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Molecular dynamics simulation study of ultrasound induced cavitation [PDF]

Ultrasonics Sonochemistry
Cavitation, 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, Xudong Duan, Song He, Jiarui Wang, Simin Wang   +4 more
doaj   +2 more sources

Molecular dynamics simulation of an entire cell

Frontiers in Chemistry, 2023
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell’s components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge.
Jan A. Stevens, Fabian Grünewald, P. A. Marco van Tilburg, Melanie König, Benjamin R. Gilbert, Troy A. Brier, Zane R. Thornburg, Zaida Luthey-Schulten, Siewert J. Marrink   +8 more
doaj   +4 more sources

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

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, Kento Kasahara, Hisham M. Dokainish, Hiraku Oshima, Yuji Sugita   +4 more
doaj   +1 more source

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, Safar Farajnia, Younes Ghasemi, Mojtaba Mortazavi, Samaneh Ghasemali, Mostafa Zakariazadeh, Nosratollah Zarghami, Nasser Samadi   +7 more
doaj   +1 more source

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, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita   +10 more
doaj   +1 more source

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
doaj   +1 more source

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, Gary Yu, Thomas D. Potter, Martin Walker, Sarah J. Gray, Jing Li, Nicola Jane Boyd   +6 more
doaj   +1 more source

Encapsulation mechanism of α-mangostin by β-cyclodextrin: Methods of molecular docking and molecular dynamics

Journal of Advanced Pharmaceutical Technology & Research, 2021
The study aimed to investigate the interaction of host-guest between α-mangostin and β-cyclodextrin (βCD) and also to calculate the energy of the complex system between α-mangostin with βCD for drug delivery using methods of 15 molecular dynamics and ...
Dian Triwahyuningtyas, Sandra Megantara, Tai Tze Hong, Muhammad Yusuf, Muchtaridi Muchtaridi   +4 more
doaj   +1 more source

Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease

Biophysics and Physicobiology, 2021
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), spread rapidly around the globe. The main protease encoded by SARS-CoV-2 is essential for processing of the polyproteins translated from ...
Daisuke Kuroda, Kouhei Tsumoto
doaj   +1 more source

Melting of metal nanowires: molecular dynamics simulation [PDF]

Физико-химические аспекты изучения кластеров, наноструктур и наноматериалов, 2018
A comparative molecular dynamics study has been carried out of the melting of infinite metallic nanowires and free spherical metallic nanoparticles of the same diameter.
S.A. Vasilyev, A.Yu. Kartoshkin, M.V. Samsonov, E.V. Dyakova   +3 more
doaj   +1 more source