[HTML][HTML] Classical molecular dynamics

CL Brooks, DA Case, S Plimpton, B Roux… - The Journal of …, 2021 - pubs.aip.org
This issue of JCP highlights both developments in and applications of classical molecular
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …

Coarse-graining organic semiconductors: the path to multiscale design

NE Jackson - The Journal of Physical Chemistry B, 2020 - ACS Publications
Four decades of molecular theory and computation have helped form the modern
understanding of the physical chemistry of organic semiconductors. Whereas these efforts …

Tracking the structural dynamics of proteins with time-resolved X-ray solution scattering

K Pounot, G Schirò, M Levantino - Current Opinion in Structural Biology, 2023 - Elsevier
Relevant events during protein function such as ligand binding/release and interaction with
substrates or with light are often accompanied by out-of-equilibrium structural dynamics …

Ligand-centered to metal-centered activation of a Rh (III) photosensitizer revealed by ab initio molecular dynamics simulations

IB Losada, P Persson - Chemical Science, 2023 - pubs.rsc.org
Excited state evolution of the rhodium (III) complex [Rh (III)(phen) 2 (NH3) 2] 2+(phen= 1, 10-
phenanthroline) has been investigated theoretically to gain a better understanding of light …

Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations

DJ Hsu, D Leshchev, I Kosheleva… - The Journal of …, 2021 - pubs.aip.org
The protein folding process often proceeds through partially folded transient states.
Therefore, a structural understanding of these disordered states is crucial for develo** …

Eliminating finite-size effects on the calculation of x-ray scattering from molecular dynamics simulations

AO Dohn, V Markmann, A Nimmrich… - The Journal of …, 2023 - pubs.aip.org
Structural studies using x-ray scattering methods for investigating molecules in solution are
shifting focus toward describing the role and effects of the surrounding solvent. However …

Early Folding Dynamics of i-Motif DNA Revealed by pH-Jump Time-Resolved X-ray Solution Scattering

AM Chan, SB Ebrahimi, D Samanta… - Journal of the …, 2024 - ACS Publications
The i-motif is a pH-responsive cytosine-rich oligonucleotide sequence that forms, under
acidic conditions, a quadruplex structure. This tunable structural switching has made the i …

Molecular features of hydration layers: Insights from simulation, microscopy, and spectroscopy

K Kim, S Choi, Z Zhang, L Bai, S Chung… - The Journal of Physical …, 2022 - ACS Publications
Water molecules are orderly when stacked on a material surface in a liquid or under ambient
conditions. Such a hydration layer plays a crucial role in various chemical and biological …

[HTML][HTML] Toward a quantitative description of solvation structure: a framework for differential solution scattering measurements

NB Thompson, KL Mulfort, DM Tiede - IUCrJ, 2024 - journals.iucr.org
Appreciating that the role of the solute–solvent and other outer-sphere interactions is
essential for understanding chemistry and chemical dynamics in solution, experimental …

Fitting high-resolution electron density maps from atomic models to solution scattering data

SR Chamberlain, S Moore, TD Grant - Biophysical Journal, 2023 - cell.com
Solution scattering techniques, such as small-and wide-angle X-ray scattering (SWAXS),
provide valuable insights into the structure and dynamics of biological macromolecules in …