D. Thirumalai

Mechanical feedback drives asynchronous cell divisions during embryogenesis

The paper models biomechanical feedback during zebrafish embryogenesis to predict the transition from synchronous to asynchronous cell divisions and explains the resulting cell cycle lengthening.

Salt-dependent self-association of trinucleotide repeat RNA sequences

The paper shows that salt concentration affects RNA self-association rates and yields through changes in free energy gaps, with implications for repeat RNA aggregation.

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.

Sizes, conformational fluctuations, and SAXS profiles for Intrinsically Disordered Proteins

This paper develops a transferable model to predict biophysical properties of IDPs, showing agreement with experimental data on size, conformation, and SAXS profiles.

A method for extracting effective interactions from Hi-C data with applications to interphase chromosomes and inverted nuclei

This paper introduces a method to extract effective interaction energies from Hi-C data to model chromosome organization, showing that heterochromatin attraction drives compartment formation in conventional and inverted nuclei.

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

The paper uses molecular simulations to study how Mg2+ ions influence the folding and misfolding kinetics of the Azoarcus ribozyme, revealing diverse folding pathways and the role of energetic and topological frustration.

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

The paper shows that odd-even differences in RNA repeat sequences affect phase separation propensity through free energy gaps between ground and slipped hairpin states.

Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis

The paper uses simulations to show that cell size polydispersity and deformability explain the viscosity plateau in non-confluent zebrafish tissue beyond a critical packing fraction.

Topological transitions, turbulent-like motion and long-time-tails driven by cell division in biological tissues

The paper shows that cell division and apoptosis in epithelial monolayers generate turbulent-like flows with energy spectra and velocity correlations similar to inertial turbulence.

Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletion

The paper shows that some Topologically Associating Domains (TADs) persist without cohesin, supported by Hi-C data, polymer simulations, and 3D structural analysis in mouse and human cells.

Reduction of RBD Binding Affinity to Glycosylated ACE2 is Entropic in Origin

The paper develops a lattice model to test if entropic forces from ACE2 glycans affect RBD binding, finding that glycans have a weak entropic effect.

Residue-dependent transition temperatures and denaturant midpoints in the folding of a multi-domain protein

The paper calculates thermal and denaturation unfolding titration curves for a multi-domain protein, showing small dispersions in melting and denaturation temperatures, consistent with thermodynamic scaling.

Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo

The paper uses a kinetic network model to show that optimal CYT-19 activity maximizes self-splicing yield of group I introns by balancing chaperone-mediated folding and self-splicing kinetics.

Molecular Mechanisms of Steric Pressure Generation and Membrane Remodeling by Intrinsically Disordered Proteins

This study measures steric pressure generated by intrinsically disordered domains of AP180 at membrane surfaces, finding that they produce significant pressure through entropic and electrostatic mechanisms, independent of molecular weight.

TMAO Destabilizes RNA Secondary Structurevia Direct Hydrogen Bond Interactions

This study investigates how TMAO interacts with RNA hairpins using molecular dynamics simulations, revealing that TMAO destabilizes RNA via hydrogen bond interactions with solvent-exposed bases.

Structural changes in chromosomes driven by multiple condensin motors during mitosis

The paper develops a computational framework to model loop extrusion by condensin I and II during mitosis, showing changes in loop size and structure across cell types.

Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages

The paper shows that N* states in Aβ40 and Aβ42 monomers follow Ostwald's rule of stages, influencing aggregation and dimer formation.

Transcription-induced active forces suppress chromatin motion

The paper introduces a polymer model to explain how transcription-induced active forces suppress chromatin mobility during transcription.

A maximum-entropy model to predict 3D structural ensembles of chromatins from pairwise distances: Applications to Interphase Chromosomes and Structural Variants

This paper introduces a computational method to predict 3D chromatin structures from pairwise distances and applies it to analyze chromosome organization and structural variants.

Universality of distribution of tumor mutation burden - a biomarker for the tumor evolution and disease risk

The paper analyzes tumor mutation burden (TMB) across 5,000 cancer patients and finds a universal distribution pattern, with implications for cancer risk and treatment response.

Statistical Mechanical theory for spatio-temporal evolution of Intra-tumor heterogeneity in cancers: Analysis of Multiregion sequencing data

The paper develops a statistical mechanical theory to quantify intra-tumor heterogeneity using multi-region sequencing data, showing that ITH increases with spatial distance between regions.

Tracer particles sense local stresses in an evolving multicellular spheroid without affecting the anomalous dynamics of the cancer cells

The paper shows tracer particles accurately report local stresses in a growing multicellular spheroid without altering cancer cell dynamics.

Differences in Ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts

The paper uses molecular dynamics simulations to show that Na+ stabilizes RNA more than K+ due to differences in ion-RNA binding modes related to charge density.

Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers

The paper investigates how mechanical feedback in growing tissue monolayers leads to dynamical memory effects through cell division and intercellular interactions.

Cooperativity and folding kinetics in a multi-domain protein with interwoven chain topology

This study uses a coarse-grained model to simulate the folding of Adenylate Kinase, revealing cooperative domain interactions and folding heterogeneity in a multiply connected multidomain protein.

Role of Water-bridged Interactions in Metal Ion Coupled Protein Allostery

This study reveals that water-bridged interactions facilitate Ca2+ binding and allostery in calmodulin by reducing energy landscape ruggedness and enabling asymmetric EF-hand responses.

Information flow, Gating, and Energetics in dimeric molecular motors

This study develops a theoretical framework to quantify gating in dimeric molecular motors using information theory and stochastic thermodynamics, showing that information flow between motor heads is critical for coordination and transport efficiency.

Adhesion strength between cells regulate non-monotonic growth by a biomechanical feedback mechanism

The paper uses simulations to show that cell adhesion strength regulates non-monotonic growth in multicellular spheroids through a biomechanical feedback mechanism involving pressure fluctuations.

Plus and minus ends of microtubule respond asymmetrically to kinesin binding by a long range directionally driven allosteric mechanism

This study investigates how kinesin binding induces directional asymmetry in microtubule structure through long-range allosteric effects, explaining the directionality of kinesin stepping.