D. Thirumalai

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.

The paper shows that folded proteins exhibit orientational order through nematic droplets, which may enable allosteric function by resisting mechanical stress in some regions while allowing flexibility in others.

This study uses a coarse-grained model to simulate RNA repeat sequences, showing that condensates exhibit reptation-like dynamics and complex intermolecular networks.

The paper models chromatin dynamics to show how epigenetic domains form through nucleosome modification spreading and chromatin relaxation rates, with experimental validation in mouse embryonic stem cells.

The paper shows that upward curvature in log ku(f) as a function of force indicates parallel unfolding pathways in single-domain proteins, supported by simulations of β-sandwich proteins and mutants.

The paper develops a theory and simulations showing that crowding particles increase protein stability, with applications to lambda repressor, and explains modest destabilization in cellular environments.

The paper develops a theoretical method to study pH effects on intrinsically disordered proteins using a molecular transfer model and mean-field approximation.

This study uses computational methods to analyze how long-range allosteric communication affects the stability and disassembly of SARS-CoV-2 RBD-ACE2 complexes.

The paper uses t-SNE to reveal phase separation in tumors based on cell movement patterns driven by self-generated forces.

The paper uses molecular dynamics simulations to study how water-mediated interactions influence helix formation in confined polypeptides, showing hydrophobic side chains are stabilized in nanotubes.

The paper shows that the assisted folding rate of rhodanese in the GroEL/ES nanocage decreases, suggesting the chaperonin machinery optimizes the product of folding rate and yield rather than maximizing either individually.

This paper uses simulations to show that nucleosome unwrapping has asymmetric HPC rotation depending on force direction, explaining hysteresis in DNA stretching experiments.

This paper explains the faster aggregation rate of Aβ42 compared to Aβ40 by showing that their distinct populations of high free energy excited states encode their aggregation propensities.

The paper uses simulations to study Cytochrome c folding, showing dramatic shape changes from an unfolded prolate ellipsoid to a spherical native state through a sequential mechanism.

The paper develops a theoretical model and simulations to explain condensin-mediated loop extrusion in DNA, showing how ATP binding induces conformational changes that drive loop formation.

This paper introduces HIPPS, a method to calculate 3D chromosome structures from Hi-C contact maps without assuming an energy function, showing conformational heterogeneity in human chromosomes.

This study shows that divalent cations bind to RNA in a nucleotide-specific manner through inner or outer shell coordination, with Mg2+ preferring outer shell and Ca2+ inner shell, and bridging interactions playing a key role in RNA folding.

This study identifies TMB-related chromosomal patterns and links them to cancer risk and patient outcomes across multiple cancer types.

The paper uses molecular simulations to study Mg2+-induced folding of the central domain of bacterial 16S rRNA, showing cooperative folding and heterogeneous structural assembly.

This study shows that tracer particles in growing cancer spheroids exhibit sub- and super-diffusive behavior due to cell proliferation and apoptosis, without affecting cell dynamics.

The paper shows that mechanical heterogeneity along cell-cell junctions during vertebrate axis elongation is driven by cadherin clustering and Planar Cell Polarity signaling.

The paper shows that cell-cell adhesion strength influences tumor growth rates through a pressure-adhesion feedback loop, with an optimal adhesion level maximizing proliferation.

This paper investigates how gold nanoparticles affect kinesin stepping trajectories and finds that they can exaggerate rightward bias and fail to track the stepping head accurately.

The paper develops a hydrodynamic model to show that shell rigidity and turgor pressure control bacterial and viral sizes through a dimensionless compliance parameter.

The paper compares theoretical simulations and experimental data on cell movement in tumor spheroids, revealing distinct subdiffusive and superdiffusive dynamics in core and peripheral cells.

This paper uses molecular dynamics simulations to show that step-wise hydration of Mg2+ by four water molecules precedes phosphate release in myosin VI, revealing a general mechanism for Pi release in ATPases and GTPases.

This paper develops a theory and simulation approach to accurately predict RNA folding in mixed ion solutions, showing good agreement with experimental data.

The paper resolves the FISH-Hi-C paradox by showing that conformational heterogeneity in human interphase chromosomes explains discrepancies between Hi-C contact probabilities and FISH distances.

The paper develops a theoretical framework to model molecular motor movement, including alternative stepping mechanisms, and applies it to myosin VI to predict motility features and energy consumption.

This study shows ion condensation on ribozymes is site-specific and fold-dependent, contrasting with uniform interactions on rigid charged rods.