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List of works by Dave Thirumalai

A Förster Resonance Energy Transfer-Based Sensor of Steric Pressure on Membrane Surfaces

scientific article published on 25 November 2020

A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants

scientific article published in 2023

Accurate, smooth, local, energy-dependent optical potentials for electron scattering

article

Activated dynamics, loss of ergodicity, and transport in supercooled liquids

scientific article published on 01 January 1993

Allosteric communication between ACE2 active site and binding interface with SARS-CoV-2

scientific article published in 2023

Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back

scientific article published on 25 August 2007

Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks ⬇️

scientific article published on April 2009

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

scientific article

Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle

scientific article published on 24 December 2008

Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures

Annealing function of GroEL: structural and bioinformatic analysis

scientific article

Application of the matrix-effective-potential formalism to electron-neon scattering at 150 - 700-eV impact energy and comparison to optical-potential calculations

scholarly article by Devarajan Thirumalai & Donald Truhlar published 1 June 1982 in Physical Review A

Aqueous urea solution destabilizes Abeta(16-22) oligomers

scholarly article

Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures

scientific article published on 05 October 2009

Bryngelson and Thirumalai Reply

scientific article published on 01 November 1996

Caging helps proteins fold ⬇️

scientific article published on September 23, 2003

Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?

scientific article published on 21 August 2003

Capturing the essence of folding and functions of biomolecules using coarse-grained models

scientific article published on 27 September 2011

Chain length determines the folding rates of RNA.

scientific article published on 7 February 2012

Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

scientific article published on 03 December 2018

Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism

scientific article published on April 1996

Chaperonin-mediated protein folding

scientific article

Charge Density of Cation Determines Inner Versus Outer Shell Coordination to Phosphate in RNA

scientific article published on 28 April 2020

Charge density of divalent metal cations determines RNA stability

scientific article published on 13 February 2007

Charge fluctuation effects on the shape of flexible polyampholytes with applications to intrinsically disordered proteins

scientific article published on 01 October 2018

Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant

scientific article published on July 2002

Chromatin Is Stretched but Intact When the Nucleus Is Squeezed through Constrictions

scientific article published on 15 December 2016

Coarse-grained model for predicting RNA folding thermodynamics

scientific article published on 16 April 2013

Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin.

scientific article published on 11 January 2017

Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins ⬇️

scientific article published on April 21, 2011

Collapse transition in proteins

scientific article

Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments

scientific article published in Physical Review Letters

Compaction of a bacterial group I ribozyme coincides with the assembly of core helices

scientific article published in February 2004

Comparison between dynamical theories and metastable states in regular and glassy mean-field spin models with underlying first-order-like phase transitions

scientific article published on 01 June 1988

Comparison of convergence for the schwinger, optimized anomaly-free, and optimized minimum-norm variational methods for potential scattering

Compression and stretching of a self-avoiding chain in cylindrical nanopores

scientific article published on 22 September 2008

Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization

scientific article published in Physical Review Letters

Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox

scientific article published on 29 August 2019

Conformations of a polyelectrolyte chain

scientific article published on 01 September 1992

Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis

scientific article published in May 2004

Cooperativity in protein folding: from lattice models with sidechains to real proteins ⬇️

scientific article published on 01 January 1998

Correction

Correction: Spatially heterogeneous dynamics of cells in a growing tumor spheroid: comparison between theory and experiments

scientific article published on 30 June 2020

Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States

scientific article published on 30 March 2006

Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein

scholarly article

Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II

scientific article

Criterion that determines the foldability of proteins

scientific article published on 01 May 1996

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA ⬇️

scientific article published on July 15, 2011

Crowding effects on the mechanical stability and unfolding pathways of ubiquitin

scientific article published on January 2009

Crowding effects on the structural transitions in a flexible helical homopolymer

scientific article published on 16 March 2009

Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models

scientific article

Denaturant-dependent folding of GFP ⬇️

scientific article published on July 9, 2012

Denaturants Alter the Flux Through Multiple Pathways in the Folding of PDZ Domain.

scientific article published on 5 January 2018

Denaturants can accelerate folding rates in a class of globular proteins

scientific article

Design principles governing the motility of myosin V.

scientific article

Determination of network of residues that regulate allostery in protein families using sequence analysis

scientific article

Development and Applications of Coarse-Grained Models for RNA

article

Development of novel statistical potentials for protein fold recognition

scientific article published on April 2004

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities

scientific article published on 30 July 2020

Directly measuring single-molecule heterogeneity using force spectroscopy

scientific article published on 17 June 2016

Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-Gaussian Velocity Distributions under Force. ⬇️

scientific article published on 8 August 2016

Dispersion-equation approach to obtaining complex optical potentials for electron scattering

Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

scientific article published on 10 July 2015

Dissecting contact potentials for proteins: Relative contributions of individual amino acids

scientific article published on 01 January 2008

Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets.

scientific article published in March 2003

Dissecting the kinematics of the kinesin step.

scientific article

Drag reduction in turbulent flows by polymers

scientific article published on 01 July 1991

Dramatic shape changes occur as Cytochrome c folds

scientific article published on 25 August 2020

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires ⬇️

scientific article published on November 22, 2010

Dynamic Transition in tRNA is Solvent Induced

article

Dynamic competition between catch and slip bonds in selectins bound to ligands.

scientific article

Dynamical Transition and Heterogeneous Hydration Dynamics in RNA

article

Dynamics of Allosteric Transitions in Dynein

article

Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers

article

Dynamics of Random Hydrophobic-Hydrophilic Copolymers with Implications for Protein Folding

scientific article published on 01 December 1996

Dynamics of allosteric transitions in GroEL.

scientific article

Dynamics of locking of peptides onto growing amyloid fibrils

scholarly article

Dynamics of tRNA at different levels of hydration.

scientific article published on April 2009

Dynamics of the structural glass transition and the p-spin-interaction spin-glass model

scientific article published on 01 May 1987

Dynamics of unbinding of cell adhesion molecules: transition from catch to slip bonds

scientific article

Early events in RNA folding

scientific article (publication date: 2001)

Effect of finite size on cooperativity and rates of protein folding.

scientific article published in January 2006

Effects of Macromolecular Crowding on the Collapse of Biopolymers ⬇️

scientific article published in Physical Review Letters

Effects of crowding and confinement on the structures of the transition state ensemble in proteins

scientific article published on 22 June 2007

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

scholarly article

Effects of pH on Proteins: Predictions for Ensemble and Single-Molecule Pulling Experiments ⬇️

scientific article published on December 27, 2011

Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins.

scientific article

Electron scattering by CO2: Elastic scattering, rotational excitation, and excitation of the asymmetric stretch at 10 eV impact energy

Electron scattering by methane: Elastic scattering and rotational excitation cross sections calculated with ab initio interaction potentials

article

Emerging ideas on the molecular basis of protein and peptide aggregation ⬇️

scientific article published on April 1, 2003

Energy-dependent polarization potential, dispersion-relation absorption potential, and matrix effective potential for electron-neon scattering at 10 — 100 eV

scholarly article by Devarajan Thirumalai & Donald Truhlar published 1 August 1982 in Physical Review A

Entropic stabilization of proteins by TMAO

scientific article (publication date: 17 November 2011)

Entropic stabilization of the folded states of RNA due to macromolecular crowding

scientific article

Entropy and enthalpy of interaction between amino acid side chains in nanopores. ⬇️

scientific article published in December 2014

Ergodic behavior in supercooled liquids and in glasses

scientific article published on 01 April 1989

Ergodic convergence properties of supercooled liquids and glasses

scientific article published on 01 October 1990

Ergodicity and activated dynamics in supercooled liquids

scientific article published on 01 March 1992

Erratum: Energy-dependent polarization potential, dispersion-relation absorption potential, and matrix effective potential for electron-neon scattering at 10-100 eV

scholarly article by Devarajan Thirumalai & Donald Truhlar published 1 November 1983 in Physical Review A

Estimations of the size of nucleation regions in globular proteins

scientific article published in December 2008

Evidence of disorder in biological molecules from single molecule pulling experiments ⬇️

scientific article published on 31 March 2014

Exact solution of the Zwanzig-Lauritzen model of polymer crystallization under tension

scientific article published on March 2013

Excitation of the asymmetric stretch mode of CO2by electron impact

Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics

scientific article published on May 2002

Exploring the energy landscape in proteins

scientific article

Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity

scientific article published on 01 April 1999

Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments

scientific article

Extracting stacking interaction parameters for RNA from the data set of native structures

scientific article

Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models

scientific article published in Physical Review Letters

Factors governing helix formation in peptides confined to carbon nanotubes

scientific article published on 26 September 2008

Factors governing the foldability of proteins

scientific article published on 01 December 1996

Finite size effects on thermal denaturation of globular proteins

Fishing for folding nuclei in lattice models and proteins

scientific article published on 01 January 1998

Folding PDZ2 Domain Using the Molecular Transfer Model

scientific article published on 15 March 2016

Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations ⬇️

scientific article published on November 30, 2011

Folding of RNA involves parallel pathways

Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size

scientific article published in July 2004

Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures

scientific article

Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes

scholarly article

Force-dependent switch in protein unfolding pathways and transition-state movements ⬇️

scientific article published on 27 January 2016

Force-induced unzipping transitions in an athermal crowded environment

scientific article

Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states

scientific article published in March 2018

Forced-unfolding and force-quench refolding of RNA hairpins

scientific article

Fragile-to-strong crossover, growing length scales, and dynamic heterogeneity in Wigner glasses

scientific article published on 01 March 2020

Free polymer in a colloidal solution

scientific article published on 01 October 1991

Freezing of a colloidal liquid subject to shear flow

scientific article published on 01 April 1988

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover

scientific article published on 18 September 2018

From mechanical folding trajectories to intrinsic energy landscapes of biopolymers.

scientific article

Full‐response pseudochannels: A new method for converging coupled‐channels scattering calculations. Theory and examples

article

Gene regulation by riboswitches with and without negative feedback loop

scientific article

Generalized iterative annealing model for the action of RNA chaperones

scientific article published in September 2013

Giant Casimir Nonequilibrium Forces Drive Coil to Globule Transition in Polymers

scientific article published on 14 May 2019

HOPE: a homotopy optimization method for protein structure prediction.

scientific article

Helicase processivity and not the unwinding velocity exhibits universal increase with force

scientific article

Helices 2 and 3 are the initiation sites in the PrP(C) → PrP(SC) transition

scientific article published on 31 December 2012

Hidden complexity in the isomerization dynamics of Holliday junctions

scientific article published on 7 October 2012

How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?

scientific article published on March 2009

How do metal ions direct ribozyme folding?

scientific article published on 31 August 2015

How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics

scientific article published on 28 October 2019

Hydration for a series of hydrocarbons ⬇️

scientific article published on July 21, 1998

Hydrophobic Interactions in Aqueous Urea Solutions with Implications for the Mechanism of Protein Denaturation

scientific article published in January 1998

Hydrophobic and ionic interactions in nanosized water droplets.

scientific article published in October 2006

Identifying natural substrates for chaperonins using a sequence-based approach

scientific article

Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein.

scientific article published on 24 August 2016

Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin.

scientific article published on 6 January 2016

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide ⬇️

scientific article published on May 19, 2011

Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation

scientific article

Influence of surface interactions on folding and forced unbinding of semiflexible chains.

scientific article published in November 2005

Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer ⬇️

scientific article published on July 26, 2012

Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability

scholarly article

Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism

scientific article published on 16 May 2007

Interface Residues That Drive Allosteric Transitions Also Control the Assembly of l-Lactate Dehydrogenase

scientific article published on 27 August 2018

Intermediates and transition states in protein folding.

scientific article published in January 2007

Internal constraints induce localization in an isolated polymer molecule

scientific article published on 01 January 1996

Interphase human chromosome exhibits out of equilibrium glassy dynamics

scientific article published in Nature Communications

Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent

scientific article published on 11 May 2019

Is there a unique melting temperature for two-state proteins?

scientific article published in January 2002

Isolated polymer molecule in a random environment

scientific article published on 01 January 1988

Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones

scientific article published on 23 December 2019

Kinematics of the lever arm swing in myosin VI.

scientific article published on 16 May 2017

Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation

scientific article published on 31 January 2008

Kinetics and thermodynamics of folding in model proteins

scientific article

Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein

scientific article published on 01 October 1996

Kinetics of Loop Formation in Polymer Chains†

scientific article published on 13 February 2008

Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape

scientific article published on 22 October 2013

Kinetics of interior loop formation in semiflexible chains

scientific article published in March 2006

Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water.

scientific article published on September 1997

Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism 1 1Edited by A. R. Fersht ⬇️

scientific article published on September 18, 1998

Localized second-order optical potential for electron scattering in terms of imaginary-frequency susceptibilities

article by Steven M. Valone et al published 1 June 1982 in Physical Review A

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

scholarly article

Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics

scientific article published on May 1999

Manifestation of random first-order transition theory in Wigner glasses.

scientific article

Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: theory and applications

scientific article

Maximizing RNA folding rates: a balancing act.

scientific article

Mean-field Potts glass model: Initial-condition effects on dynamics and properties of metastable states.

scientific article

Mean-field soft-spin Potts glass model: Statics and dynamics

scientific article published on 01 April 1988

Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments

article by Changbong Hyeon & D Thirumalai published 27 February 2007 in Journal of Physics: Condensed Matter

Mechanical unfolding of RNA hairpins

scientific article

Mechanical unfolding of RNA: from hairpins to structures with internal multiloops

scientific article

Mechanisms and kinetics of beta-hairpin formation

scientific article

Membrane-Protein Interactions Are Key to Understanding Amyloid Formation

scientific article published on 01 February 2014

Metal ion dependence of cooperative collapse transitions in RNA

scientific article published on 25 August 2009

Metastability of the folded states of globular proteins

scientific article

Minimal models for proteins and RNA from folding to function

scientific article published on January 2008

Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped

scientific article

Minimum energy compact structures of random sequences of heteropolymers

scientific article published on 01 October 1993

Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways ⬇️

scientific article published on May 1, 1995

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding

scientific article published on 05 December 2018

Molecular Transfer Model for pH Effects on Intrinsically Disordered Proteins: Theory and Applications

scientific article published on 10 February 2021

Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium

scientific article published on 7 December 2017

Molecular crowding enhances native state stability and refolding rates of globular proteins

scientific article

Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution

scientific article

Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins

scientific article published on May 2009

Molecular-dynamics study of glassy and supercooled states of a binary mixture of soft spheres

scientific article published on 01 October 1987

Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism.

scholarly article

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

article published in the Proceedings of the National Academy of Sciences of the United States of America

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

preprint dated 19 October 2017

Multiple Probes are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins

scientific article published in 2008

Multiple barriers in forced rupture of protein complexes

scientific article

Multiple protein folding nuclei and the transition state ensemble in two-state proteins

scientific article

Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions

scholarly article

Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin

scientific article published on 12 July 2021

Myosin V executes steps of variable length via structurally constrained diffusion

scientific article published on 15 January 2020

Myosin VI: How Do Charged Tails Exert Control? ⬇️

scientific article published on November 10, 2010

Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces

scientific article

Native secondary structure formation in RNA may be a slave to tertiary folding ⬇️

scientific article published on September 29, 1998

Native topology determines force-induced unfolding pathways in globular proteins

scientific article published on June 2000

Navigating the folding routes

scientific article published on March 1995

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved

scientific article published on 01 April 2005

Noise Control in Gene Regulatory Networks with Negative Feedback.

scientific article published on 12 May 2016

Non-empirical model for the imaginary part of the optical potential for electron scattering

article

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

scientific article published on 9 January 2023

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

scientific article published on 13 June 2023

On the Development of Coarse-Grained Protein Models

article

On the Emergence of Orientational Order in Folded Proteins with Implications for Allostery

scientific article published on 29 April 2021

On the Simulation of Quantum Systems: Path Integral Methods

On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model

scientific article published on 01 December 2009

On the origin of the unusual behavior in the stretching of single-stranded DNA.

scientific article

Optimal information transfer in enzymatic networks: A field theoretic formulation

scientific article published on 14 July 2017

Order-disorder transition in colloidal suspensions

scientific article published on 01 December 1987

Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases

Orientational potentials extracted from protein structures improve native fold recognition

scientific article published on April 2004

Origin of superdiffusive behavior in a class of nonequilibrium systems

scientific article published on 01 March 2019

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

scientific article

Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin

scientific article published on 30 October 2017

Path-integral Monte Carlo simulations of electron localization in water clusters

scientific article published in June 1986

Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins

scientific article published in November 2006

Persistence Length Changes Dramatically as RNA Folds

scientific article published in Physical Review Letters

Perspective: Reaches of chemical physics in biology

scientific article published in September 2013

Phenomenological and microscopic theories for catch bonds.

scientific article published on April 2016

Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes ⬇️

scientific article

Polarization and absorption effects in electron-helium scattering at 30-400 eV

article

Polymer-induced drag reduction in turbulent flows

scientific article published on 01 January 1996

Principles governing oligomer formation in amyloidogenic peptides

scientific article

Probing protein-protein interactions by dynamic force correlation spectroscopy.

scientific article

Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations

scientific article published on 01 July 2005

Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization

scientific article

Probing the instabilities in the dynamics of helical fragments from mouse PrPC.

scholarly article

Probing the mechanisms of fibril formation using lattice models

scientific article

Processivity and Velocity for Motors Stepping on Periodic Tracks

scientific article published on 25 February 2020

Processivity, Velocity, and Universal Characteristics of Nucleic Acid Unwinding by Helicases

scientific article published on 20 July 2019

Promoter melting triggered by bacterial RNA polymerase occurs in three steps

scientific article

Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins ⬇️

scientific article published on 17 May 2014

Protein collapse is encoded in the folded state architecture.

scientific article published on 27 April 2017

Protein folding guides disulfide bond formation

scientific article

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

scientific article published on 01 January 1997

Protein folding: from theory to practice

scientific article published on 21 December 2012

Protein thermodynamics: Are native proteins metastable?

scientific article published on 23 November 2011

Proteins associated with diseases show enhanced sequence correlation between charged residues

scientific article

Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure

scientific article published on 17 August 2013

Pulling-speed-dependent force-extension profiles for semiflexible chains

scientific article

Quasifree-scattering model for the imaginary part of the optical potential for electron scattering

article

RNA and protein folding: common themes and variations

scientific article

RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme

scientific article

RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and Molecular Tensegrity

scientific article published on November 2012

Rational fraction analytic continuation method for complex resonance energies in multidimensional systems

Refolding dynamics of stretched biopolymers upon force quench.

scientific article

Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds.

scientific article published on 7 August 2018

Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers

scientific article (publication date: 29 October 2008)

Reply to Alberti: Are in vitro folding experiments relevant in vivo?

scientific article published on 25 May 2016

Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state

scholarly article

Response

scientific article published on 01 May 1995

Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations

scholarly article

Ribosome exit tunnel can entropically stabilize alpha-helices

scholarly article

Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture

scientific article published in March 2010

Ripping RNA by Force Using Gaussian Network Models

scientific article published on 2 December 2016

Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2

scientific article published on 01 December 2020

Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations

Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics

scientific article published in May 2001

Role of internal chain dynamics on the rupture kinetic of adhesive contacts

scientific article published on 20 June 2008

Role of water in protein aggregation and amyloid polymorphism

scientific article published on 15 July 2011

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension ⬇️

scientific article published on 14 June 2016

Scaling concepts for the dynamics of viscous liquids near an ideal glassy state

scientific article published on 01 July 1989

Self-generated persistent random forces drive phase separation in growing tumors

scientific article published on 01 November 2020

Semiflexible chains in confined spaces.

scientific article published on 30 January 2009

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins

scientific article published on 15 April 2019

Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide

scientific article published on June 2009

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA

scientific article published on 26 June 2018

Sequence-dependent folding landscapes of adenine riboswitch aptamers

scientific article published on 23 December 2013

Sequence-resolved free energy profiles of stress-bearing vimentin intermediate filaments

scientific article

Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA

scientific article published on 9 March 2021

Share, but unequally: a plausible mechanism for emergence and maintenance of intratumour heterogeneity

scientific article published on 01 January 2019

Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins

scientific article published on 01 June 2018

Simulations of beta-hairpin folding confined to spherical pores using distributed computing

scientific article

Size, shape, and flexibility of RNA structures

scientific article published in November 2006

Spatially heterogeneous dynamics of cells in a growing tumor spheroid: comparison between theory and experiments

scientific article published on 28 May 2020

Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains

scientific article

Stretching Homopolymers

article published in 2007

Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding

scientific article published on May 1999

Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection

scientific article

Structure and dynamics of screened-Coulomb colloidal liquids

scientific article published on 01 June 1986

Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization.

scientific article published on 24 April 2018

Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions

scientific article published on 14 May 2008

Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase

scientific article published on December 2009

Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways

scientific article published on 29 September 2005

Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines

scientific article published on 24 April 2019

Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing

scientific article published in Nature Communications

Tests of the quasiclassical trajectory cross‐correlation moment method against accurate quantum dynamics for V–V energy transfer in HF–HF collisions

Tests of the semiclassical polarization approximation for electron scattering by helium and neon

scholarly article by Devarajan Thirumalai & Donald Truhlar published 1 January 1983 in Physical Review A

The different electronic natures displayed by the alkylthio groups in simple and higher conjugated aniline systems

scientific article published on 08 August 2006

The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study

scientific article published in March 2003

The nature of folded states of globular proteins

scientific article

The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus ⬇️

scientific article published on January 1, 1997

The shape of a flexible polymer in a cylindrical pore

scientific article published on 01 May 2005

Theoretical perspectives on protein folding

scientific article published on January 2010

Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor

scientific article

Theoretical probes of conformational fluctuations in S-peptide and RNase A/3'-UMP enzyme product complex

scientific article published on 01 April 1993

Theory and computations in biology: Kamal's legacy

scientific article published on 08 February 2017

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

scientific article published on 30 September 2019

Theory of Biopolymer Stretching at High Forces

scientific article published on 7 April 2010

Theory of RNA Folding: From Hairpins to Ribozymes

Theory of the Molecular Transfer Model for Proteins with Applications to the Folding of the src-SH3 Domain ⬇️

scientific article published on April 30, 2012

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

scientific article

Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes.

scientific article published on 6 January 2017

Toward a Molecular Theory of Early and Late Events in Monomer to Amyloid Fibril Formation ⬇️

scientific article published on January 1, 2011

Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations

scientific article published on March 2009

Ultrasensitivity of Water Exchange Kinetics to the Size of Metal Ion.

scientific article published on 30 August 2017

Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment

scientific article published on 19 August 2015

Universal Nature of Collapsibility in the Context of Protein Folding and Evolution

scientific article published on 29 May 2019

Universal relations in the self-assembly of proteins and RNA ⬇️

scientific article published on 08 October 2014

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding

scholarly article

Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases

scientific article published on December 2009

Urea-induced denaturation of preQ1-riboswitch

scientific article published on 31 July 2013

Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches

scientific article

Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics

scientific article published on January 1998

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

preprint dated 6 February 2023

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

scientific article published on 27 October 2023

Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores

scientific article published on March 2009

p-spin-interaction spin-glass models: Connections with the structural glass problem

scientific article published on 01 October 1987

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