264 citations · 2.7k across the 64 of their papers we have counts for
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Scaling regimes for wormlike chains confined to cylindrical surfaces under tension
Greg Morrison, D. Thirumalai
We compute the free energy of confinement for a wormlike chain (WLC), with persistence length , that is confined to the surface of a cylinder of radius under a…
On the emergence of orientational order in folded proteins with implications for allostery
Debayan Chakraborty, Mauro Lorenzo Mugnai, D. Thirumalai
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully u…
Theory and simulations for crowding-induced changes in stability of proteins with applications to repressor
Natalia D. Denesyuk, D. Thirumalai
Experiments and theories have shown that when steric interactions between crowding particles and proteins are dominant, which give rise to Asakura-Oosawa depletion forces, then the…
Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines
D. Thirumalai, Changbong Hyeon, Pavel I. Zhuravlev +1
Allosteric signaling in biological molecules, which may be viewed as specific action at a distance due to localized perturbation upon binding of ligands or changes in environmental…
Confinement-induced glassy dynamics in a model for chromosome organization
Hongsuk Kang, Young-Gui Yoon, D. Thirumalai +1
Recent experiments showing scaling of the intrachromosomal contact probability, with the genomic distance , are interpreted to mean a self-similar fractal-like…
Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins
Pavel I. Zhuravlev, Govardhan Reddy, John E. Straub +1
Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH…
Membrane-protein interactions hold the key to understanding amyloid formation
John E. Straub, D. Thirumalai
In this perspective we describe the critical role membranes play in modulating the structures of the Amyloid Precursor Proteins to produce the peptides involved in the Alzheimer's…
Hidden Complexity in the Isomerization Dynamics of Holliday Junctions
Changbong Hyeon, Jinwoo Lee, Jeseong Yoon +2
A plausible consequence of rugged energy landscapes of biomolecules is that functionally competent folded states may not be unique, as is generally assumed. Indeed, molecule-to-mol…
Chain Length Determines the Folding Rates of RNA
Changbong Hyeon, D. Thirumalai
We show that the folding rates (k_F) of RNA are determined by N, the number of nucleotides. By assuming that the distribution of free energy barriers separating the folded and the…
Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models
Changbong Hyeon, D. Thirumalai
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chr…
Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments
Greg Morrison, Changbong Hyeon, Michael Hinczewski +1
We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ens…
Compression and stretching of a self-avoiding chain in cylindrical nanopores
Suckjoon Jun, D. Thirumalai, Bae-Yeun Ha
Force-induced deformations of a self-avoiding chain confined inside a cylindrical cavity, with diameter , are probed using molecular dynamics simulations, scaling analysis, and…
Force Dependent Hopping Rates of RNA Hairpins can be Estimated from Accurate Measurement of the Folding Landscapes
Changbong Hyeon, Greg Morrison, D. Thirumalai
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule for…
Stretching Homopolymers
Greg Morrison, Changbong Hyeon, N. M. Toan +2
Force induced stretching of polymers is important in a variety of contexts. We have used theory and simulations to describe the response of homopolymers, with monomers, to forc…
Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments
Changbong Hyeon, D. Thirumalai
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the ene…
The shape of a flexible polymer in a cylindrical pore
G. Morrison, D. Thirumalai
We calculate the mean end-to-end distance () of a self-avoiding polymer encapsulated in an infinitely long cylinder with radius . A self-consistent perturbation theory is use…
Dependence of folding rates on protein length
Mai Suan Li, D. K. Klimov, D. Thirumalai
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical pr…
Bending rigidity of stiff polyelectrolyte chains: Single chain and a bundle of multichains
Bae-Yeun Ha, D. Thirumalai
We study the bending rigidity of highly charged stiff polyelectrolytes, for both a single chain and many chains forming a bundle. A theory is developed to account for the interplay…
Introducing Protein Folding Using Simple Models
D. Thirumalai, D. K. Klimov
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mech…
Dynamics of Collapse of flexible Polyelectrolytes and Polyampholytes
Namkyung Lee, D. Thirumalai
We provide a theory for the dynamics of collapse of strongly charged polyelectrolytes (PEs) and flexible polyampholytes (PAs) using Langevin equation. After the initial stage, in w…
Emergence of stable and fast folding protein structures
D. Thirumalai, D. K. Klimov
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we…
Kinetics of condensation of flexible polyelectrolytes in poor solvents: effects of solvent quality, valence and size of counterions
Namkyung Lee, D. Thirumalai
The collapse kinetics of strongly charged polyelectrolytes in poor solvents is investigated by Langevin simulations and scaling arguments. The rate of collapse increases sharply as…
Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins
D. K. Klimov, D. Thirumalai
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, , is introduced to quantitatively assess the…
Thermodynamic stability of folded proteins against mutations
H. J. Bussemaker, D. Thirumalai, J. K. Bhattacharjee
By balancing the average energy gap with its typical change due to mutations for protein-like heteropolymers with M residues, we show that native states are unstable to mutations o…