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The Journal of Physical Chemistry B
Scopus
ISSN 1520-5207 · American Chemical Society · 4 articles in the index
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Journal Article Full text
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and…
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Journal Article
Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane
This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure…
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Journal Article Full text
Superhydrophobic Surfaces: Insights from Theory and Experiment
Biomimetic nanosurfaces with distinct wettability and versatility have found special enthusiasm in both fundamental research and industrial applications. With the advent of nanotechnology, it is doable to acclimate surface architecture and surface chemistry to attain superhydrophobicity. The…
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Journal Article
Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations
The formation of membraneless organelles in cells commonly occurs via liquid-liquid phase separation (LLPS) and is in many cases driven by multivalent interactions between intrinsically disordered proteins (IDPs). Investigating the nature of these interactions, and their effect on dynamics within…