From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology

S Mondal, B Bagchi - Current Opinion in Structural Biology, 2022 - Elsevier
Biological activity requires a solvent that can provide a suitable environment, which satisfies
the twin need for stability and the ability to change. Among all the solvents water plays the …

[HTML][HTML] Ions' motion in water

P Banerjee, B Bagchi - The Journal of chemical physics, 2019 - pubs.aip.org
Over the decades, a great deal of attention has been focused on the solvation and transport
properties of small rigid monatomic ions such as Na+, K+, Li+, Cl−, and Br− due to their …

Structural stability of insulin oligomers and protein association–dissociation processes: Free energy landscape and universal role of water

S Mukherjee, S Acharya, S Mondal… - The Journal of …, 2021 - ACS Publications
Association and dissociation of proteins are important biochemical events. In this Feature
Article, we analyze the available studies of these processes for insulin oligomers in aqueous …

Unusual similarity of DNA solvation dynamics in high-salinity crowding with divalent cations of varying concentrations

D Sardana, P Alam, K Yadav, NS Clovis… - Physical Chemistry …, 2023 - pubs.rsc.org
Double-stranded DNA bears the highest linear negative charge density (2e− per base-pair)
among all biopolymers, leading to strong interactions with cations and dipolar water …

Probing adaptation of hydration and protein dynamics to temperature

LC Doan, JN Dahanayake, KR Mitchell-Koch… - Acs Omega, 2022 - ACS Publications
Protein dynamics is strongly influenced by the surrounding environment and physiological
conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the …

[HTML][HTML] Long-range DNA-water interactions

AK Singh, C Wen, S Cheng, NQ Vinh - Biophysical journal, 2021 - cell.com
DNA functions only in aqueous environments and adopts different conformations depending
on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating …

Molecular picture of the effect of cosolvent crowding on ligand binding and dispersed solvation dynamics in G-quadruplex DNA

K Yadav, D Sardana, H Shweta… - The Journal of …, 2022 - ACS Publications
Understanding molecular interactions and dynamics of proteins and DNA in a cell-like
crowded environment is crucial for predicting their functions within the cell. Noncanonical G …

Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations

S Mukherjee, S Mondal, B Bagchi - The Journal of Physical …, 2023 - ACS Publications
The coupling between the conformational fluctuations of DNA and its surrounding
environment, consisting of water and ions in solution, remains poorly understood and …

[图书][B] Nonequilibrium Statistical Mechanics: An Introduction with Applications

B Bagchi - 2024 - taylorfrancis.com
Nonequilibrium statistical mechanics (NESM), practically synonymous with time-dependent
statistical mechanics (TDSM), is a beautiful and profound subject, vast in scope, diverse in …

DNA photoionization: from high to low energies

E Balanikas, D Markovitsi - 2021 - books.rsc.org
Absorption of one or more ultraviolet (UV) photons directly by DNA may lead to its ionization:
an electron is ejected, generating an electron hole (radical cation) on the nucleic acid. 1–3 …