Dave Thirumalai
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Researcher in soft-matter physics at UT Austin
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Physics
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(Suggest an Edit or Addition)Dave Thirumalai's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Navigating the folding routes (1995) (1023)
- Scaling concepts for the dynamics of viscous liquids near an ideal glassy state. (1989) (674)
- On the Simulation of Quantum Systems: Path Integral Methods (1986) (570)
- Molecular crowding enhances native state stability and refolding rates of globular proteins. (2005) (491)
- Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding (2008) (452)
- Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism (2007) (341)
- Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. (1996) (338)
- Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes (2008) (313)
- p-spin-interaction spin-glass models: Connections with the structural glass problem. (1987) (312)
- The nature of folded states of globular proteins (1992) (310)
- Emerging ideas on the molecular basis of protein and peptide aggregation. (2003) (310)
- Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. (2007) (310)
- Kinetics and thermodynamics of folding in model proteins. (1993) (302)
- Kinetics of protein folding: Nucleation mechanism, time scales, and pathways (1995) (296)
- Dissecting the Assembly of Aβ16–22 Amyloid Peptides into Antiparallel β Sheets (2003) (292)
- Role of water in protein aggregation and amyloid polymorphism. (2011) (279)
- Metastability of the folded states of globular proteins. (1990) (258)
- RNA and protein folding: common themes and variations. (2005) (247)
- HYDROPHOBIC INTERACTIONS IN AQUEOUS UREA SOLUTIONS WITH IMPLICATIONS FOR THE MECHANISM OF PROTEIN DENATURATION (1998) (232)
- Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism. (1996) (231)
- Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations (2006) (230)
- Toward a molecular theory of early and late events in monomer to amyloid fibril formation. (2011) (229)
- Dynamics of the structural glass transition and the p-spin-interaction spin-glass model. (1987) (226)
- Capturing the essence of folding and functions of biomolecules using coarse-grained models. (2011) (223)
- Kinetics of Folding of Proteins and RNA (1996) (222)
- From Minimal Models to Real Proteins: Time Scales for Protein Folding Kinetics (1995) (199)
- Viscosity Dependence of the Folding Rates of Proteins (1997) (197)
- Quasifree-scattering model for the imaginary part of the optical potential for electron scattering (1983) (196)
- Mechanical unfolding of RNA hairpins. (2005) (190)
- Early events in RNA folding. (2001) (190)
- Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. (2006) (184)
- Folding of RNA involves parallel pathways. (1997) (180)
- Entropic stabilization of proteins by TMAO. (2011) (176)
- Theoretical perspectives on protein folding. (2010) (173)
- Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. (2006) (173)
- Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model (2008) (169)
- Simulations of β-hairpin folding confined to spherical pores using distributed computing (2002) (168)
- Chaperonin-mediated protein folding. (2004) (167)
- An iterative scheme for the evaluation of discretized path integrals (1983) (165)
- Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. (2001) (164)
- Native topology determines force-induced unfolding pathways in globular proteins. (2000) (157)
- Criterion that determines the foldability of proteins. (1996) (156)
- Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. (1996) (152)
- Exploring protein aggregation and self‐propagation using lattice models: Phase diagram and kinetics (2002) (152)
- Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations (2007) (150)
- Asymmetry in the shapes of folded and denatured states of proteins (2003) (148)
- Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. (1999) (148)
- Charge density of divalent metal cations determines RNA stability. (2007) (144)
- Mechanisms and kinetics of beta-hairpin formation. (2000) (142)
- Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? (2003) (137)
- Dynamics of unbinding of cell adhesion molecules: transition from catch to slip bonds. (2005) (136)
- Aqueous urea solution destabilizes Aβ16–22 oligomers (2004) (135)
- Dynamics of allosteric transitions in GroEL (2006) (134)
- 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. (2009) (132)
- Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. (1999) (130)
- Ribosome exit tunnel can entropically stabilize α-helices (2005) (125)
- Ergodic behavior in supercooled liquids and in glasses. (1989) (122)
- Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. (2003) (122)
- Development of novel statistical potentials for protein fold recognition. (2004) (121)
- On the calculation of time correlation functions in quantum systems: Path integral techniquesa) (1983) (120)
- Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. (2007) (120)
- Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics. (2001) (119)
- Path integral Monte Carlo studies of the behavior of excess electrons in simple fluids (1987) (119)
- Dynamics of locking of peptides onto growing amyloid fibrils (2009) (117)
- Probing the instabilities in the dynamics of helical fragments from mouse PrPC. (2004) (116)
- Size, shape, and flexibility of RNA structures. (2006) (113)
- Collapse transition in proteins. (2009) (112)
- Minimum energy compact structures of random sequences of heteropolymers. (1993) (111)
- Cooperativity in protein folding: from lattice models with sidechains to real proteins. (1998) (110)
- Coarse-grained model for predicting RNA folding thermodynamics. (2013) (110)
- Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. (2005) (108)
- Non-empirical model for the imaginary part of the optical potential for electron scattering (1983) (106)
- Folding kinetics of proteins : a model study (1992) (102)
- Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments (2006) (100)
- Principles governing oligomer formation in amyloidogenic peptides. (2010) (99)
- Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization. (2005) (99)
- Random solutions from a regular density functional Hamiltonian: a static and dynamical theory for the structural glass transition (1989) (99)
- Factors governing the foldability of proteins (1996) (99)
- Dynamic transition in tRNA is solvent induced. (2006) (99)
- Path integral Monte Carlo study of the hydrated electron (1987) (98)
- Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures (2009) (97)
- Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. (2002) (94)
- Orientational potentials extracted from protein structures improve native fold recognition (2004) (94)
- Factors governing fibrillogenesis of polypeptide chains revealed by lattice models. (2010) (92)
- Activated dynamics, loss of ergodicity, and transport in supercooled liquids. (1993) (92)
- Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. (2009) (92)
- Forced-unfolding and force-quench refolding of RNA hairpins. (2006) (92)
- Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. (1998) (92)
- A Path Integral Monte Carlo Study of Liquid Neon and the Quantum Effective Pair Potential (1984) (91)
- Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. (2003) (91)
- Localization of an excess electron in water clusters (1986) (91)
- The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study (2003) (89)
- Interphase human chromosome exhibits out of equilibrium glassy dynamics (2017) (88)
- Protein folding guides disulfide bond formation (2015) (88)
- Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires (2010) (88)
- Kinetic partitioning mechanism as a unifying theme in the folding of biomolecules (1997) (86)
- Effects of macromolecular crowding on the collapse of biopolymers. (2014) (86)
- Kinetics of loop formation in polymer chains. (2007) (86)
- 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. (2009) (86)
- Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. (1999) (85)
- Colloquium : Random first order transition theory concepts in biology and physics (2015) (83)
- How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins? (2009) (83)
- Comparison between dynamical theories and metastable states in regular and glassy mean-field spin models with underlying first-order-like phase transitions. (1988) (82)
- Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. (1999) (82)
- Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. (2006) (82)
- Determination of network of residues that regulate allostery in protein families using sequence analysis (2006) (81)
- Probing the mechanisms of fibril formation using lattice models. (2008) (81)
- How do metal ions direct ribozyme folding? (2015) (80)
- Thermal denaturation and folding rates of single domain proteins: size matters (2003) (79)
- Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin (2000) (79)
- Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. (2009) (79)
- From mechanical folding trajectories to intrinsic energy landscapes of biopolymers (2013) (79)
- Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. (2008) (79)
- Hidden complexity in the isomerization dynamics of Holliday junctions. (2012) (78)
- Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. (2006) (78)
- Dynamics of tRNA at different levels of hydration. (2009) (77)
- Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. (2009) (77)
- Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. (1995) (76)
- Nucleation mechanism for protein folding and theoretical predictions for hydrogen‐exchange labeling experiments (1995) (76)
- Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. (2008) (76)
- Dissecting the kinematics of the kinesin step. (2012) (75)
- Metal ion dependence of cooperative collapse transitions in RNA. (2009) (75)
- Mean-field soft-spin Potts glass model: Statics and dynamics. (1988) (75)
- Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes (2008) (74)
- Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA. (2011) (74)
- LINKING RATES OF FOLDING IN LATTICE MODELS OF PROTEINS WITH UNDERLYING THERMODYNAMIC CHARACTERISTICS (1998) (74)
- Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins (2011) (74)
- Compression and stretching of a self-avoiding chain in cylindrical nanopores. (2008) (73)
- Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways (1995) (73)
- Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins. (2019) (73)
- Electrostatic Persistence Length of a Polyelectrolyte Chain (1995) (72)
- Multiple protein folding nuclei and the transition state ensemble in two‐state proteins (2001) (71)
- The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus. (1997) (71)
- Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. (2007) (71)
- Effects of crowding and confinement on the structures of the transition state ensemble in proteins. (2007) (70)
- Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. (2008) (69)
- Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. (2009) (68)
- Caging helps proteins fold (2003) (68)
- Denaturant-dependent folding of GFP (2012) (67)
- On the use of semiclassical dynamics in determining electronic spectra of Br2 in an Ar matrix (1985) (66)
- Effects of pH on proteins: predictions for ensemble and single-molecule pulling experiments. (2012) (65)
- Persistence length changes dramatically as RNA folds. (2005) (64)
- 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. (2008) (64)
- Extracting stacking interaction parameters for RNA from the data set of native structures. (2005) (64)
- Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing (2018) (63)
- Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. (2002) (62)
- Quantative measure of efficiency of Monte Carlo simulations (1994) (62)
- Exploring the energy landscape in proteins. (1993) (61)
- Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein (2016) (61)
- Promoter melting triggered by bacterial RNA polymerase occurs in three steps (2010) (60)
- RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. (2005) (60)
- Static properties of polymer chains in porous media (1989) (60)
- Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. (2004) (59)
- Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. (1997) (59)
- Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. (2004) (58)
- Semiflexible chains under tension (1996) (56)
- Time correlation functions in quantum systems (1984) (56)
- Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture. (2010) (56)
- Kinetics of interior loop formation in semiflexible chains. (2006) (55)
- Charge states rather than propensity for β‐structure determine enhanced fibrillogenesis in wild‐type Alzheimer's β‐amyloid peptide compared to E22Q Dutch mutant (2002) (55)
- Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures (2003) (55)
- Ribosome exit tunnel can entropically stabilize alpha-helices. (2005) (54)
- Effect of finite size on cooperativity and rates of protein folding. (2006) (54)
- A MEAN-FIELD MODEL FOR SEMIFLEXIBLE CHAINS (1995) (54)
- Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide and Ribonuclease A (1994) (54)
- Hydrophobic and ionic interactions in nanosized water droplets. (2006) (53)
- Mean-field Potts glass model: Initial-condition effects on dynamics and properties of metastable states. (1988) (53)
- Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization. (2015) (53)
- Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci (2018) (52)
- Protein folding: from theory to practice. (2013) (52)
- Infinite-range Ising spin glass in a transverse field (1989) (51)
- Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. (1998) (51)
- Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins. (2014) (50)
- Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines. (2018) (50)
- Force-dependent switch in protein unfolding pathways and transition-state movements (2015) (49)
- Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. (2006) (49)
- Semiflexible chains in confined spaces. (2008) (49)
- Maximizing RNA folding rates: a balancing act. (2000) (48)
- Native secondary structure formation in RNA may be a slave to tertiary folding. (1998) (48)
- Counterion charge density determines the position and plasticity of RNA folding transition states. (2006) (48)
- Refolding dynamics of stretched biopolymers upon force quench (2009) (47)
- Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. (2005) (47)
- Free polymer in a colloidal solution. (1991) (46)
- Time Scales for the Formation of the Most Probable Tertiary Contacts in Proteins with Applications to Cytochrome c (1999) (46)
- Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature. (2014) (46)
- Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. (2009) (46)
- Minimal models for proteins and RNA from folding to function. (2008) (46)
- Conformations of a polyelectrolyte chain. (1992) (46)
- Importance of Excluded Volume on the Solvation of Urea in Water (2004) (45)
- Measures of effective ergodic convergence in liquids (1989) (45)
- Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. (2009) (45)
- Dynamics of Collapse of Flexible Polyelectrolytes in Poor Solvents (2000) (44)
- Cell growth rate dictates the onset of glass to fluid-like transition and long time super-diffusion in an evolving cell colony (2017) (44)
- Chain length determines the folding rates of RNA. (2012) (43)
- Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide. (2009) (43)
- Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations. (2011) (42)
- Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability (2008) (42)
- Alterations in Water Structure Induced by Guanidinium and Sodium Ions (2004) (42)
- Urea-induced denaturation of preQ1-riboswitch. (2013) (42)
- Thermodynamic stability of folded proteins against mutations (1997) (42)
- Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein (2007) (41)
- Finite size effects on thermal denaturation of globular proteins. (2004) (41)
- Persistence length of flexible polyelectrolyte chains (1998) (40)
- Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state. (2006) (40)
- Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide. (2011) (40)
- Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. (2009) (40)
- Annealing function of GroEL: structural and bioinformatic analysis. (2002) (40)
- Ergodic convergence properties of supercooled liquids and glasses. (1990) (40)
- Isolated polymer molecule in a random environment. (1988) (39)
- Phenomenological and microscopic theories for catch bonds. (2016) (39)
- Ultrasensitivity of Water Exchange Kinetics to the Size of Metal Ion. (2017) (39)
- Structural Heterogeneity in Transmembrane Amyloid Precursor Protein Homodimer Is a Consequence of Environmental Selection (2014) (38)
- Hydration for a series of hydrocarbons. (1998) (38)
- Electron scattering by methane: Elastic scattering and rotational excitation cross sections calculated with ab initio interaction potentials (1983) (38)
- Design principles governing the motility of myosin V (2013) (37)
- Charge fluctuation effects on the shape of flexible polyampholytes with applications to Intrinsically disordered proteins (2018) (37)
- Order-disorder transition in colloidal suspensions. (1987) (37)
- Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model. (2015) (36)
- Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes (2014) (36)
- The shape of a flexible polymer in a cylindrical pore. (2005) (36)
- Are disordered spin glass models relevant for the structural glass problem (1995) (35)
- On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model (2009) (35)
- Theory of the molecular transfer model for proteins with applications to the folding of the src-SH3 domain. (2012) (34)
- Shape of Confined Polymer Chains (1997) (33)
- HOPE: A Homotopy Optimization Method for Protein Structure Prediction (2005) (33)
- Factors governing helix formation in peptides confined to carbon nanotubes. (2008) (33)
- Crowding effects on the structural transitions in a flexible helical homopolymer. (2009) (32)
- Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation. (2008) (32)
- Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments. (2011) (32)
- Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds (2018) (32)
- Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures (2012) (32)
- Protein thermodynamics: Are native proteins metastable? (2011) (32)
- Theoretical perspectives on biological machines (2019) (31)
- Dynamics of collapse of flexible polyampholytes (2000) (31)
- Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin. (2017) (31)
- Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities (2020) (31)
- Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium (2017) (31)
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA. (2018) (30)
- Internal constraints induce localization in an isolated polymer molecule. (1996) (30)
- Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment. (2015) (30)
- Cellular signaling networks function as generalized Wiener-Kolmogorov filters to suppress noise (2014) (30)
- Theory and simulations for RNA folding in mixtures of monovalent and divalent cations (2019) (30)
- Bending rigidity of stiff polyelectrolyte chains: A single chain and a bundle of multichains (2002) (29)
- On the origin of the unusual behavior in the stretching of single-stranded DNA. (2012) (29)
- Fishing for folding nuclei in lattice models and proteins. (1998) (29)
- Helices 2 and 3 are the initiation sites in the PrP(C) → PrP(SC) transition. (2013) (29)
- Theory of Biopolymer Stretching at High Forces. (2009) (29)
- Crowding effects on the mechanical stability and unfolding pathways of ubiquitin. (2008) (29)
- Pulling-speed-dependent force-extension profiles for semiflexible chains. (2004) (28)
- Stretching Homopolymers (2007) (28)
- Membrane-Protein Interactions Are Key to Understanding Amyloid Formation. (2014) (27)
- Methods for simulating time correlation functions in quantum systems (1991) (27)
- Mechanisms and kinetics of b-hairpin formation (2000) (27)
- Molecular-dynamics study of glassy and supercooled states of a binary mixture of soft spheres. (1987) (27)
- Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin (2017) (27)
- Multiple barriers in forced rupture of protein complexes. (2012) (27)
- Effect of elongational flow on the isotropic-nematic phase transition in rod-like systems (1986) (26)
- The use of citalopram in resistant cataplexy. (2000) (26)
- Directly measuring single-molecule heterogeneity using force spectroscopy (2016) (26)
- Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations. (2005) (26)
- Influence of the shape of crowding particles on the structural transitions in a polymer. (2012) (25)
- Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization. (2018) (25)
- Statistical Mechanics of Semiflexible Chains: A Meanfield Variational Approach (1997) (24)
- Proteins associated with diseases show enhanced sequence correlation between charged residues (2004) (24)
- Identifying natural substrates for chaperonins using a sequence‐based approach (2005) (23)
- Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension. (2016) (23)
- Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. (2004) (23)
- Evidence of disorder in biological molecules from single molecule pulling experiments. (2014) (23)
- Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape. (2013) (23)
- Liquid and crystalline states of monodisperse charged colloidal particles (1989) (22)
- A CRITERION THAT DETERMINES FAST FOLDING OF PROTEINS : A MODEL STUDY (1996) (22)
- FRACTAL ANALYSIS OF PROTEIN POTENTIAL ENERGY LANDSCAPES (1998) (22)
- Entropic stabilization of the folded states of RNA due to macromolecular crowding (2013) (22)
- Evaluation of microcanonical rate constants for bimolecular reactions by path integral techniques (1985) (22)
- Mechanical heterogeneity along single cell-cell junctions is driven by lateral clustering of cadherins during vertebrate axis elongation (2020) (22)
- Dynamics of Random Hydrophobic-Hydrophilic Copolymers with Implications for Protein Folding. (1996) (22)
- Protein Sequence Design by Energy Landscaping (2002) (22)
- Insights into Specific Problems in Protein Folding Using Simple Concepts (2002) (22)
- 1/p expansion for a p-spin interaction spin-glass model in a transverse field (1990) (22)
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot (2017) (22)
- Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases (2004) (21)
- LETTER TO THE EDITOR: Liquid, crystalline and glassy states of binary charged colloidal suspensions (1989) (21)
- Structure and dynamics of screened-Coulomb colloidal liquids. (1986) (21)
- Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding. (2018) (21)
- Exploring the Propensities of Helices in PrP to Form Sheet Using NMR Structures and Sequence Alignments (2002) (21)
- Dynamic competition between catch and slip bonds in selectins bound to ligands. (2006) (21)
- Dependence of Folding Rates on Protein Length (2002) (20)
- Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent. (2019) (20)
- Aqueous urea solution destabilizes Abeta(16-22) oligomers. (2004) (20)
- Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. (2002) (20)
- Role of internal chain dynamics on the rupture kinetic of adhesive contacts. (2008) (20)
- Probing protein-protein interactions by dynamic force correlation spectroscopy. (2005) (20)
- Dynamical transition and heterogeneous hydration dynamics in RNA. (2014) (20)
- Is there a unique melting temperature for two‐state proteins? (2002) (20)
- From Hi-C Contact Map to Three-dimensional Organization of Interphase Human Chromosomes (2020) (20)
- Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. (2013) (20)
- Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: theory and applications. (2006) (20)
- Universal Nature of Collapsibility in the Context of Protein Folding and Evolution. (2019) (20)
- Protein Collapse is Encoded in the Folded State Architecture (2016) (19)
- Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox (2019) (19)
- Lattice Model Studies of Force-Induced Unfolding of Proteins † (2001) (19)
- Computational Investigation of Carbene-Phosphinidenes: Correlation between 31P Chemical Shifts and Bonding Features to Estimate the π-Backdonation of Carbenes. (2018) (19)
- Theoretical Perspectives on In Vitro and In Vivo Protein Folding (1994) (19)
- Folding PDZ2 Domain Using the Molecular Transfer Model. (2016) (19)
- Theoretical probes of conformational fluctuations in S‐peptide and RNase A/3′–UMP enzyme product complex (1993) (19)
- Perspective: Reaches of chemical physics in biology. (2013) (19)
- Share, but unequally: a plausible mechanism for emergence and maintenance of intratumour heterogeneity (2018) (18)
- J an 2 00 0 Dynamics of Collapse of flexible Polyelectrolytes and Polyampholytes (2008) (18)
- Tests of the quasiclassical trajectory cross-correlation moment method against accurate quantum dynamics for V-V energy transfer in HF-HF collisions (1983) (18)
- Denaturants can accelerate folding rates in a class of globular proteins (1996) (18)
- Theory of RNA Folding: From Hairpins to Ribozymes (2009) (18)
- Folding in lattice models with side chains (2002) (17)
- Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-Gaussian Velocity Distributions under Force. (2016) (17)
- RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and Molecular Tensegrity. (2012) (17)
- Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins (2017) (16)
- Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones (2019) (16)
- Localized second-order optical potential for electron scattering in terms of imaginary-frequency susceptibilities (1982) (16)
- Helicase processivity and not the unwinding velocity exhibits universal increase with force. (2015) (16)
- A Kinetic Model for Chaperonin Assisted Folding of Proteins (1997) (16)
- Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped (2011) (16)
- Noise Control in Gene Regulatory Networks with Negative Feedback. (2016) (15)
- Kinematics of the lever arm swing in myosin VI (2016) (15)
- Polymer-induced drag reduction in turbulent flows. (1996) (15)
- Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA (2020) (15)
- Dissecting contact potentials for proteins: Relative contributions of individual amino acids (2007) (15)
- Sequence-dependent folding landscapes of adenine riboswitch aptamers. (2013) (15)
- Drag reduction in turbulent flows by polymers. (1991) (14)
- Path integral methods for simulating electronic spectra (1985) (14)
- Ergodicity and activated dynamics in supercooled liquids. (1992) (14)
- Elastic scattering and rotational excitation of a polyatomic molecule by electron impact - Acetylene (1981) (14)
- Sequence-resolved free energy profiles of stress-bearing vimentin intermediate filaments (2014) (14)
- Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics (2021) (14)
- Influence of optimal cavity shapes on the size of polymer molecules in random media (1990) (14)
- Gene regulation by riboswitches with and without negative feedback loop. (2012) (14)
- Generalized iterative annealing model for the action of RNA chaperones. (2013) (13)
- Random First‐Order Phase Transition Theory of the Structural Glass Transition (2009) (13)
- Electron scattering by CO2 - Elastic scattering, rotational excitation, and excitation of the asymmetric stretch at 10 eV impact energy (1981) (13)
- Intermediates and transition states in protein folding. (2007) (13)
- Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin. (2015) (13)
- Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2 (2020) (13)
- Studies on in vitro Antibacterial, Antifungal Property and Antioxidant Potency of Murraya paniculata (2011) (13)
- Spatially heterogeneous dynamics of cells in a growing tumor spheroid: comparison between theory and experiments. (2019) (13)
- Progressing from folding trajectories to transition state ensemble in proteins (2004) (12)
- Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches. (2014) (12)
- Persistence Length of Intrinsically Stiff Polyampholyte Chains (1997) (12)
- Stretching DNA: Role of electrostatic interactions (1998) (12)
- Comparison of convergence for the schwinger, optimized anomaly-free, and optimized minimum-norm variational methods for potential scattering (1980) (12)
- Bimolecular Reactive Collisions: Adiabatic and Nonadiabatic Methods for Energies, Lifetimes, and Branching Probabilities (1984) (12)
- Variational theories for localized states of an excess electron in fluids (1990) (12)
- ANALYTICAL THEORIES OF PROTEIN FOLDING (1996) (12)
- Estimations of the size of nucleation regions in globular proteins. (2008) (12)
- Rapid convergence of V–V energy transfer calculated using adiabatic basis functions. I. An accurate two‐state model for low‐energy resonant V–V energy transfer. II. (1982) (11)
- How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics (2019) (11)
- Dynamics of Allosteric Transitions in Dynein. (2018) (11)
- Polarization and absorption effects in electron-helium scattering at 30--400 eV (1982) (11)
- Ergodic measures for the simulation of dialectric properties of water (1991) (10)
- A Förster Resonance Energy Transfer-Based Sensor of Steric Pressure on Membrane Surfaces. (2020) (10)
- Distribution Function of the End-to-End Distance of Semiflexible Polymers (1997) (10)
- MDMap: A system for data-driven layout and exploration of molecular dynamics simulations (2011) (10)
- Energy-dependent polarization potential, dispersion-relation absorption potential, and matrix effective potential for electron-neon scattering at 10--100 eV (1982) (10)
- Charge Density of Cation Determines Inner Versus Outer Shell Coordination to Phosphate in RNA. (2020) (10)
- The Asakura-Oosawa theory: Entropic forces in physics, biology, and soft matter. (2022) (10)
- Cadherin clustering controls heterogeneous, asymmetric junction dynamics during vertebrate axis elongation (2020) (9)
- Rational fraction analytic continuation method for complex resonance energies in multidimensional systems (1984) (9)
- Determination of factors governing fibrillogenesis of polypeptide chains using lattice models (2010) (9)
- Theory and simulations of condensin mediated loop extrusion in DNA (2020) (9)
- Relaxation of anisotropic correlations in (two-component) supercooled liquids (1987) (9)
- Donor Stabilized Diatomic Gr.14 E2 (E = C-Pb) Molecule D-E2-D (D = NHC, aNHC, NNHC, NHSi, NHGe, cAAC, cAASi, cAAGe): A Theoretical Insight. (2019) (9)
- Spatially heterogeneous dynamics of cells in a growing tumor spheroid: Comparison between Theory and Experiments (2019) (9)
- Path-integral Monte Carlo simulations of electron localization in water clusters (1986) (9)
- Application of the matrix-effective-potential formalism to electron-neon scattering at 150 - 700-eV impact energy and comparison to optical-potential calculations (1982) (9)
- Manifestation of random first-order transition theory in Wigner glasses. (2012) (9)
- Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent (2019) (9)
- Interface residues that drive allosteric transitions also control the assembly of L-lactate Dehydrogenase (2018) (9)
- Finite size effects on calorimetric cooperativity of two-state proteins (2004) (8)
- Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins (2011) (8)
- Freezing of a colloidal liquid subject to shear flow. (1988) (8)
- Universal nature of collapsibility in the context of protein folding and evolution (2018) (8)
- Chromatin dynamics controls epigenetic domain formation (2021) (8)
- Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores. (2009) (8)
- Origin of superdiffusive behavior in a class of nonequilibrium systems. (2018) (8)
- Optimal information transfer in enzymatic networks: A field theoretic formulation. (2017) (7)
- Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover. (2018) (7)
- Dynamics of Asp 23-Lys 28 Salt-Bridge Formation in A â 1035 Monomers (7)
- Improved calculation of the cross section for excitation of the asymmetric stretch of CO2 by electron impact (1981) (6)
- Excitation of the asymmetric stretch mode of CO2 by electron impact (1980) (6)
- Emergence of stable and fast folding protein structures (1999) (6)
- Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants. (2021) (6)
- Processivity, velocity and universal characteristics of nucleic acid unwinding by helicases (2018) (6)
- Influence of surface interactions on folding and forced unbinding of semiflexible chains. (2005) (6)
- The Cavity Approach for Metastable Glassy States Near Random First Order Phase Transitions (1995) (6)
- Self-generated persistent random forces drive phase separation in growing tumors. (2020) (6)
- dock-lock mechanism Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage (2007) (5)
- Cooperation Among Tumor Cell Subpopulations Leads to Intratumor Heterogeneity (2020) (5)
- Dynamical aspects of anisotropic correlations in supercooled liquids (1990) (5)
- Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain. (2018) (5)
- Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers (2022) (5)
- Force-induced unzipping transitions in an athermal crowded environment. (2013) (5)
- Sequence Determines the Switch in the Fibril Forming Regions in the Low Complexity FUS Protein and Its Variants (2021) (5)
- Accurate, smooth, local, energy-dependent optical potentials for electron scattering (1983) (5)
- Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states. (2017) (5)
- Charge density of cation determines inner versus outer shell coordination to phosphate in RNA (2020) (5)
- Generalized Rayleigh-Plesset Theory for Cell Size Maintenance in Viruses and Bacteria (2019) (5)
- Interplay of Driver, Mini-Driver, and Deleterious Passenger Mutations on Cancer Progression (2016) (5)
- Tests of the semiclassical polarization approximation for electron scattering by helium and neon (1983) (4)
- Probes of equipartition in nonlinear Hamiltonian systems (1989) (4)
- Universal relations in the self-assembly of proteins and RNA (2014) (4)
- Myosin VI: how do charged tails exert control? (2010) (4)
- Development and applications of Coarse Grained models for RNA (2014) (4)
- Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their distinct aggregation propensities (2020) (4)
- Polyelectrolyte and Polyampholyte Effects in Synthetic and Biological Macromolecules (2011) (4)
- Far from equilibrium dynamics of tracer particles embedded in a growing multicellular spheroid (2020) (4)
- Myosin V executes steps of variable length via structurally constrained diffusion (2019) (4)
- Kinetics and Mechanism of RNA Folding studied by SAXS (2009) (4)
- A mathematical model for phenotypic heterogeneity in breast cancer with implications for therapeutic strategies (2021) (4)
- Studies on phytochemicals, antibacterial efficacy and antioxidant potency of Capparis sepiaria on enteric pathogens (2015) (4)
- Dual Role of Cell-Cell Adhesion In Tumor Suppression and Proliferation (2019) (4)
- Polymer chains in porous media (1989) (4)
- Self-generated persistent random forces drive phase separation in growing tumors (2020) (4)
- Energy Landscape of Ubiquitin Is Weakly Multidimensional. (2021) (4)
- Information flow, Gating, and Energetics in dimeric molecular motors (2021) (4)
- ERGODIC CONVERGENCE IN LIQUIDS AND GLASSES (1990) (4)
- Entropy and enthalpy of interaction between amino acid side chains in nanopores. (2014) (3)
- Transcription-induced active forces suppress chromatin motion by inducing a transient disorder-to-order transition (2022) (3)
- Structure of APP-C991-99 and Implications for Role of Extra-Membrane Domains in Function and Oligomerization (2018) (3)
- Step-wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor (2019) (3)
- Processivity and Velocity for Motors Stepping on Periodic Tracks (2019) (3)
- Low Force Unfolding of a Single-Domain Protein by Parallel Pathways. (2021) (3)
- Lifshitz tails in a spatially correlated random potential (1986) (3)
- On the emergence of orientational order in folded proteins with implications for allostery (2021) (3)
- Probing the role of local propensity in peptide turn formation (2000) (3)
- Exact solution of the Zwanzig-Lauritzen model of polymer crystallization under tension. (2012) (3)
- Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts (2022) (3)
- Dramatic shape changes occur as Cytochrome c folds (2020) (3)
- Topologically entangled polymers (1992) (3)
- Molecular Transfer Model for pH Effects on Intrinsically Disordered Proteins: Theory and Applications. (2021) (3)
- Response to ‘‘Comment on a proposed method for finding barrier height distributions’’ [J. Chem. Phys. 103, 1235 (1995)] (1995) (2)
- Imprints of tumor mutation burden on chromosomes and relation to cancer risk in humans: A pan-cancer analysis (2020) (2)
- Loss of ergodicity in glassy systems (2008) (2)
- Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology (2022) (2)
- D Thirumalai schemes sensitivity of predicted native states to variations in the interaction Pair potentials for protein folding : choice of reference states and (1999) (2)
- Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald’s rule of stages (2022) (2)
- Hydrophobic and Ionic Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins (2012) (2)
- On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions (2008) (2)
- Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins (2018) (2)
- Role of water-bridged interactions in metal ion coupled protein allostery (2022) (2)
- Fragile-to-strong crossover, growing length scales, and dynamic heterogeneity in Wigner glasses. (2019) (2)
- Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing (2018) (2)
- Adhesion strength between cells regulate non-monotonic growth by a biomechanical feedback mechanism (2021) (2)
- Ripping RNA by Force using Gaussian Network Models (2016) (2)
- Random First Order Theory concepts in Biology and Condensed Matter physics (2014) (2)
- Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes. (2017) (2)
- A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants (2022) (2)
- Molecular Transfer Model for pH effects on Intrinsically Disordered Proteins: Theory and Applications (2020) (2)
- Membrane-protein interactions hold the key to understanding amyloid formation (2014) (2)
- Step-Wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor. (2021) (2)
- Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin. (2021) (2)
- ROTATIONAL RELAXATION OF A SPHEROCYLINDER AND A SEMIRIGID MOLECULE IN CONCENTRATED SOLUTIONS (1994) (2)
- Adhesion strength between cells regulate non-monotonic growth by a biomechanical feedback mechanism. (2022) (2)
- On the theory of condensin mediated loop extrusion in genomes (2020) (2)
- Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin (2016) (2)
- Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin (2020) (1)
- Two landmarks in polymer physics: the Edwards model and de Gennes' observation (1999) (1)
- Extracting folding landscape characteristics of biomolecules using mechanical forces (2015) (1)
- Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99. (2022) (1)
- Factors governing fibrillogenesis of polypeptide chains (2010) (1)
- Glassy dynamics distinguishes chromosome organization across organisms (2015) (1)
- C2.5 Introducing protein folding using simple models (2001) (1)
- Architecture of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci (2017) (1)
- Energy Landscape of Ubiquitin is Weakly Multidimensional (2021) (1)
- Random First Order Transition Theory for Glassy Dynamics in a Single Condensed Polymer. (2020) (1)
- The Conformations of Confined Polymers in an External Potential (2017) (1)
- Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes. (2021) (1)
- Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA (2018) (1)
- Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome (2020) (1)
- Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin. (2021) (1)
- Reduction in RBD Binding Affinity to Glycosylated ACE2 is Entropic in Origin (2022) (1)
- Chromatin Is Stretched but Intact When the Nucleus Is Squeezed through Constrictions. (2017) (1)
- Relationship between the fluctuation metric and the non-ergodicity parameter: incoherent scattering function (1993) (1)
- Low force unfolding of a single-domain protein by parallel pathways (2020) (1)
- Share, but unequally: A mechanism for emergence and maintenance of intratumor heterogeneity (2018) (1)
- Dispersion‐equation approach to obtaining complex optical potentials for electron scattering (2009) (1)
- Introducing Protein Folding Using Simple Models (2001) (1)
- Temperature and Guanidine Hydrochloride Effects on the Folding Thermodynamics of WW Domain and Variants. (2021) (1)
- Giant Casimir Nonequilibrium Forces Drive Coil to Globule Transition in Polymers. (2017) (1)
- Elucidation of ion effects on the Thermodynamics of RNA Folding (2018) (1)
- Signaling Networks and Dynamics of Allosteric Transitions in Bacterial Chaperonin GroEL: Implications for Iterative Annealing of Misfolded Proteins (2017) (1)
- Flow induced transitions in smectic liquid crystals (1987) (1)
- Retardation of folding rates of substrate proteins in the nanocage of GroEL (2020) (1)
- Kinetics of condensation of flexible polyelectrolytes in poor solvents: effects of solvent quality, valence and size of counterions (1999) (1)
- Folding RNA in mixtures of monovalent and divalent cations: Theory and simulations (2019) (1)
- Bryngelson and Thirumalai Reply. (1996) (1)
- Dynamics of Allosteric Transitions in Dynein (2018) (1)
- Electron Localization by Atomic and Molecular Clusters (1987) (1)
- Faculty Opinions recommendation of Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding. (2011) (0)
- Watching ion-driven folding kinetics of a ribozyme one molecule at a time (2023) (0)
- 22] for General Reviews on Spin Glasses See: Mean--eld Potts Glass Model: Initial Condition Eeects on Dynamics and Properties of Glassy Dynamical Transition and Aging in a Model without Disorder Preprint Cond-mat/9408079 4.1 Ferromagnetic Ordering with J 0 = 0 (1994) (0)
- Hydration of Magnesium is Required for Myosin VI Phosphate Release (2018) (0)
- Noise Control In Gene Regulatory Networks With Negative Feedback (2016) (0)
- Structural and functional allostery wiring diagrams in GroEL/GroES (2009) (0)
- On the origin of the integrity of a subset of Topologically Associating Domains upon Cohesin loss in Interphase Chromosomes (2022) (0)
- Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo (2022) (0)
- Plus and minus ends of microtubules respond asymmetrically to kinesin binding by a long-range directionally driven allosteric mechanism (2021) (0)
- Correction: Spatially heterogeneous dynamics of cells in a growing tumor spheroid: comparison between theory and experiments. (2020) (0)
- Searching, Stepping, and Stomping: What Polymer Theory can teach us about the Molecular Motor Myosin V (2013) (0)
- Molecular Simulations of Mg2+-induced Folding of the Central Domain of the 16S Ribosomal RNA (2020) (0)
- Dependence of Water Exchange Kinetics on the Size and Charge of Metal Ion (2017) (0)
- Full‐response pseudochannels: A new method for converging coupled‐channels scattering calculations. Theory and examples (1982) (0)
- Molecular Mechanisms of Transition from Catch to Slip Bonds in Fibrin (2019) (0)
- Principles Governing the Stability and Folding Kinetics of Proteins From Extremophiles (2012) (0)
- Semiexible Chains in Conned Spaces (2013) (0)
- Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis (2023) (0)
- Residue-dependent transition temperatures and denaturant midpoints in the folding of a multi-domain protein (2022) (0)
- Crowding Effects on the Unfolding of Ubiquitin (2009) (0)
- Topological transitions, turbulent-like motion and long-time-tails driven by cell division in biological tissues (2022) (0)
- Coarse-grained model of chaperonin-mediated protein folding (2006) (0)
- Solution of the FISH-Hi-C paradox for Human Interphase Chromosomes (2019) (0)
- Tracer particles sense local stresses in an evolving multicellular spheroid without affecting the anomalous dynamics of the cancer cells (2022) (0)
- Denaturants alter the flux through multiple pathways in the folding of PDZ domain (2017) (0)
- On the origin of viscosity saturation at high densities during zebrafish morphogenesis (2022) (0)
- Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation (2023) (0)
- Interphase human chromosome exhibits out of equilibrium glassy dynamics (2018) (0)
- Liquid-Liquid Phase Separation of Repeat Disorder Sequences Leads to RNA Conformational and Dynamical Heterogeneity (2021) (0)
- Folding PDZ2 domain using the Molecular Transfer Model (2016) (0)
- A ug 1 99 8 Fractal Analysis of Protein Potential Energy Landscapes (2018) (0)
- Friends in need: How chaperonins recognize and remodel proteins that require folding assistance (2022) (0)
- Impact of TMAO on the preQ1 RNA Riboswitch Studied using Molecular Dynamics Simulations (2012) (0)
- Frictional effects on RNA folding: Speed limit and Kramers turnover (2018) (0)
- Growth mechanism of amyloid fibrils (2009) (0)
- Intrinsically Disordered Proteins Sense Membrane Curvature (2019) (0)
- Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension (2016) (0)
- Impact of divalent ions on the conformations of single and double stranded DNA: A coarse-grained molecular dynamics study. (2023) (0)
- Sizes, conformational fluctuations, and SAXS profiles for Intrinsically Disordered Proteins (2023) (0)
- Networks of Functional Residues in GroEL and GroES (2009) (0)
- Loss of CTCF loops on human interphase chromosome organization (2020) (0)
- Crowding Induced Conformational Switch (2011) (0)
- Molecular chaperones maximize the native state yield per unit time by driving substrates out of equilibrium (2017) (0)
- Shape of Confined Polymer (2002) (0)
- Mechanical Force and Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot (2016) (0)
- Mechanical Unbinding of Leukocyte Function-Associated Antigen-1 with ICAM-1 and ICAM-3 Complexes involves a Single Energetic Barrier (2010) (0)
- Translating the energy landscape paradigm to experimental observables in biomolecular folding (1998) (0)
- Localization of a Polymer with Internal Constraints (1996) (0)
- Multistep Folding Kinetics of Group I Intron RNA Studied by Mg2+-Concentration Jump Simulations (2017) (0)
- Cissus quadrangualaris as green corrosion inhibitor for mild steel in acid medium (0)
- Theory and simulations for crowding-induced changes in stability of proteins with applications to λ repressor (2020) (0)
- Confinement effects on folding of proteins and RNA (2009) (0)
- A FRET-based Sensor of Steric Pressure on Membrane Surfaces (2021) (0)
- Response of proteins to mechanical force (2016) (0)
- Discrete step sizes of molecular motors lead to bimodal non-Gaussian velocity distributions under force (2016) (0)
- Structure and dynamics of RNA in biomolecular condensate. (2023) (0)
- Age at first birth in women is genetically associated with increased risk of schizophrenia (2018) (0)
- Entropic stabilization of the folded states of RNA due to macromolecular crowding (2013) (0)
- Regulation of telomerase activity by macromolecular crowding (2011) (0)
- Protein misfolding and aggregation (2012) (0)
- RFOT theory explains fragile-to-strong crossover in Wigner glasses (2020) (0)
- Parsing the Contributions of Polypeptide Backbones and Sidechains to Denaturation in Concentrated Aqueous Solutions of Urea and Guanidinium Chloride (2014) (0)
- Live discussion: Protein folding and neurodegeneration: Biophysics to the rescue? 1 (2004) (0)
- Predicting the Organization of Mitotic Chromosomes using the Generalized Rouse Model (2020) (0)
- Theory and simulations for crowding-induced changes in stability of proteins with applications to $\lambda$ repressor (2020) (0)
- Molecular simulations of the monovalent-ion dependent Folding Thermodynamics of RNA (2018) (0)
- Probing the low-resolution dynamics of biopolymers under force (2006) (0)
- 48 Design principles governing the motility of myosin motors (2015) (0)
- Statistical Mechanical theory for spatio-temporal evolution of Intra-tumor heterogeneity in cancers: Analysis of Multiregion sequencing data (2022) (0)
- Glass-like dynamics in the folded state of human interphase chromosome (2017) (0)
- Faculty of 1000 evaluation for Regulated noise in the epigenetic landscape of development and disease. (2012) (0)
- A method for extracting effective interactions from Hi-C data with applications to interphase chromosomes and inverted nuclei (2023) (0)
- Theory and computations in biology: Kamal’s legacy (2017) (0)
- Kinetic Model for Myosin Gating and Backward Stepping Mechanisms (2019) (0)
- Irving Langmuir Prize in Chemical Physics Talk: Interphase Human Chromosome Exhibits Glassy Dynamics (2019) (0)
- Role of Water Mediated Interactions in Calcium-Coupled Allostery of Calmodulin Domains (2019) (0)
- Directly measuring single molecule heterogeneity in proteins and RNA using force spectroscopy (2016) (0)
- Structural changes in chromosomes driven by multiple condensin motors during mitosis (2022) (0)
- Detection and Estimation of Phenolic Acid and Flavonods in Leaves of Cadaba indica Lam by High Performance Thin Layer Chromatography (2018) (0)
- Remarks on the Connection Between Intrinsic Temperature Scales and Foldability of Proteins (1996) (0)
- Multi-Scale Coarse Grained Model for the Stepping of Molecular Motors with application to Kinesin (2021) (0)
- Calculation of Ion-Dependent RNA Folding Free Energy using Coarse-Grained Simulation (2018) (0)
- AN ABSTRACT OF THE THESIS OF Gowtham Vemulapalli for the degree of Master of Science in Electrical and Computer Engineering presented on October 17, 2003. Title: Accurately Tunable Low-voltage Continuous-time Filters (2009) (0)
- Autobiography of Dave Thirumalai. (2021) (0)
- Water-mediated interactions determine helix formation of peptides in open nanotubes (2020) (0)
- Document heading Pharmacognosy of Coccinia grandis : a review (2011) (0)
- Synthesis , characterization and biological evaluation of chromen and pyrano chromen-5-one derivatives impregnated into a novel collagen based scaffold for tissue engineering application † (2015) (0)
- Hypolipidaemic and antioxidant effect of Enicostemma littorale (2013) (0)
- Temperature and guanidine hydrochloride effects on the folding thermodynamics of WW domain and variants (2021) (0)
- Universality of distribution of tumor mutation burden - a biomarker for the tumor evolution and disease risk (2022) (0)
- Methodsfor simulatingtime correlationfunctions in quantumsystems (0)
- Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletion (2023) (0)
- Folding Pathways of RNA by Cation Condensation (2003) (0)
- How do neck linker docking and microtubule control dynamics of a kinesin step (2011) (0)
- TMAO and Solvent Exposed RNA Bases Stabilizes Unfolded State via Hydrogen Bonding (2009) (0)
- Conformational Fluctuations and Phases in Fused in Sarcoma (FUS) Low-Complexity Domain. (2023) (0)
- Molecular Mechanisms of Steric Pressure Generation and Membrane Remodeling by Intrinsically Disordered Proteins (2022) (0)
- Forced-rupture of Cell-Adhesion Complexes Reveals abrupt switch between two Brittle States (2017) (0)
- Exploring Rugged Energy Landscape in Large Systems. (1997) (0)
- Scenarios for protein aggregation: Molecular Dynamics simulations and Bioinformatic Analysis (2006) (0)
- TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions (2022) (0)
- 21aEF-12 The Structure Prediction of APP Dimer and Monomer (2010) (0)
- B M ] 2 3 Se p 20 06 Size , shape , and flexibility of RNA structures (2017) (0)
- On the Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin (2016) (0)
- Optimal information transfer in enzymatic networks: A field theoretic formulation (2017) (0)
- Effect of the Cation Size on the Stability of RNA Structures (2021) (0)
- Reply to Alberti: Are in vitro folding experiments relevant in vivo? (2016) (0)
- Assembly Mechanisms of RNA Pseudoknots are Determined by the Stabilities of the Constituent Secondary Structures (2010) (0)
- Chapter 11:Scenarios for Protein Aggregation: Molecular Dynamics Simulations and Bioinformatics Analysis (2008) (0)
- Decision letter: Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization (2020) (0)
- Effect of Force and Discrete Step-Size on the Velocity Distribution of Processive Molecular Motors (2015) (0)
- Erratum: Spatially heterogeneous dynamics of cells in a growing tumor spheroid: Comparison between theory and experiments (Soft Matter (2020) 16 (5294-5304) DOI: 10.1039/C9SM02277E) (2020) (0)
- Broad Velocity Distributions in SFIV Helicases are a Consequence of Heterogeneity (2016) (0)
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What Schools Are Affiliated With Dave Thirumalai?
Dave Thirumalai is affiliated with the following schools:
