83 citations · 178 across the 7 of their papers we have counts for
7 papers
Reaction-transport coupling drives spatiotemporal organization in fuel-driven supramolecular polymerization
Akta Singh, Nayana Mukherjee, Jagannath Mondal +1
Chemically fueled supramolecular systems provide a versatile platform for generating nonequilibrium structures and dynamical instabilities, including chemical oscillations and trav…
A Deep Autoencoder Framework for Discovery of Metastable Ensembles in Biomacromolecules
Satyabrata Bandyopadhyay, Jagannath Mondal
Mini-proteins and peptides manifest dynamic conformational fluctuation and involve mutual interconversion among metastable states. A robust mapping of the conformational landscape…
On the Role of Solvent in Hydrophobic Cavity-ligand Recognition Kinetics
Navjeet Ahalawat, Satyabrata Bandyopadhyay, Jagannath Mondal
Solvent often manifests itself as the key determinant of the kinetic aspect of molecular recognition process. While the solvent is often depicted as a source of barrier in the liga…
Role of and relaxations in Collapsing Dynamics of a Polymer Chain in Supercooled Glass-forming Liquid
Mrinmoy Mukherjee, Jagannath Mondal, Smarajit Karmakar
Understanding the effect of glassy dynamics on the stability of bio-macromolecules and investigating the underlying relaxation processes governing degradation processes of these ma…
The role of water and steric constraints in the kinetics of cavity-ligand unbinding
Pratyush Tiwary, Jagannath Mondal, Joseph A. Morrone +1
A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and t…
When does TMAO fold a polymer chain and urea unfold it?
Jagannath Mondal, Guillaume Stirnemann, B. J. Berne
Longstanding mechanistic questions about the role of protecting osmolyte trimethylamine N- oxide (TMAO) which favors protein folding and the denaturing osmolyte urea are addressed…
How hydrophobic drying forces impact the kinetics of molecular recognition
Jagannath Mondal, Joseph A. Morrone, B. J. Berne
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solv…