Thermodynamics
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subject area of
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pubid_109424 Journal Article
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pubid_109425 Journal Article
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pubid_121008 Journal Article
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pubid_129862 Journal Article
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pubid_149308 Journal Article
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pubid_66859 Journal Article
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A New Analysis of Mars "Special Regions": Findings of the Second MEPAG Special Regions Science Analysis Group (SR-SAG2) Journal Article
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A POSITIVE ENTROPY CHANGE FOR GUANOSINE BINDING AND FOR THE CHEMICAL STEP IN THE TETRAHYMENA RIBOZYME REACTION Journal Article
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A comparison of ether- and alkyl-derivatized imidazolium-based room-temperature ionic liquids: a molecular dynamics simulation study Journal Article
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A coupled equilibrium approach to study nucleosome thermodynamics. Journal Article
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A motor that makes its own track: Helicase unwinding of DNA Journal Article
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A moving story Journal Article
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A mutation in the beta-myosin rod associated with hypertrophic cardiomyopathy has an unexpected molecular phenotype Journal Article
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A new look at the microtubule binding patterns of dimeric kinesins Journal Article
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A supramolecular hydrogel prepared from a thymine-containing artificial nucleolipid: study of assembly and lyotropic mesophases Journal Article
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A thermodynamic model for Nap1-histone interactions. Journal Article
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A universal mode of helix packing in RNA Journal Article
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Accurate and efficient corrections for missing dispersion interactions in molecular Simulations Journal Article
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Activation Thermodynamics and H/D Kinetic Isotope Effect of the H-ox to HredH+ Transition in [FeFe] Hydrogenase Journal Article
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Advances in fluorescence labeling strategies for dynamic cellular imaging Journal Article
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Aggregation of granulocyte colony stimulating factor under physiological conditions: Characterization and thermodynamic inhibition Journal Article
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An early transition state for folding of the P4-P6 RNA domain Journal Article
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An introduction to best practices in free energy calculations. Journal Article
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Anomalous heat conduction and anomalous diffusion in nonlinear lattices, single walled nanotubes, and billiard gas channels Journal Article
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Apparent Activation Energies Associated with Protein Dynamics on Hydrophobic and Hydrophilic Surfaces Journal Article
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Application of a thermodynamic model to the prediction of phase separations in freeze-concentrated formulations for protein lyophilization Journal Article
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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Journal Article
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B-12 cofactors directly stabilize an mRNA regulatory switch Journal Article
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Best practices in free energy calculations for drug design. Journal Article
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Biochemical and physicochemical properties of phosphorodithioate DNA Journal Article
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Biological potential of martian hydrothermal systems Journal Article
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Biophysically Defined and Cytocompatible Covalently Adaptable Networks as Viscoelastic 3D Cell Culture Systems Journal Article
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Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge Journal Article
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CALCIUM(II) SITE SPECIFICITY - EFFECT OF SIZE AND CHARGE ON METAL-ION BINDING TO AN EF-HAND-LIKE SITE Journal Article
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CATALYSIS OF RNA CLEAVAGE BY A RIBOZYME DERIVED FROM THE GROUP-I INTRON OF ANABAENA PRE-TRNA(LEU) Journal Article
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CONTRIBUTIONS OF 2'-HYDROXYL GROUPS OF THE RNA SUBSTRATE TO BINDING AND CATALYSIS BY THE TETRAHYMENA RIBOZYME - AN ENERGETIC PICTURE OF AN ACTIVE-SITE COMPOSED OF RNA Journal Article
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CUUCGG HAIRPINS - EXTRAORDINARILY STABLE RNA SECONDARY STRUCTURES ASSOCIATED WITH VARIOUS BIOCHEMICAL PROCESSES Journal Article
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Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution Journal Article
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Calorimetric Measurement of SH2 Domain Ligand Affinities. Journal Article
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Characterization of protein-protein interactions critical for poliovirus replication: Analysis of 3AB and VPg binding to the RNA-dependent RNA polymerase Journal Article
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Charge Transfer Dynamics between Photoexcited CdS Nanorods and Mononuclear Ru Water-Oxidation Catalysts Journal Article
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Chloroplast thylakoid structure in evergreen leaves employing strong thermal energy dissipation Journal Article
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Collapsing bacterial cylinders Journal Article
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Comparative Hydrogen-Deuterium Exchange for a Mesophilic vs Thermophilic Dihydrofolate Reductase at 25 degrees C: Identification of a Single Active Site Region with Enhanced Flexibility in the Mesophilic Protein Journal Article
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Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials Journal Article
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Comparison of crystal structure interactions and thermodynamics for stabilizing mutations in the Tetrahymena ribozyme Journal Article
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Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. Journal Article
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Computational exploration of heterolytic halogen-carbon bond scission photoreactions in ruthenium polypyridyl complexes. Journal Article
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Configurational Preferences of Arylamide alpha-Helix Mimetics via Alchemical Free Energy Calculations of Relative Binding Affinities Journal Article
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Congo red populates partially unfolded states of an amyloidogenic protein to enhance aggregation and amyloid fibril formation Journal Article
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Connecting Protein Conformation and Dynamics with Ligand-Receptor Binding Using Three-Color Forster Resonance Energy Transfer Tracking Journal Article
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Conserved thermochemistry of guanosine nucleophile binding for structurally distinct group I ribozymes Journal Article
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Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. Journal Article
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Cooperative binding of single-stranded telomeric DNA by the Pot1 protein of Schizosaccharomyces pombe Journal Article
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Counteracting effects of renal solutes on amyloid fibril formation by immunoglobulin light chains Journal Article
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Cryogenic Ion Spectroscopy of the Green Fluorescent Protein Chromophore in Vacuo Journal Article
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Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. Journal Article
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De novo designed peptide-based amyloid fibrils Journal Article
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Deciphering the mechanism of thermodynamic accommodation of telomeric oligonucleotide sequences by the Schizosaccharomyces pombe protection of telomeres 1 (Pot1pN) protein Journal Article
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Direct calculation of the binding free energies of FKBP ligands. Journal Article
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Diversity in peptide recognition by the SH2 domain of SH2B1 Journal Article
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Dynamics of Protein Kinases: Insights from Nuclear Magnetic Resonance Journal Article
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EFFECT OF MONOVALENT CATION-INDUCED TELOMERIC DNA-STRUCTURE ON THE BINDING OF OXYTRICHA TELOMERIC PROTEIN Journal Article
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EFFICIENT PROTEIN-FACILITATED SPLICING OF THE YEAST MITOCHONDRIAL BI5 INTRON Journal Article
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Effects of phase separating systems on lyophilized hemoglobin Journal Article
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Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15 Journal Article
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Effects of sucrose on conformational equilibria and fluctuations within the native-state ensemble of proteins Journal Article
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End-to-end stacking and liquid crystal condensation of 6-to 20-base pair DNA duplexes Journal Article
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Energetics and affinity of the histone octamer for defined DNA sequences. Journal Article
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Energetics and cooperativity of tertiary hydrogen bonds in RNA structure Journal Article
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Entrapping intermediates of thermal aggregation in alpha-helical proteins with low concentration of guanidine hydrochloride Journal Article
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Evaluation of Solid Fuel Char Briquettes from Human Waste Journal Article
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Evidence for increased local flexibility in psychrophilic alcohol dehydrogenase relative to its thermophilic homologue Journal Article
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Exocyclic amine of the conserved G center dot U pair at the cleavage site of the Tetrahymena ribozyme contributes to 5'-splice site selection and transition state stabilization Journal Article
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Exploiting conformational dynamics to facilitate formation and trapping of electron-transfer photoproducts in metal complexes. Journal Article
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Extreme Dynamics in the BamA beta-Barrel Seam Journal Article
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FEATHER: Automated Analysis of Force Spectroscopy Unbinding and Unfolding Data via a Bayesian Algorithm Journal Article
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FREE-ENERGY CONTRIBUTIONS OF G.U AND OTHER TERMINAL MISMATCHES TO HELIX STABILITY Journal Article
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Formation of Mercury Sulfide from Hg(II)-Thiolate Complexes in Natural Organic Matter Journal Article
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From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica Journal Article
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GUANOSINE BINDING TO THE TETRAHYMENA RIBOZYME - THERMODYNAMIC COUPLING WITH OLIGONUCLEOTIDE BINDING Journal Article
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Gas-phase carbene radical anions: New mechanistic insights Journal Article
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Gas-phase water-mediated equilibrium between methylglyoxal and its geminal diol Journal Article
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Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy Journal Article
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Graphene Blisters with Switchable Shapes Controlled by Pressure and Adhesion Journal Article
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Ground-State Thermodynamics of Bistable Redox-Active Donor-Acceptor Mechanically Interlocked Molecules Journal Article
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Hammerhead cleavage of the phosphorodithioate linkage Journal Article
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Heat current limiter and constant heat current source Journal Article
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High concentration formulations of recombinant human interleukin-1 receptor antagonist: II. Aggregation kinetics Journal Article
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High pressure refolding of recombinant human growth hormone from insoluble aggregates - Structural transformations, kinetic barriers, and energetics Journal Article
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High-pressure refolding of bikunin: Efficacy and thermodynamics Journal Article
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High-pressure refolding of disulfide-cross-linked lysozyme aggregates: Thermodynamics and optimization Journal Article
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High-pressure studies of aggregation of recombinant human interleukin-1 receptor antagonist: Thermodynamics, kinetics, and application to accelerated formulation studies Journal Article
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Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments. Journal Article
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Homochirality and the Need for Energy Journal Article
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IMPROVED FREE-ENERGY PARAMETERS FOR PREDICTIONS OF RNA DUPLEX STABILITY Journal Article
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Identification of the determinants for the specific recognition of single-strand telomeric DNA by Cdc13 Journal Article
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Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. Journal Article
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Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction Journal Article
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Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy Journal Article
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Influence of hydrostatic pressure and cosolutes on RNA tertiary structure Journal Article
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Insights into the Dynamics of Specific Telomeric Single-Stranded DNA Recognition by Pot1pN Journal Article
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Interactions between Hofmeister Anions and the Binding Pocket of a Protein Journal Article
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Intermolecular Forces Model for Lipid Microbubble Shells Journal Article
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Kinetics and energetics of assembly, nucleation, and growth of aggregates and fibrils for an amyloidogenic protein - Insights into transition states from pressure, temperature, and co-solute studies Journal Article
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Lattice study of the conformal window in QCD-like theories Journal Article
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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset Journal Article
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Ligand-dependent folding of the three-way junction in the purine riboswitch Journal Article
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Low-energy spectrum of iron-sulfur clusters directly from many-particle quantum mechanics Journal Article
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MECHANISM OF DNA-REPLICATION FIDELITY FOR 3 MUTANTS OF DNA-POLYMERASE-I - KLENOW FRAGMENT KF(EXO+), KF(POLA5), AND KF(EXO-) Journal Article
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MUTATIONS IN A NONCONSERVED SEQUENCE OF THE TETRAHYMENA RIBOZYME INCREASE ACTIVITY AND SPECIFICITY Journal Article
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Maintenance of quaternary structure in the frozen state stabilizes lactate dehydrogenase during freeze-drying Journal Article
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Mathematical model of the role of degradation on matrix development in hydrogel scaffold. Journal Article
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Mediating Electrostatic Binding of 1-Butyl-3-methylimidazolium Chloride to Enzyme Surfaces Improves Conformational Stability Journal Article
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Membrane orientation and position of the C2 domain from cPLA2 by site-directed spin labeling Journal Article
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Minimum Energy Path to Membrane Pore Formation and Rupture Journal Article
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Mixing Properties of Lyophilized Protein Systems: A Spectroscopic and Calorimetric Study Journal Article
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Molecular Thermometry Journal Article
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Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude. Journal Article
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Mutational analysis of the purine riboswitch aptamer domain Journal Article
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Mutations at the same amino acid in myosin that cause either skeletal or cardiac myopathy have distinct molecular phenotypes Journal Article
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Negative-ion photoelectron spectroscopy, gas-phase acidity, and thermochemistry of the peroxyl radicals CH3OO and CH3CH2OO Journal Article
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Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding. Journal Article
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Ocean-Atmosphere Interactions in the Emergence of Complexity in Simple Chemical Systems Journal Article
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On the role of hydrogel structure and degradation in controlling the transport of cell-secreted matrix molecules for engineered cartilage Journal Article
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Organic aerosols and the origin of life: An hypothesis Journal Article
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Overview of the SAMPL5 host-guest challenge: Are we doing better? Journal Article
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Oxidation of methionine residues in recombinant human interleukin-1 receptor antagonist: Implications of conformational stability on protein oxidation kinetics Journal Article
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PLEISTOCENE GEOCHRONOLOGY AND PALAEOTHERMOMETRY FROM PROTEIN DIAGENESIS IN OSTRICH EGGSHELLS - IMPLICATIONS FOR THE EVOLUTION OF MODERN HUMANS Journal Article
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POLYMER-SUPPORTED RNA-SYNTHESIS AND ITS APPLICATION TO TEST THE NEAREST-NEIGHBOR MODEL FOR DUPLEX STABILITY Journal Article
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Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. Journal Article
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Partial molar volume, surface area, and hydration changes for equilibrium unfolding and formation of aggregation transition state: High-pressure and cosolute studies on recombinant human IFN-gamma Journal Article
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Photoelectron Spectroscopy and Thermochemistry of the Peroxyformate Anion Journal Article
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Photoelectron spectroscopy of isolated multiply negatively charged oligonucleotides Journal Article
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Preferential exclusion of sucrose from recombinant interleukin-1 receptor antagonist: Role in restricted conformational mobility and compaction of native state Journal Article
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Probing Hydrophobic Interactions Using Trajectories of Amphiphilic Molecules at a Hydrophobic/Water Interface Journal Article
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Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods. Journal Article
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Product binding varies dramatically between processive and nonprocessive cellulase enzymes. Journal Article
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Protein-solute interactions affect the outcome of ultrafiltration/diafiltration operations Journal Article
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QUANTITATING AND ENGINEERING THE ION SPECIFICITY OF AN EF-HAND-LIKE CA2+ BINDING-SITE Journal Article
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Quantifying chromatin-associated interactions: the HI-FI system. Journal Article
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Quantifying the energetic interplay of RNA tertiary and secondary structure interactions Journal Article
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Quantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping Journal Article
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RIBOZYME-CATALYZED AND NONENZYMATIC REACTIONS OF PHOSPHATE DIESTERS - RATE EFFECTS UPON SUBSTITUTION OF SULFUR FOR A NONBRIDGING PHOSPHORYL OXYGEN ATOM Journal Article
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RNA SUBSTRATE BINDING-SITE IN THE CATALYTIC CORE OF THE TETRAHYMENA RIBOZYME Journal Article
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Rapid and simple protein-stability screens: application to membrane proteins Journal Article
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Reconstituting Intracellular Vesicle Fusion Reactions: The Essential Role of Macromolecular Crowding Journal Article
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Refolding of Proteins From Inclusion Bodies Is Favored by a Diminished Hydrophobic Effect at Elevated Pressures Journal Article
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Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. Journal Article
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Role of the loop containing residue 115 in the induced-fit mechanism of the bacterial cell wall biosynthetic enzyme MurA Journal Article
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Roles of conformational stability and colloidal stability in the aggregation of recombinant human granulocyte colony-stimulating factor Journal Article
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SELF-SPLICING RNA - IMPLICATIONS FOR EVOLUTION Journal Article
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STABILITY OF XGCGCP, GCGCYP, AND XGCGCYP HELIXES - AN EMPIRICAL ESTIMATE OF THE ENERGETICS OF HYDROGEN-BONDS IN NUCLEIC-ACIDS Journal Article
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Schools of skyrmions with electrically tunable elastic interactions Journal Article
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Search for Flavor-Changing Neutral Currents in Top-Quark Decays t -> Zq in pp Collisions at root s=8 TeV Journal Article
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Self-Organized Gels in DNA/F-Actin Mixtures without Crosslinkers: Networks of Induced Nematic Domains with Tunable Density Journal Article
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Self-organization in leaky threshold systems: The influence of near-mean field dynamics and its implications for earthquakes, neurobiology, and forecasting Journal Article
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Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides. Journal Article
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Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal Article
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Single polymer dynamics in an elongational flow Journal Article
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Single-Molecule Conformational Dynamics of a Biologically Functional Hydroxocobalamin Riboswitch Journal Article
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Single-Molecule Tracking of Polymer Surface Diffusion Journal Article
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Site-Specific Patterning of Highly Ordered Nanocrystal Super lattices through Biomolecular Surface Confinement Journal Article
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Site-directed mutagenesis reveals the thermodynamic requirements for single-stranded DNA recognition by the telomere-binding protein Cdc13 Journal Article
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Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. Journal Article
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Specific volume and adiabatic compressibility measurements of native and aggregated recombinant human interleukin-1 receptor antagonist: Density differences enable pressure-modulated refolding Journal Article
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Spectroscopy and Photochemistry of Sodium Chromate Ester Cluster Ions Journal Article
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Stability of p53 Homologs Journal Article
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Stability, surface features, and atom leaching of palladium nanoparticles: toward prediction of catalytic functionality Journal Article
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Stable ordering in Langmuir-Blodgett films Journal Article
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Statistically optimal analysis of samples from multiple equilibrium states. Journal Article
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Structural and biophysical studies of human PARP-1 in complex with damaged DNA. Journal Article
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Structure and mechanism of purine-binding riboswitches Journal Article
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Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine Journal Article
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Structure-guided Mutational Analysis of Gene Regulation by the Bacillus subtilis pbuE Adenine-responsive Riboswitch in a Cellular Context Journal Article
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Submicrosecond Time Resolution Atomic Force Microscopy for Probing Nanoscale Dynamics Journal Article
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Suppression of eukaryotic translation termination by selected RNAs Journal Article
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Surfactant-induced unfolding of cellulase: Kinetic studies Journal Article
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Synthetic oligorotaxanes exert high forces when folding under mechanical load Journal Article
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TERTIARY INTERACTIONS WITH THE INTERNAL GUIDE SEQUENCE MEDIATE DOCKING OF THE P1 HELIX INTO THE CATALYTIC CORE OF THE TETRAHYMENA RIBOZYME Journal Article
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TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability Journal Article
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THE 2,6-DIAMINOPURINE RIBOSIDE-CENTER-DOT-5-METHYLISOCYTIDINE WOBBLE BASE-PAIR - AN ISOENERGETIC SUBSTITUTION FOR THE STUDY OF G-CENTER-DOT-U PAIRS IN RNA Journal Article
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THE IMPORTANCE OF BEING RIBOSE AT THE CLEAVAGE SITE IN THE TETRAHYMENA RIBOZYME REACTION Journal Article
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Temperature Dependence of the Reaction between the Hydroxyl Radical and Organic Matter Journal Article
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Temperature dependence of benzyl alcohol- and 8-anilinonaphthalene-1-sulfonate-induced aggregation of recombinant human interleukin-1 receptor antagonist Journal Article
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Temperature dependence of protein motions in a thermophilic dihydrofolate reductase and its relationship to catalytic efficiency Journal Article
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The Energetic Difference between Synthesis of Correct and Incorrect Base Pairs Accounts for Highly Accurate DNA Replication Journal Article
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The Formation of CO by Thermal Decomposition of Formic Acid under Electrochemical Conditions of CO2 Reduction Journal Article
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The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition Journal Article
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The Structure of a Tetrahydrofolate-Sensing Riboswitch Reveals Two Ligand Binding Sites in a Single Aptamer Journal Article
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The Tetrahymena ribozyme cleaves a 5 '-methylene phosphonate monoester similar to 10(2)-fold faster than a normal phosphate diester: Implications for enzyme catalysis of phosphoryl transfer reactions Journal Article
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The Trouble with Chemical Energy: Why Understanding Bond Energies Requires an Interdisciplinary Systems Approach Journal Article
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The application of statistical physics to evolutionary biology Journal Article
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The energetics of organic synthesis inside and outside the cell Journal Article
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The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Journal Article
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The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions. Journal Article
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The kinetic cycle of cardiac troponin C: Calcium binding and dissociation at site II trigger slow conformational rearrangements Journal Article
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The origin of the RNA world: Co-evolution of genes and metabolism Journal Article
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The sequence at specific positions in the early transcribed region sets the rate of transcript synthesis by RNA polymerase II in vitro Journal Article
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Thermodynamic Underpinnings of Cell Alignment on Controlled Topographies Journal Article
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Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain Journal Article
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Thermodynamic modulation of light chain amyloid fibril formation Journal Article
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Thermodynamic stability of small-world oscillator networks: A case study of proteins Journal Article
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Thermodynamic stability of the P4-P6 domain RNA tertiary structure measured by temperature gradient gel electrophoresis Journal Article
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Thermodynamic stability of wild-type and mutant p53 core domain. Journal Article
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Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field Journal Article
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Thermodynamics of Coupled Protein Adsorption and Stability Using Hybrid Monte Carlo Simulations Journal Article
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Toward Understanding Amino Acid Adsorption at Metallic Interfaces: A Density Functional Theory Study Journal Article
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Tuning the equilibrium ion affinity and selectivity of the EF-hand calcium binding motif: Substitutions at the gateway position Journal Article
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Two-state model for helicase translocation and unwinding of nucleic acids Journal Article
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Understanding the origin of liquid crystal ordering of ultrashort double-stranded DNA Journal Article
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Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase Journal Article
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Yeast CAF-1 assembles histone (H3-H4)2 tetramers prior to DNA deposition. Journal Article
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