Editorial: Molecular Dynamics Simulations of Metalloproteins and Metalloenzymes by Kshatresh Dutta Dubey, Binju Wang, Yubing Si, Syed Tarique Moin

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Stereochemical errors and their implications for molecular dynamics simulations by Freddolino Peter L, Trabuco Leonardo G, Schreiner Eduard, Schulten Klaus

“…<p>Abstract</p> <p>Background</p> <p>Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. …”
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Molecular dynamics modeling of the Hugoniot states of aluminum by Xin Yang, Xiangguo Zeng, Chuanjin Pu, Wenjun Chen, Huayan Chen, Fang Wang

“…In this study, molecular dynamics (MD) simulations coupled with multi-scale shock technique (MSST) are used to predict the Hugoniot curve PH, Grüneisen coefficient γ and melting temperature Tm of single crystal (SC) and nanocrystalline (NC) aluminum (Al) with grain sizes of 6 and 60 nm at dynamic high pressure. …”
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Molecular dynamic simulation on the transport properties of alcohols by Jing Fan, Shuangshuo Liu, Chang Gao, Fenhong Song

“…In this work, NEMD (nonequilibrium molecular dynamics) method has been applied to calculate the thermal conductivity and RNEMD (reverse nonequilibrium molecular dynamics) method has been used to calculate the viscosity of alcohols. …”
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What is a Multiscale Problem in Molecular Dynamics? by Luigi Delle Site

“…In this work, we make an attempt to answer the question of what a multiscale problem is in Molecular Dynamics (MD), or, more in general, in Molecular Simulation (MS). …”
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Molecular dynamics of liquid Zirconia: effect of pressure by ON Nenuwe, OJ Azi

Subjects: “…molecular dynamics…”
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Hybrid quantum annealing via molecular dynamics by Hirotaka Irie, Haozhao Liang, Takumi Doi, Shinya Gongyo, Tetsuo Hatsuda

“…The key concept is to introduce a Hamiltonian dynamics of the classical flux variables associated with the quantum spins of the transverse-field Ising model. Molecular dynamics of the classical fluxes can be used as a powerful preconditioner to sort out the frozen and ambivalent spins for quantum annealers. …”
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Digital quantum simulation of molecular dynamics and control by Alicia B. Magann, Matthew D. Grace, Herschel A. Rabitz, Mohan Sarovar

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Fluctuations of conserved charges in hydrodynamics and molecular dynamics by Vovchenko Volodymyr

“…We also cover recent developments on critical fluctuations in molecular dynamics simulations.…”
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Applications of Molecular Dynamics Simulation in Protein Study by Siddharth Sinha, Benjamin Tam, San Ming Wang

Subjects: “…molecular dynamics simulations…”
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Coarse-grained molecular dynamics simulations of biomolecules by Ken Takahashi, Takayuki Oda, Keiji Naruse

Subjects: “…coarse-grained molecular dynamics…”
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Coarse-grained molecular dynamics simulations of biomolecules by Ken Takahashi, Takayuki Oda, Keiji Naruse

Subjects: “…coarse-grained molecular dynamics， all atom-molecular dynamics， reverse graining，protein-protein interactions， protein-lipid interactions， in silico drug design…”
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Intracellular molecular dynamics studied by neutron scattering by Zaccai Giuseppe, Madern Dominique, Franzetti Bruno

“…Incoherent neutron scattering experiments have produced important insights into intracellular molecular dynamics in vivo. Selected results highlight the role of water dynamics in cancer and brain cells, as well as cellular adaptation through the evolution of appropriate molecular dynamics, in order to respond to environmental challenges.…”
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Reliability and reproducibility checklist for molecular dynamics simulations

“…We present a checklist to improve the reliability and reproducibility of molecular dynamics simulations and related methods.…”
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Molecular dynamic simulation of heating of titanium nanoclusters by N.A. Pan'kin

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Molecular Dynamics Simulation of Polyacrylamide Adsorption on Calcite by Keat Yung Hue, Jin Hau Lew, Maung Maung Myo Thant, Omar K. Matar, Paul F. Luckham, Erich A. Müller

“…Classical atomistic molecular dynamics (MD) simulation is employed to model the interaction of polyacrylamide-based polymer additives with a calcite structure, which is the main component of carbonate formations. …”
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Protobiotic Systems Chemistry Analyzed by Molecular Dynamics by Amit Kahana, Doron Lancet

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Molecular Dynamics Simulation of the Thermal Behavior of Hydroxyapatite by Ilya Likhachev, Nikolay Balabaev, Vladimir Bystrov, Ekaterina Paramonova, Leon Avakyan, Natalia Bulina

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Molecular Dynamics Simulation of the Nanoindentation of Coal Vitrinite by Hewu Liu, Hewu Liu, Chenliang Hou, Yu Song

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Molecular Dynamics Simulations of Deformable Viral Capsomers by Lauren B. Nilsson, Fanbo Sun, J. C. S. Kadupitiya, Vikram Jadhao

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