From adaptive resolution to molecular dynamics of open systems
We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on
discussing its basic principles and presenting its current numerical and theoretical …
discussing its basic principles and presenting its current numerical and theoretical …
BAR‐Based Multi‐Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region
Z Sun, Z Liu - Advanced Theory and Simulations, 2021 - Wiley Online Library
The indirect free energy simulation at quantum mechanics (QM)/molecular mechanics (MM)
levels provides a feasible alternative to direct QM/MM simulations. The main idea under the …
levels provides a feasible alternative to direct QM/MM simulations. The main idea under the …
SAMPL7 trimertrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations
Z Sun - Journal of Computer-Aided Molecular Design, 2021 - Springer
Host–guest binding remains a major challenge in modern computational modelling. The
newest 7th statistical assessment of the modeling of proteins and ligands (SAMPL) …
newest 7th statistical assessment of the modeling of proteins and ligands (SAMPL) …
Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR–ligand binding
The transcriptional regulator TtgR belongs to the TetR family of transcriptional repressors. It
depresses the transcription of the TtgABC operon and itself and thus regulates the extrusion …
depresses the transcription of the TtgABC operon and itself and thus regulates the extrusion …
[HTML][HTML] Steering a solute between coexisting solvation states: revisiting nonequilibrium work relations and the calculation of free energy differences
By analogy with single-molecule pulling experiments, we present a computational
framework to obtain free energy differences between complex solvation states. To illustrate …
framework to obtain free energy differences between complex solvation states. To illustrate …
Thermodynamic insights of base flipping in TNA duplex: force fields, salt concentrations, and free energy simulation methods
Threofuranosyl nucleic acid (TNA) is an analogue of DNA. Its inter-nucleotide linkages are
shifted from the wild-type 5'-to-3'one to the 3'-to-2'one. As a result, the number of covalent …
shifted from the wild-type 5'-to-3'one to the 3'-to-2'one. As a result, the number of covalent …
[PDF][PDF] Topical Issue on Dielectric Spectroscopy Applied to Soft Matter
S Napolitano - The European Physical Journal E, 2020 - Springer
Broadband Dielectric spectroscopy (BDS) is a well-established experimental technique,
successfully employed to characterize soft matter at the molecular level. The technique is …
successfully employed to characterize soft matter at the molecular level. The technique is …
[PDF][PDF] Predicting affinities of ligands targeting G-protein coupled receptors: Advances in hybrid multiscale simulation approaches
K Korshunova - 2021 - scholar.archive.org
Abstract Human G-Protein Coupled Receptors (hGPCRs) play an immense role for modern
pharmacology: as many as 34% of all FDA-approved drugs target these membrane …
pharmacology: as many as 34% of all FDA-approved drugs target these membrane …
[PDF][PDF] Topical Issue on Advances in Computational Methods for Soft Matter Systems
L Rovigatti, F Romano, J Russo - The European Physical Journal E, 2018 - Springer
We like to think of scientific articles as stories, and this Topical Issue is a collection of some
of the best stories in the computational Soft Matter genre. As a field, Soft Matter is rapidly …
of the best stories in the computational Soft Matter genre. As a field, Soft Matter is rapidly …
[PDF][PDF] Thermodynamic Insights of Base Flipping in TNA
JZH Zhang - 2020 - pdfs.semanticscholar.org
Threofuranosyl nucleic acid (TNA) is an analogue of DNA. Its inter-nucleotide linkages are
shifted from the wild-type 5'-to-3'one to the 3'-to-2'one. As a result, the number of covalent …
shifted from the wild-type 5'-to-3'one to the 3'-to-2'one. As a result, the number of covalent …