B. Mondal

Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences

The paper develops a computational model to study ion-DNA interactions and shows it accurately predicts experimental results without parameter tuning.

Brewing COFFEE: a sequence-specific coarse-grained energy function for simulations of DNA-protein complexes

The paper introduces COFFEE, a sequence-specific coarse-grained energy function for simulating DNA-protein complexes, showing it accurately reproduces experimental data and explains nucleosome behavior.

Redox state and cellular uptake of copper is regulated by the N-terminus of human Copper Transporter-1

The paper shows that the N-terminus of hCTR1 regulates copper uptake by coordinating Cu(I) and facilitating its reduction from Cu(II).

Energy Landscape of Ubiquitin is Weakly Multidimensional

The paper investigates the energy landscape of ubiquitin using simulations, finding it weakly multidimensional with a single dominant barrier and a force-dependent transition state location.

Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation

This study identifies double domain swapping as a mechanism driving early aggregation in human γC and γD crystallin proteins through molecular dynamics simulations.

A Transient Intermediate Populated in Prion Folding Leads to Domain Swapping

This study identifies a transient intermediate state in prion folding that leads to domain swapping, suggesting a pathogenic mechanism for prion aggregation.

Cosolvent Effects on the Growth of Protein Aggregates Formed by a Single Domain Globular Protein and an Intrinsically Disordered Protein

This study investigates how cosolvents affect the growth of protein aggregates formed by a globular protein and an intrinsically disordered protein using simulations.