Operando characterization of organic mixed ionic/electronic conducting materials
Operando characterization plays an important role in revealing the structure–property
relationships of organic mixed ionic/electronic conductors (OMIECs), enabling the direct …
relationships of organic mixed ionic/electronic conductors (OMIECs), enabling the direct …
Recent progress in general force fields of small molecules
Recent advances in computational hardware and free energy algorithms enable a broader
application of molecular simulation of binding interactions between receptors and small …
application of molecular simulation of binding interactions between receptors and small …
Automation of AMOEBA polarizable force field for small molecules: Poltype 2
A next‐generation protocol (Poltype 2) has been developed which automatically generates
AMOEBA polarizable force field parameters for small molecules. Both features and …
AMOEBA polarizable force field parameters for small molecules. Both features and …
Spatiotemporal characterization of water diffusion anomalies in saline solutions using machine learning force field
Understanding water behavior in salt solutions remains a notable challenge in
computational chemistry. Conventional force fields have shown limitations in accurately …
computational chemistry. Conventional force fields have shown limitations in accurately …
Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ
In this work the 4-point polarizable SWM4 Drude water model is reparametrized. Multiple
models were developed using different strategies toward reproduction of specific target data …
models were developed using different strategies toward reproduction of specific target data …
The importance of charge transfer and solvent screening in the interactions of backbones and functional groups in amino acid residues and nucleotides
V Sladek, DG Fedorov - International Journal of Molecular Sciences, 2022 - mdpi.com
Quantum mechanical (QM) calculations at the level of density-functional tight-binding are
applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 …
applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 …
CHARMM-GUI implicit solvent modeler for various generalized born models in different simulation programs
Implicit solvent models are widely used because they are advantageous to speed up
simulations by drastically decreasing the number of solvent degrees of freedom, which …
simulations by drastically decreasing the number of solvent degrees of freedom, which …
How much can physics do for protein design?
E Michael, T Simonson - Current Opinion in Structural Biology, 2022 - Elsevier
Physics and physical chemistry are an important thread in computational protein design,
complementary to knowledge-based tools. They provide molecular mechanics scoring …
complementary to knowledge-based tools. They provide molecular mechanics scoring …
A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model
RA Corrigan, AC Thiel, JR Lynn, TL Casavant… - The Journal of …, 2023 - pubs.aip.org
Computational simulation of biomolecules can provide important insights into protein
design, protein-ligand binding interactions, and ab initio biomolecular folding, among other …
design, protein-ligand binding interactions, and ab initio biomolecular folding, among other …
Development of a QM/MM (ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX (8-oxo-G) tetrad
Y Wang, L Liu, Y Gao, J Zhao, C Liu, L Gong… - Physical Chemistry …, 2024 - pubs.rsc.org
The rapid deprotonation of G˙+ in the DNA strand impedes positive charge (hole) transfer,
whereas the slow deprotonation rate of G˙+ in the G-tetrad makes it a more suitable carrier …
whereas the slow deprotonation rate of G˙+ in the G-tetrad makes it a more suitable carrier …