring faster and deeper insights into the fundamental mechanisms driving the cement hydration reactions. Molecular simulations have the potential to provide such understanding
Aslam Kunhi Mohamed, Amine Bouibes, Mathieu Bauchy, Ziga Casar   +3 more
doaj   +1 more source

A Complexity O(1) Priority Queue for Event Driven Molecular Dynamics Simulations [PDF]

, 2006
We propose and implement a priority queue suitable for use in event driven molecular dynamics simulations. All operations on the queue take on average O(1) time per collision.
Alder, Allen, Allen, Bentley, Blackstone, Brown, Brown, Daggett, Donev, Donev, Erpenbeck, Fredman, Frenkel, Gerald Paul, Handy, Hennessy, Jones, Knuth, Krantz, Lubachevsky, Marín, Marín, Rapaport, Rapaport, Saavedra, Shida, Sleator, Sudus, Tarjan, Urbanc, Vuillemin, Williams   +31 more
core   +2 more sources

Molecular dynamics simulations on dextran hydrogels

e-Polymers, 2013
To probe the detailed structure of dextran hydrogels, periodical models for three dextran hydrogel systems with different dextran contents have been constructed and compared using molecular dynamic simulations.
Chen Jun, Zhou Si-Min, Ma Bao-Guang, Zhang Li-Ming, Yi Ju-Zhen   +4 more
doaj   +1 more source

Stationarity, soft ergodicity, and entropy in relativistic systems [PDF]

, 2009
Recent molecular dynamics simulations show that a dilute relativistic gas equilibrates to a Juettner velocity distribution if ensemble velocities are measured simultaneously in the observer frame.
Abramowitz M., Becker R., D. Cubero, Dunkel J., Dunkel J. Hänggi P. Hilbert S., Genovese L. Ospici M. Deutsch T. Méhaut J.-F. Neelov A. Goedecker S., J. Dunkel, Januszewski M. Kostur M., Johns K. A., Johns K. A., Lindner B., Montesinos M., Thomson A. C. Fluke C. J. Barnes D. G. Barsdell B. R., Weinberg S., Wolfe B. Melia F.   +14 more
core   +3 more sources

Molecular Dynamics of Yukawa System using the Fast Multipole Method [PDF]

, 2001
In order to perform the large-scale molecular dynamics simulation of the Yukawa system, a mathematical expression for molecular dynamics using the fast multipole method is described. The model simulations are also performed to test the performance of our
Kishimoto, Tokunari, Totsuji, Chieko, Totsuji, Hiroo, Tsuruta, Kenji   +3 more
core   +1 more source

Molecular Dynamics Simulation [PDF]

, 2014
The contributions collected in this book move from the quantum-statistical description to the validity of classical modeling; they present some perspectives in the algorithmic and in the enhanced sampling approaches, tackling some longstanding challenges to simulation in the area of non-equilibrium, rare events, mesoscale and quantum-classical ...
Ciccotti, Giovanni, FERRARIO, Mauro, Schuette, Christof   +2 more
openaire   +3 more sources

Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors

Molecules, 2023
Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD,
Rosario Tomarchio, Vincenzo Patamia, Chiara Zagni, Letizia Crocetti, Agostino Cilibrizzi, Giuseppe Floresta, Antonio Rescifina   +6 more
doaj   +1 more source

Extended Dislocations in Plastically Deformed Metallic Nanoparticles

Nanomaterials and Nanotechnology, 2016
In the present study, the sawtooth nature of compressive loading of metallic nanoparticles is observed using a molecular dynamics simulation. The atomic structure evolution confirmed that extended dislocations are the main defects split into two ...
Bin Zheng, Yi-Nong Wang, Min Qi, Huiling Du   +3 more
doaj   +1 more source