Results 1 to 10 of about 176,064 (165)
Molecular Dynamics Simulation in Virus Research [PDF]
Frontiers in Microbiology, 2012 Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these
Hirotaka eOde +8 more
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Molecular dynamics simulation study of ultrasound induced cavitation [PDF]
Ultrasonics SonochemistryCavitation, though widely studied, has aspects that remain poorly understood, especially at the microlevel. This study employs molecular dynamics simulations using LAMMPS to investigate cavitation processes under sinusoidal ultrasonic forces, examining ...
Weixiang Lin +4 more
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Molecular Dynamics Simulation for Membrane Fusion. [PDF]
Methods Mol BiolThe soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein complex drives membrane fusion, and this process is further aided by accessory proteins, including complexin and α-synuclein. To understand the molecular mechanism underlying membrane fusion, we introduce an all-atom molecular dynamics (MD) simulation method. This
Tyoe O, Zhang K, Diao J.
europepmc +4 more sources
Molecules, 2022 Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs).
Daiki Matsubara +4 more
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Engineering of Ocriplasmin Variants by Bioinformatics Methods for the Reduction of Proteolytic and Autolytic Activities [PDF]
Iranian Journal of Medical Sciences, 2021 Background: Ocriplasmin has been developed for the induction of posterior vitreous detachment in patients with vitreomacular adhesion. At physiological pH, ocriplasmin is susceptible to autolytic and proteolytic degradation, limiting its activity ...
Roghayyeh Baghban +7 more
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Reduced efficacy of a Src kinase inhibitor in crowded protein solution
Nature Communications, 2021 The intracellular compartment is a crowded environment. Here, the authors use molecular dynamics (MD) simulations to assess inhibitor binding to c-Src kinase and show how ligand binding pathways differ in crowded and dilute protein solutions ...
Kento Kasahara +10 more
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Molecular dynamics simulations in photosynthesis [PDF]
Photosynthesis Research, 2020 AbstractPhotosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and
Nicoletta Liguori +3 more
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Molecular dynamics simulations [PDF]
Journal of Physics: Condensed Matter, 2004 38 pages, 11 figures, to appear in J.
Binder, K. +4 more
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The Novel Mechanism of Vibration Effect on Head Loss—Experiment, Simulation and Theory Analysis
Applied Sciences, 2022 As is known to us all, head loss affects the water transmission process, especially under the vibration condition. However, the detailed mechanism of the vibration effect on head loss was unclear, and most studies only focused on the pipeline property ...
Liu Yang, Haijun Wang
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Molecular Simulation Approaches to the Study of Thermotropic and Lyotropic Liquid Crystals
Crystals, 2022 Over the last decade, the availability of computer time, together with new algorithms capable of exploiting parallel computer architectures, has opened up many possibilities in molecularly modelling liquid crystalline systems.
Mark R. Wilson +6 more
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