Convergence of Kirkwood–Buff integrals of ideal and nonideal aqueous solutions using molecular dynamics simulations

J Milzetti, D Nayar… - The Journal of Physical …, 2018 - ACS Publications
The computation of Kirkwood–Buff integrals (KBIs) using molecular simulations of closed
systems is challenging due to finite system-size effects. One of the problems involves the …

Kirkwood–Buff-derived force field for peptides and proteins: philosophy and development of KBFF20

EA Ploetz, S Karunaweera, N Bentenitis… - Journal of Chemical …, 2021 - ACS Publications
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and
proteins is presented. The force field relies heavily on the use of Kirkwood–Buff theory to …

Origin of non-linearity in phase solubility: solubilisation by cyclodextrin beyond stoichiometric complexation

TWJ Nicol, N Matubayasi, S Shimizu - Physical Chemistry Chemical …, 2016 - pubs.rsc.org
The low solubility of drugs, which poses a serious problem in drug development, can in part
be overcome by the use of cyclodextrins (CDs) and their derivatives. Here, the key to …

Temperature Dependence of Hydrotropy

S Shimizu, N Matubayasi - The Journal of Physical Chemistry B, 2024 - ACS Publications
The solubility of hydrophobic solutes increases dramatically with the temperature when
hydrotropes are added to water. In this paper, the mechanism of this well-known observation …

Preferential solvation in binary and ternary mixtures

GN Pallewela, PE Smith - The Journal of Physical Chemistry B, 2015 - ACS Publications
Preferential solvation has become a useful tool to help characterize and understand the
properties of liquid mixtures. Here, we provide a new quantitative measure of preferential …

How osmolytes counteract pressure denaturation on a molecular scale

S Shimizu, PE Smith - ChemPhysChem, 2017 - Wiley Online Library
Life in the deep sea exposes enzymes to high hydrostatic pressure, which decreases their
stability. For survival, deep sea organisms tend to accumulate various osmolytes, most …

Real Space Triplets in Quantum Condensed Matter: Numerical Experiments Using Path Integrals, Closures, and Hard Spheres

LM Sesé - Entropy, 2020 - mdpi.com
Path integral Monte Carlo and closure computations are utilized to study real space triplet
correlations in the quantum hard-sphere system. The conditions cover from the normal fluid …

Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes

NL Kariyawasam, EA Ploetz, L Swint-Kruse… - Biophysical …, 2024 - Elsevier
The functions of many proteins are associated with interconversions among conformational
substates. However, these substates can be difficult to measure experimentally, and …

Fluctuation solution theory of pure fluids

EA Ploetz, GN Pallewela, PE Smith - The Journal of Chemical Physics, 2017 - pubs.aip.org
Fluctuation Solution Theory (FST) provides an alternative view of fluid thermodynamics in
terms of pair fluctuations in the particle number and excess energy observed for an …

Gaussian and non-Gaussian fluctuations in pure classical fluids

N Naleem, EA Ploetz, PE Smith - The Journal of Chemical Physics, 2017 - pubs.aip.org
The particle number, energy, and volume probability distributions in the canonical,
isothermal-isobaric, grand canonical, and isobaric-isenthalpic ensembles are investigated …