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Thirumalai, Devarajan - Institute for Physical Science and Technology, University of Maryland at College Park

University of Maryland Chemistry GAANN Program Fellowship Application Packet
N.G. Walter et al. (eds.) Non-Protein Coding RNAs 27 doi: 10.1007/978-3-540-70840-7_2, Springer-Verlag Berlin Heidelberg 2009
Tensor renormalization group: Local magnetizations, correlation functions, and phase diagrams of systems with quenched randomness
Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures
Faculty Section Alexander, M 0301
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Topic: Ideal gases, Charles's Law Courses: General Chemistry, Physical Chemistry
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Mechanical Unfolding of RNA: From Hairpins to Structures with Internal Multiloops
Mechanisms and kinetics of -hairpin formation D. K. Klimov* and D. Thirumalai
Finite-temperature phase diagram of nonmagnetic impurities in high-temperature superconductors using a d=3 tJ model with quenched disorder
Caging helps proteins fold D. Thirumalai*, Dmitri K. Klimov, and George H. Lorimer
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Probing the mechanisms of fibril formation using lattice models Mai Suan Li,1
Deconvolution of dynamic mechanical networks Michael Hinczewskia,b,1
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Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments
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Effects of Crowding and Confinement on the Structures of the Transition State Ensemble in Margaret S. Cheung and D. Thirumalai*,,
A mean-field model for semiflexible chains B.-Y. Ha and D. Thirumalai
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties
Kinetics of Folding of Proteins and RNA D. THIRUMALAI* AND S. A. WOODSON
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model
Metal Ion Dependence of Cooperative Collapse Transitions in RNA
10.1110/ps.8.2.361Access the most recent version at doi: 1999 8: 361-369Protein Sci.
Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models Mai Suan Li,1
Frustrated further-neighbor antiferromagnetic and electron-hopping interactions in the d=3 t-J model: Finite-temperature global phase diagrams from renormalization group theory
Monday March 7, 2005 Chem 247-Majors Organic Chemistry Molecule of the week: Oleic Acid
Can energy landscape roughness of proteins and RNA be measured by using mechanical
Excitation spectrum gap and spin-wave velocity of XXZ Heisenberg chains: Global renormalization-group calculation
Stretching Homopolymers Greg Morrison,, Changbong Hyeon, N. M. Toan, Bae-Yeun Ha,| and
Inverted Berezinskii-Kosterlitz-Thouless singularity and high-temperature algebraic order in an Ising model on a scale-free hierarchical-lattice small-world network
Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to
Topic: Material and chemical properties, Enthalpy of solution Courses: General chemistry, Physical Chemistry
Monday March 28, 2005 Chem 247-Majors Organic Chemistry Molecule of the week: Capsaicin
Z .Physics of the Earth and Planetary Interiors 117 2000 139151 www.elsevier.comrlocaterpepi
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Multiple Probes are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins
J. Am. Chem. SOC.1994,116, 2049-2063 2049 Dynamics in Rugged Energy Landscapes with Applications to
VOLUME 76, NUMBER 21 P H Y S I C A L R E V I E W L E T T E R S 20 MAY 1996 Criterion that Determines the Foldability of Proteins
Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores
Solar Energy Materials & Solar Cells 91 (2007) 17261732 Optical and structural properties of Ta2O5CeO2 thin films
Macromolecules 1996,28, 577-581 677 Electrostatic Persistence Length of a Polyelectrolyte Chain
Virtual atom representation of hydrogen bonds in minimal off-lattice models of helices: effect on stability, cooperativity
Subscriber access provided by UNIV OF MARYLAND COLL PARK The Journal of Physical Chemistry B is published by the American Chemical
Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures
Interactions between Hydrophobic and Ionic Solutes in Aqueous Guanidinium Chloride and Urea Solutions: Lessons
Department of Chemistry & Biochemistry The University of Maryland at College Park
Theoretical Perspectives on Protein Folding
Semiflexible chains in confined spaces Greg Morrison1,2
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Griffiths singularities and algebraic order in the exact solution of an Ising model on a fractal modular network
Solar Energy Materials & Solar Cells 87 (2005) 181196 Optical filters from SiO2 and TiO2 multi-layers
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Biochemistry Graduate program Department of Chemistry & Biochemistry
Available online at www.sciencedirect.com Principles governing oligomer formation in amyloidogenic
Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures
Topic: Maxwell-Boltzmann statistics, Kinetic theory of gases Courses: General Chemistry, Physical Chemistry
Dynamics of locking of peptides onto growing amyloid fibrils
arXiv:0908.0376v1[cond-mat.soft]4Aug2009 Anisotropic Mean-Field Theory for Semiflexible Polymer Dynamics under Tension
Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments
Native topology determines force-induced unfolding pathways in globular proteins
Semiflexible chains under tension B.-Y. Ha and D. Thirumalai
Topic: Sublimation Courses: General Chemistry, Physical Chemistry
Page 1 of 3 Toan M. Ngo, Ph.D
The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus
Global cross-over dynamics of single semiflexible polymers This article has been downloaded from IOPscience. Please scroll down to see the full text article.
arXiv:0802.0771v1[cond-mat.dis-nn]6Feb2008 Reentrant and Forward Phase Diagrams of
Research Interests Jason D. Kahn University of Maryland, College Park
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Eur. Phys. J. B 48, 117 (2005) DOI: 10.1140/epjb/e2005-00376-y THE EUROPEAN
DNA-protein binding rates: Bending fluctuation and hydrodynamic coupling effects
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Dissecting contact potentials for proteins
Monday Feb. 28, 2005 Chem 247-Majors Organic Chemistry Molecule of the week: Polystyrene
Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins
Topic: Radical Reactions Courses: Organic Chemistry
Lattice Model Studies of Force-Induced Unfolding of Proteins D. K. Klimov* and D. Thirumalai*
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High-precision thermodynamic and critical properties from tensor renormalization-group flows Michael Hinczewski1
Solar Energy Materials & Solar Cells 92 (2008) 821829 Modeling the optical properties of WO3 and WO3SiO2 thin films
Determination of network of residues that regulate allostery in protein families using
Promoter melting triggered by bacterial RNA polymerase occurs in three steps
Critical percolation phase and thermal Berezinskii-Kosterlitz-Thouless transition in a scale-free network with short-range and long-range random bonds
University of Maryland Department of Chemistry and Biochemistry
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Topic: Atomic structure, Emission spectra Courses: General Chemistry
Publication List Devarajan (Dave) Thirumalai
pubs.acs.org/Macromolecules Published on Web 04/07/2010 r 2010 American Chemical Society 4394 Macromolecules 2010, 43, 43944400
Rigor to Post-Rigor Transition in Myosin V: Link between the Dynamics and the
Urea Destabilizes RNA by Forming Stacking Interactions and Multiple Hydrogen Bonds with Nucleic Acid Bases
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS On the accuracy of inferring energetic
Refolding dynamics of stretched biopolymers upon force quench
Thermodynamic Perspective on the Dock-Lock Growth Mechanism of Amyloid Fibrils Edward P. O'Brien,,
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent
Sequence and Crowding Effects in the Aggregation of a 10-Residue Fragment Derived from Islet Amyloid Polypeptide
Molecular Origin of Constant m-Values, Denatured State Collapse, and Residue-Dependent Transition Midpoints in Globular Proteins
How accurate are polymer models in the analysis of Frster resonance energy transfer experiments on proteins?
Crowding Effects on the Structural Transitions in a Flexible Helical Homopolymer Alexander Kudlay,1
Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II
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Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle
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Collapse transition in proteins D. Thirumalaib
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Minimal Models for Proteins and RNA: From Folding
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the
Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the Stability of RNA Hairpins
Structures and Free-Energy Landscapes of the Wild Type and Mutants of the A2130 Peptide Are Determined
Kinetics of Loop Formation in Polymer Chains Ngo Minh Toan,, Greg Morrison,, Changbong Hyeon, and D. Thirumalai*,,#
Kinetic Model for the Coupling between Allosteric Transitions in GroEL and Substrate Protein Folding
Allosteric Transitions in the Chaperonin GroEL are Captured by a Dominant Normal Mode that is Most Robust to Sequence Variations
Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein
Charge Density of Divalent Metal Cations Determines RNA Stability
Monomer adds to preformed structured oligomers of A -peptides by a two-stage docklock mechanism
Mechanical unfolding of RNA hairpins Changbong Hyeon* and D. Thirumalai
Current Topics RNA and Protein Folding: Common Themes and Variations
Molecular crowding enhances native state stability and refolding rates of globular proteins
Pulling-Speed-Dependent Force-Extension Profiles for Semiflexible Chains
Compaction of a Bacterial Group I Ribozyme Coincides with the Assembly of Core Ursula A. Perez-Salas,*,#, Prashanth Rangan,#, Susan Krueger, R. M. Briber,*,| D. Thirumalai, and
Molecular Dynamics Simulations of End-to-End Contact Formation in Hydrocarbon Chains in Water and Aqueous Urea
Abstract. We describe a unied approach to describe the kinetics of protein and RNA folding. The underlying
Emerging ideas on the molecular basis of protein and peptide1 aggregation2
Role of Counterion Condensation in Folding of the Tetrahymena Ribozyme II. Counterion-dependence of
Finite Size Effects on Thermal Denaturation of Globular Proteins Mai Suan Li,1,2
How the diffusivity profile reduces the arbitrariness of protein folding free energies
Physica A 389 (2010) 29932996 Contents lists available at ScienceDirect
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TABLE I. Thermal denaturation parameters of two-state proteins protein N c c T/TF T/TF
TABLE I. Chemical denaturation parameters of two-state proteins protein N C/Cm (C/Cm)
Infinitely robust order and local order-parameter tulips in Apollonian networks with quenched disorder
Multicritical point relations in three dual pairs of hierarchical-lattice Ising spin glasses Michael Hinczewski and A. Nihat Berker
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Effects of pH on Proteins: Predictions for Ensemble and Single-Molecule Pulling Experiments
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