Models, Chemical

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  Subject Areas on Research

  • 'Seeing' Strain in Soft Materials. 
  • A Monte Carlo model reveals independent signaling at central glutamatergic synapses. 
  • A combined explicit-implicit method for high accuracy reaction path integration. 
  • A crystal clear view of the beta2-adrenergic receptor. 
  • A crystal structure of a dimer of the antibiotic ramoplanin illustrates membrane positioning and a potential Lipid II docking interface. 
  • A mathematical model of the folate cycle: new insights into folate homeostasis. 
  • A mathematical model of tumor oxygen and glucose mass transport and metabolism with complex reaction kinetics. 
  • A mechanistic study of evolvability using the mitogen-activated protein kinase cascade. 
  • A mechano-chemical model for the passive swelling response of an isolated chondron under osmotic loading. 
  • A molecular basis for inositol polyphosphate synthesis in Drosophila melanogaster. 
  • A mutation-induced activated state of the beta 2-adrenergic receptor. Extending the ternary complex model. 
  • A perspective for understanding the modes of juvenile hormone action as a lipid signaling system. 
  • A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data 
  • A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes. 
  • A rapid fluorescence assay for FtsZ assembly indicates cooperative assembly with a dimer nucleus. 
  • A reappraisal of the concept of an abnormality of glutamine metabolism in primary gout. 
  • A robust framework to predict mercury speciation in combustion flue gases. 
  • A simple route towards CuO nanowires and nanorods. 
  • A stable dimer in the pH-induced equilibrium unfolding of the homo-hexameric enzyme 4-oxalocrotonate tautomerase (4-OT). 
  • A statistical thermodynamic model of the protein ensemble. 
  • AFLOW-CHULL: Cloud-Oriented Platform for Autonomous Phase Stability Analysis. 
  • Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach. 
  • Accelerated deamination of cytosine residues in UV-induced cyclobutane pyrimidine dimers leads to CC-->TT transitions. 
  • Activation of human plasminogen by urokinase. Partial characterization of a pre-activation peptide. 
  • Active-site heterogeneity in Limulus hemocyanin as revealed by reaction with peroxides. 
  • Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes. 
  • Addressing biological uncertainties in engineering gene circuits. 
  • Adsorption of clofibric acid and ketoprofen onto powdered activated carbon: effect of natural organic matter. 
  • Affinity of (alpha-P-borano)-NTP analogs to rabbit muscle pyruvate kinase. 
  • Alternative explanation for the apparent "two-step" binding kinetics of high-affinity racemic antagonist radioligands. 
  • An algebraic geometry approach to protein structure determination from NMR data 
  • An assessment of the effects of shell cross-linked nanoparticle size, core composition, and surface PEGylation on in vivo biodistribution. 
  • An efficient and accurate algorithm for assigning nuclear overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings 
  • An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. 
  • An equilibrium binding study of the interaction of aspartate transcarbamylase with cytidine 5'-triphosphate and adenosine 5'-triphosphate. 
  • An infrared spectroscopic study of the conformational transition of elastin-like polypeptides. 
  • An unbiased evaluation of CK2 inhibitors by chemoproteomics: characterization of inhibitor effects on CK2 and identification of novel inhibitor targets. 
  • Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimum number of residual dipolar couplings 
  • Analysis of medaka cytochrome P450 3A homotropic and heterotropic cooperativity. 
  • Analytical Debye-Huckel model for electrostatic potentials around dissolved DNA. 
  • Analyzing site selectivity in Rh2(esp)2-catalyzed intermolecular C-H amination reactions. 
  • Anti-AIDS agents--XXVII. Synthesis and anti-HIV activity of betulinic acid and dihydrobetulinic acid derivatives. 
  • Antibody-antigen binding kinetics. A model for multivalency antibodies for large antigen systems. 
  • Application of the finite difference method to model pH and substrate concentration in a double-chamber microbial fuel cell. 
  • Architecture of Limulus polyphemus hemocyanin. 
  • Assembly dynamics of Mycobacterium tuberculosis FtsZ. 
  • Assessment of the number of nucleotide binding sites on chloroplast coupling factor 1 by the continuous variation method. 
  • Assignment of the absolute configuration of [n]-ladderanes by TD-DFT optical rotation calculations. 
  • Atomic contributions to the optical rotation angle as a quantitative probe of molecular chirality. 
  • Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods. 
  • Basophile: accurate fragment charge state prediction improves peptide identification rates. 
  • Beyond diffusion-limited aggregation kinetics in microparticle suspensions. 
  • Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. 
  • Biochemistry. Photosynthesis from the protein's perspective. 
  • Biological charge transfer via flickering resonance. 
  • CYP7B1: one cytochrome P450, two human genetic diseases, and multiple physiological functions. 
  • Cadmium is a potent inhibitor of PPM phosphatases and targets the M1 binding site. 
  • Calcineurin. Structure, function, and inhibition. 
  • Calmodulin binds to caldesmon in an antiparallel manner. 
  • Calorimetric determination of the standard transformed enthalpy of a biochemical reaction at specified pH and pMg. 
  • Can regular solution theory be applied to lipid bilayer membranes? 
  • Cardiac transient outward potassium current: a pulse chemistry model of frequency-dependent properties. 
  • Cellular mechanisms of cyclophosphamide resistance: model studies in human medulloblastoma cell lines. 
  • Cellular mechanisms regulating protein phosphatase-1. A key functional interaction between inhibitor-2 and the type 1 protein phosphatase catalytic subunit. 
  • Characterization of Fe(III) sequestration by an analog of the cytotoxic siderophore brasilibactin A: implications for the iron transport mechanism in mycobacteria. 
  • Characterization of a slow folding reaction for the alpha subunit of tryptophan synthase. 
  • Characterization of nucleotide binding sites on chloroplast coupling factor 1. 
  • Characterization of the cytotoxic activities of novel analogues of the antitumor agent, lavendamycin. 
  • Characterizing the peroxisome proliferator-activated receptor (PPARγ) ligand binding potential of several major flame retardants, their metabolites, and chemical mixtures in house dust. 
  • Charged fullerenes as high-capacity hydrogen storage media. 
  • Chemical characterization of a protein-4-hydroxy-2-nonenal cross-link: immunochemical detection in mitochondria exposed to oxidative stress. 
  • Chemical evolutionary games. 
  • Chemical stability of metallic nanoparticles: a parameter controlling their potential cellular toxicity in vitro. 
  • Chiral control of electron transmission through molecules. 
  • Cloretazine (VNP40101M), a novel sulfonylhydrazine alkylating agent, in patients age 60 years or older with previously untreated acute myeloid leukemia. 
  • Co-operativity in protein-protein association. The structure and stability of the actin filament. 
  • Coefficient of restitution for wet particles. 
  • Colloid osmotic pressure of steer alpha- and beta-crystallins: possible functional roles for lens crystallin distribution and structural diversity. 
  • Communication: An exact short-time solver for the time-dependent Schrödinger equation. 
  • Comparative proteomic analysis of differentially expressed proteins in β-aminobutyric acid enhanced Arabidopsis thaliana tolerance to simulated acid rain. 
  • Comparative quantitative trait loci mapping of aliphatic, indolic and benzylic glucosinolate production in Arabidopsis thaliana leaves and seeds. 
  • Comparison of manufactured and black carbon nanoparticle concentrations in aquatic sediments. 
  • Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity. 
  • Computational studies of small carbon and iron-carbon systems relevant to carbon nanotube growth. 
  • Concerted O atom-proton transfer in the O-O bond forming step in water oxidation. 
  • Conformation of xylocholine. 
  • Conformation-assisted inhibition of protein-tyrosine phosphatase-1B elicits inhibitor selectivity over T-cell protein-tyrosine phosphatase. 
  • Conformational mechanics, adsorption, and normal force interactions of lubricin and hyaluronic acid on model surfaces. 
  • Conformational selection or induced fit: a flux description of reaction mechanism. 
  • Constitutive activity of receptors coupled to guanine nucleotide regulatory proteins. 
  • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. 
  • Control of electrical alternans in simulations of paced myocardium using extended time-delay autosynchronization. 
  • Control of electron transfer in nitrogenase. 
  • Coupling coherence distinguishes structure sensitivity in protein electron transfer. 
  • Critical redox and allosteric aspects of nitric oxide interactions with hemoglobin. 
  • Crustacean peptide and peptide-like pheromones and kairomones. 
  • Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. 
  • Cryo-EM structure of a mitochondrial calcium uniporter. 
  • Crystal structure of the human LRH-1 DBD-DNA complex reveals Ftz-F1 domain positioning is required for receptor activity. 
  • De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. 
  • Dead-end elimination with backbone flexibility. 
  • Design of a ruthenium-labeled cytochrome c derivative to study electron transfer with the cytochrome bc1 complex. 
  • Design of potent thiophene inhibitors of polo-like kinase 1 with improved solubility and reduced protein binding. 
  • Detection of vesicoureteral reflux using microwave radiometry-system characterization with tissue phantoms. 
  • Development of DX-9065a, a novel direct factor Xa antagonist, in cardiovascular disease. 
  • Development of a 3-body:many-body integrated fragmentation method for weakly bound clusters and application to water clusters (H2O)(n = 3-10, 16, 17). 
  • Dimensional study of the caging order parameter at the glass transition. 
  • Direct and cost-efficient hyperpolarization of long-lived nuclear spin states on universal (15)N2-diazirine molecular tags. 
  • Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli. 
  • Discovery and optimization of imidazo[1,2-a]pyridine inhibitors of insulin-like growth factor-1 receptor (IGF-1R). 
  • Discovery of thiophene inhibitors of polo-like kinase. 
  • Disentangling oil weathering using GC x GC. 2. Mass transfer calculations. 
  • Dissociation of nitric oxide from soluble guanylate cyclase and heme-nitric oxide/oxygen binding domain constructs. 
  • Dissociation rate constants of human fibronectin binding to fibronectin-binding proteins on living Staphylococcus aureus isolated from clinical patients. 
  • Distribution of reaction intermediates on chicken liver fatty acid synthase. 
  • Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA. 
  • Downhill kinetics of biomolecular interface binding: globally connected scenario. 
  • Dual-topology/dual-coordinate free-energy simulation using QM/MM force field. 
  • Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes. 
  • Dynamic infrared linear dichroism study of the temperature-dependent, viscoelastic behavior of a poly(ester urethane). 
  • Effect of chain length and unsaturation on elasticity of lipid bilayers. 
  • Effect of fluid shear stress on the permeability of the arterial endothelium. 
  • Effects of humic acid and electrolytes on photocatalytic reactivity and transport of carbon nanoparticle aggregates in water. 
  • Efficiency, selectivity, and robustness of nucleocytoplasmic transport. 
  • Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo. 
  • Elastic response, buckling, and instability of microtubules under radial indentation. 
  • Elasticity, strength, and water permeability of bilayers that contain raft microdomain-forming lipids. 
  • Elastin-like polypeptides as models of intrinsically disordered proteins. 
  • Electrochemical biosensor of nanocube-augmented carbon nanotube networks. 
  • Electrostatic contribution in the catalysis of O2*- dismutation by superoxide dismutase mimics. MnIIITE-2-PyP5+ versus MnIIIBr8T-2-PyP+. 
  • Elementary steps in the reaction mechanism of the alpha-ketoglutarate dehydrogenase multienzyme complex from Escherichia coli: kinetics of succinylation and desuccinylation. 
  • Energy levels in chlorophyll and electron transfer processes. 
  • Enhanced protein flexibility caused by a destabilizing amino acid replacement in BPTI. 
  • Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. 
  • Evaluation of hyperbranched poly(amino ester)s of amine constitutions similar to polyethylenimine for DNA delivery. 
  • Experimental evidence for the secondary structure of the hepatitis delta virus ribozyme. 
  • Exploration of in vitro pro-drug activation and futile cycling by glutathione S-transferases: thiol ester hydrolysis and inhibitor maturation. 
  • Exploring chemical space with discrete, gradient, and hybrid optimization methods. 
  • Expression cloning of three Rhizobium leguminosarum lipopolysaccharide core galacturonosyltransferases. 
  • False-positive rate determination of protein target discovery using a covalent modification- and mass spectrometry-based proteomics platform. 
  • Fast acquisition of high resolution 4-D amide-amide NOESY with diagonal suppression, sparse sampling and FFT-CLEAN. 
  • Fast molecular shape matching using contact maps. 
  • Fe(III) coordination properties of a new saccharide-based exocyclic trihydroxamate analogue of ferrichrome. 
  • Fe3+ coordination and redox properties of a bacterial transferrin. 
  • Flexible histone tails in a new mesoscopic oligonucleosome model. 
  • Flory theorem for structurally asymmetric mixtures. 
  • Fluorescence energy transfer between ligand binding sites on chloroplast coupling factor 1. 
  • Folding mechanism of a multiple independently-folding domain protein: double B domain of protein A. 
  • Force measurements of the alpha5beta1 integrin-fibronectin interaction. 
  • Four new adenosine deaminase mutations, altering a zinc-binding histidine, two conserved alanines, and a 5' splice site. 
  • Fractal structures of single-walled carbon nanotubes in biologically relevant conditions: role of chirality vs. media conditions. 
  • Fragility and mechanosensing in a thermalized cytoskeleton model with forced protein unfolding. 
  • Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. 
  • Full-electron calculation of effective electronic couplings and excitation energies of charge transfer states: Application to hole transfer in DNA pi-stacks. 
  • Full-electron ligand-to-ligand charge transfer in a compact Re(I) complex. 
  • Functional roles of the two domains of phosducin and phosducin-like protein. 
  • GAVA: spectral simulation for in vivo MRS applications. 
  • Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis. 
  • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. 
  • Generation of impossible cross-peaks between bulk water and biomolecules in solution NMR. 
  • Geometric phase shifts in chemical oscillators. 
  • Gold(I)-catalyzed dynamic kinetic enantioselective intramolecular hydroamination of allenes. 
  • Gold(I)-catalyzed intramolecular hydroamination of unactivated C==C bonds with alkyl ammonium salts. 
  • Growth of cationic lipid toward bilayer lipid membrane by solution spreading: scanning probe microscopy study. 
  • Hard-sphere crystallization gets rarer with increasing dimension. 
  • Harnessing localized ridges for high-aspect-ratio hierarchical patterns with dynamic tunability and multifunctionality. 
  • High-throughput 3D structural homology detection via NMR resonance assignment 
  • High-throughput screen for inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase by surrogate ligand competition. 
  • Highly parallel acoustic assembly of microparticles into well-ordered colloidal crystallites. 
  • How does protein architecture facilitate the transduction of ATP chemical-bond energy into mechanical work? The cases of nitrogenase and ATP binding-cassette proteins. 
  • How many numbers are required to specify sequence-dependent properties of polynucleotides? 
  • Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides. 
  • Hydration potential of lysozyme: protein dehydration using a single microparticle technique. 
  • Hydrocarbon emissions and health risks from cookstoves in developing countries. 
  • Hydrophobic interactions increase attachment of gum Arabic- and PVP-coated Ag nanoparticles to hydrophobic surfaces. 
  • Hyperpolarized carbon-carbon intermolecular multiple quantum coherences. 
  • IMDA/aldol strategy for transforming carbohydrates into functionalized trans-decalins. 
  • Idealization and simulation of single ion channel data. 
  • Identification of 3-methylglutarylcarnitine. A new diagnostic metabolite of 3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency. 
  • Identification of a residue critical for maintaining the functional conformation of BPTI. 
  • Identification of key amino acids responsible for the substantially higher affinities of human type 1 3beta-hydroxysteroid dehydrogenase/isomerase (3beta-HSD1) for substrates, coenzymes, and inhibitors relative to human 3beta-HSD2. 
  • Imaging actomyosin in situ. 
  • Importance of heterogeneous aggregation for NP fate in natural and engineered systems. 
  • Improved pruning algorithms and divide-and-conquer strategies for Dead-End Elimination, with application to protein design 
  • In vitro characterization of vascular endothelial growth factor and dexamethasone releasing hydrogels for implantable probe coatings. 
  • Incorporation of non-proteolytic proteins by murine alpha2-macroglobulin. 
  • Incorporation of ribonucleoside 5'-(alpha-P-borano)triphosphates into a 20-mer RNA by T7 RNA polymerase. 
  • Influence of lipid composition on physical properties and peg-mediated fusion of curved and uncurved model membrane vesicles: "nature's own" fusogenic lipid bilayer. 
  • Information content of molecular structures. 
  • Informative priors based on transcription factor structural class improve de novo motif discovery. 
  • Inside-out Z rings--constriction with and without GTP hydrolysis. 
  • Integrated single-walled carbon nanotube/microfluidic devices for the study of the sensing mechanism of nanotube sensors. 
  • Integrating statistical pair potentials into protein complex prediction. 
  • Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein-protein interactions directly from DNA. 
  • Interaction sites of the C-terminal region of the cGMP phosphodiesterase inhibitory subunit with the GDP-bound transducin alpha-subunit. 
  • Inverse design of molecules with optimal reactivity properties: acidity of 2-naphthol derivatives. 
  • Ionophore 4-BrA23187 transports Zn2+ and Mn2+ with high selectivity over Ca2+. 
  • Is it better to combine predictions? 
  • Isolation and characterization of a prenylcysteine lyase from bovine brain. 
  • Kinetic scheme for intermolecular RNA cleavage by a ribozyme derived from hepatitis delta virus RNA. 
  • Kinetic study of collagen fixation with polyepoxy fixatives. 
  • Kinetics and mechanism of iron(III) complexation by ferric binding protein: the role of phosphate. 
  • Kinetics of iron release from ferric binding protein (FbpA): mechanistic implications in bacterial periplasm-to-cytosol Fe3+ transport. 
  • Kinetics of substrate hydrolysis and inhibition by mipafox of paraoxon-preinhibited hen brain esterase activity. 
  • Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol dehydratase in metabolosomes and metabolizes 1,2-propanediol by disproportionation. 
  • Leveraging single protein polymers to measure flexural rigidity. 
  • Linear shear in a model granular system. 
  • Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein. 
  • Log-rolling micelles in sheared amphiphilic thin films. 
  • Lysolipid incorporation in dipalmitoylphosphatidylcholine bilayer membranes enhances the ion permeability and drug release rates at the membrane phase transition. 
  • Lysosomal prenylcysteine lyase is a FAD-dependent thioether oxidase. 
  • Mapping bacterial glycolipid complexity using capillary electrophoresis and electrospray mass spectrometry. 
  • Mapping of a ligand-binding site for the human thromboxane A2 receptor protein. 
  • Markov state models based on milestoning 
  • Mathematical analysis of the regulation of competing methyltransferases. 
  • Measurements of secondary organic aerosol from oxidation of cycloalkenes, terpenes, and m-xylene using an Aerodyne aerosol mass spectrometer. 
  • Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force. 
  • Mechanics considerations for microporous titanium as an orthopedic implant material. 
  • Mechanics of electrocompression of lipid bilayer membranes. 
  • Mechanism for catalysis and regulation of adenosine 5'-triphosphate hydrolysis by chloroplast coupling factor 1. 
  • Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations. 
  • Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase. 
  • Mechanism of nicotinamide-adenine dinucleotide binding to rabbit muscle glyceraldehyde 3-phosphate dehydrogenase. 
  • Mechanistic analysis of the Saccharomyces cerevisiae kinesin Kar3. 
  • Mechanistic and mutational studies of Escherichia coli molybdopterin synthase clarify the final step of molybdopterin biosynthesis. 
  • Mechanochemistry: A tour of force. 
  • Metabolism of 3-methyldiphenyl ether by Sphingomonas sp. SS31. 
  • Metallic nanoparticle arrays: a common substrate for both surface-enhanced Raman scattering and surface-enhanced infrared absorption. 
  • Microdroplet dissolution into a second-phase solvent using a micropipet technique: test of the Epstein-Plesset model for an aniline-water system. 
  • Microscale diffusion properties of the cartilage pericellular matrix measured using 3D scanning microphotolysis. 
  • Microstructure evolution during impact on granular matter. 
  • Model synthesis of nucleoside boranophosphoramidate with amino acid for prodrug purpose. 
  • Modeling biological systems using Dynetica--a simulator of dynamic networks. 
  • Modeling the biochemical differences between rabbit muscle and human liver phosphorylase. 
  • Modulating unimolecular charge transfer by exciting bridge vibrations. 
  • Molecular definition of a novel inositol polyphosphate metabolic pathway initiated by inositol 1,4,5-trisphosphate 3-kinase activity in Saccharomyces cerevisiae. 
  • Molecular encapsulation. 
  • Molybdopterin synthase mutations in a mild case of molybdenum cofactor deficiency. 
  • Monte Carlo simulation and molecular theory of tethered polyelectrolytes. 
  • Monte Carlo simulations of the transformation and removal of Ag, TiO2, and ZnO nanoparticles in wastewater treatment and land application of biosolids. 
  • Monte-Carlo-based model for the extraction of intrinsic fluorescence from turbid media. 
  • Multiplex-PCR-based recombination as a novel high-fidelity method for directed evolution. 
  • Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel. 
  • Mutagenesis of the phosphate-binding pocket of KDPG aldolase enhances selectivity for hydrophobic substrates. 
  • Mutants resistant to LpxC inhibitors by rebalancing cellular homeostasis. 
  • Mutational analysis of potential zinc-binding residues in the active site of the enterococcal D-Ala-D-Ala dipeptidase VanX. 
  • NMR structures of biomolecules using field oriented media and residual dipolar couplings. 
  • New sensitive micro-measurements of dynamic surface tension and diffusion coefficients: Validated and tested for the adsorption of 1-Octanol at a microscopic air-water interface and its dissolution into water. 
  • Nitric oxide signaling: no longer simply on or off. 
  • Numerical simulations of ethacrynic acid transport from precorneal region to trabecular meshwork. 
  • Nutrient limitation and physiology mediate the fine-scale (de)coupling of biogeochemical cycles. 
  • Off-pathway aggregation can inhibit fibrillation at high protein concentrations. 
  • OligoCalc: an online oligonucleotide properties calculator. 
  • Optical signatures of molecular dissymmetry: combining theory with experiments to address stereochemical puzzles. 
  • Optically tunable nanoparticle contrast agents for early cancer detection: model-based analysis of gold nanoshells. 
  • Optimal specificity and function for flexible biomolecular recognition. 
  • Optimization of expression of human sulfite oxidase and its molybdenum domain. 
  • Optimizing the substrate specificity of a group I intron ribozyme. 
  • Order parameter fluctuations at a buried quantum critical point. 
  • Overcoming methodological weakness in dose-intense alkylating agent studies through pharmacology. 
  • Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. 
  • Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. 
  • Pathways of folding of reduced bovine pancreatic ribonuclease. 
  • Persistence of structure over fluctuations in biological electron-transfer reactions. 
  • Phonon self-energy and origin of anomalous neutron scattering spectra in SnTe and PbTe thermoelectrics. 
  • Phosphorylation and desensitization of human endothelin A and B receptors. Evidence for G protein-coupled receptor kinase specificity. 
  • Photochemical degradation of polycyclic aromatic hydrocarbons in oil films. 
  • Photocrosslinkable polyvinyl alcohol hydrogels that can be modified with cell adhesion peptides for use in tissue engineering. 
  • Photodegradation pathways of nonabrominated diphenyl ethers, 2-ethylhexyltetrabromobenzoate and di(2-ethylhexyl)tetrabromophthalate: identifying potential markers of photodegradation. 
  • Photodisintegration cross section of the reaction (4)He(γ,p)(3)H between 22 and 30 MeV. 
  • Photopolymerizable hydrogels for tissue engineering applications. 
  • Physical and economic potential of geological CO 2 storage in saline aquifers 
  • Planar wallpaper group metamaterials for novel terahertz applications. 
  • Poly(ethylene glycol) hydrogels conjugated with a collagenase-sensitive fluorogenic substrate to visualize collagenase activity during three-dimensional cell migration. 
  • Population pharmacokinetics of piperacillin using scavenged samples from preterm infants. 
  • Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations. 
  • Preclinical and clinical pharmacodynamic assessment of L-778,123, a dual inhibitor of farnesyl:protein transferase and geranylgeranyl:protein transferase type-I. 
  • Prediction of solvent-induced morphological changes of polyelectrolyte diblock copolymer micelles. 
  • Preparation and electron paramagnetic resonance characterization of spin labeled monoderivatives of horse cytochrome c. 
  • Pretreatment of amphiphilic comb polymer surfaces dramatically affects protein adsorption. 
  • Probabilistic Analysis of Localized DNA Hybridization Circuits. 
  • Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein. 
  • Probing the interplay between the two steps of group I intron splicing: competition of exogenous guanosine with omega G. 
  • Protein S-nitrosylation: purview and parameters. 
  • Protein construct storage: Bayesian variable selection and prediction with mixtures. 
  • Protein design and folding: template trapping of self-assembled helical bundles. 
  • Protein folding dynamics: quantitative comparison between theory and experiment. 
  • Protein interfacial pocket engineering via coupled computational filtering and biological focusing criterion. 
  • Protein nitration is mediated by heme and free metals through Fenton-type chemistry: an alternative to the NO/O2- reaction. 
  • Protein-resistant polymer coatings on silicon oxide by surface-initiated atom transfer radical polymerization. 
  • Proteomic analysis of arginine adducts on glyoxal-modified ribonuclease. 
  • Pulling geometry-induced errors in single molecule force spectroscopy measurements. 
  • Quadratic string method for determining the minimum-energy path based on multiobjective optimization. 
  • Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition. 
  • Quantitation of protein-protein interactions by thermal stability shift analysis. 
  • Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step. 
  • Rapid assignment of protein side chain resonances using projection-reconstruction of (4,3)D HC(CCO)NH and intra-HC(C)NH experiments. 
  • Rapid in vitro assembly dynamics and subunit turnover of FtsZ demonstrated by fluorescence resonance energy transfer. 
  • Rational protein design: combining theory and experiment. 
  • Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods. 
  • Reactions of manganese porphyrins with peroxynitrite and carbonate radical anion. 
  • Recent advances in synthetic transformations mediated by cerium(IV) ammonium nitrate. 
  • Recognition and processing of randomly fluctuating electric signals by Na,K-ATPase. 
  • Reconfigurable core-satellite nanoassemblies as molecularly-driven plasmonic switches. 
  • Redox signaling: nitrosylation and related target interactions of nitric oxide. 
  • Reducing mass degeneracy in SAR by MS by stable isotopic labeling 
  • Regulation of enzyme activity. The activity of enzymes can be controlled by a multiplicity of conformational equilibria. 
  • Regulation of the cyanide-resistant alternative oxidase of plant mitochondria. Identification of the cysteine residue involved in alpha-keto acid stimulation and intersubunit disulfide bond formation. 
  • Relating atrazine degradation rate in soil to environmental conditions: implications for global fate modeling. 
  • Relaxation spectra of adenosine triphosphate-creatine phosphotransferase. 
  • Relaxation spectra of aspartate transcarbamylase. Interaction of the native enzyme with aspartate analogs. 
  • Relaxation spectrometry of biological systems. 
  • Resonance Raman spectroscopic characterization of the molybdopterin active site of DMSO reductase. 
  • Revealing noncovalent interactions. 
  • Reversibly cross-linked surface-grafted polymer brushes. 
  • Ribose metabolism and nucleic acid synthesis in normal and glucose-6-phosphate dehydrogenase-deficient human erythrocytes infected with Plasmodium falciparum. 
  • Roles of bilayer material properties in function and distribution of membrane proteins. 
  • S-N dissociation energies of S-nitrosothiols: on the origins of nitrosothiol decomposition rates. 
  • Sampling of the NMR time domain along concentric rings. 
  • Scaling behavior of nanopatterned polymer brushes. 
  • Scaling method for fast Monte Carlo simulation of diffuse reflectance spectra from multilayered turbid media. 
  • Secure analysis of distributed chemical databases without data integration. 
  • Self-interaction-free exchange-correlation functional for thermochemistry and kinetics. 
  • Sequential quadratic programming method for determining the minimum energy path. 
  • Signal irreproducibility in high-field solution magnetic resonance experiments caused by spin turbulence. 
  • Simulation of electron transfer between cytochrome C2 and the bacterial photosynthetic reaction center: Brownian dynamics analysis of the native proteins and double mutants. 
  • Small-molecule dynamics and mechanisms underlying the macroscopic mechanical properties of coordinatively cross-linked polymer networks. 
  • Solvent effect on optical rotation: A case study of methyloxirane in water. 
  • Spatial modeling for groundwater arsenic levels in North Carolina. 
  • Spatially refined aerosol direct radiative forcing efficiencies. 
  • Spectroelectrochemistry of heme proteins: effects of active-site heterogeneity on Nernst plots. 
  • Sphingolipidomics: high-throughput, structure-specific, and quantitative analysis of sphingolipids by liquid chromatography tandem mass spectrometry. 
  • Squeezing flows of vaginal gel formulations relevant to microbicide drug delivery. 
  • Stability analysis for drugs with multiple active ingredients. 
  • Stability of metal-glutathione complexes during oxidation by hydrogen peroxide and Cu(II)-catalysis. 
  • Standard thermodynamic formation properties for the adenosine 5'-triphosphate series. 
  • Statistical analysis of RNA backbone. 
  • Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms. 
  • Statistical prediction and molecular dynamics simulation. 
  • Stereochemical course of nucleotidyl transfer catalyzed by bacteriophage T7 induced DNA polymerase. 
  • Strategy to discover diverse optimal molecules in the small molecule universe. 
  • Stress correlations in granular materials: an entropic formulation. 
  • Strong means slow: dynamic contributions to the bulk mechanical properties of supramolecular networks. 
  • Structural and dynamic analysis of residual dipolar coupling data for proteins. 
  • Structural and mechanical study of a self-assembling protein nanotube. 
  • Structural studies of molybdopterin synthase provide insights into its catalytic mechanism. 
  • Structure and dynamics of an extended conjugated NLO chromophore within an amphiphilic 4-helix bundle peptide by molecular dynamics simulation. 
  • Structure of the N-terminal domain of GRP94. Basis for ligand specificity and regulation. 
  • Structures of Cryptococcus neoformans protein farnesyltransferase reveal strategies for developing inhibitors that target fungal pathogens. 
  • Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ. 
  • Submillisecond folding of monomeric lambda repressor. 
  • Surface-stress-induced phase transformation in metal nanowires. 
  • Surfactant-assisted synthesis of Keggin-type polyoxometalates nanorods. 
  • SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics. 
  • Synthesis and biological evaluation of an 123I-labeled bicyclic nucleoside analogue (BCNA) as potential SPECT tracer for VZV-tk reporter gene imaging. 
  • Synthesis and evaluation of a phosphonate analogue of the soluble guanylate cyclase activator YC-1. 
  • Synthesis of 5-(1-propynyl)-2'-deoxyuridine 5'-(alpha-P-borano)triphosphate and kinetic characterization as a substrate for mmlv reverse transcriptase. 
  • Synthesis of 5-ethynyl-2'-deoxyuridine-5'-boranomono phosphate as a potential thymidylate synthase inhibitor. 
  • Synthetic and model computational studies of molar rotation additivity for interacting chiral centers: a reinvestigation of van't Hoff's principle. 
  • Synthetic biomimetic hydrogels incorporated with ephrin-A1 for therapeutic angiogenesis. 
  • Ternary complex formation facilitates a redox mechanism for iron release from a siderophore. 
  • Test of the Epstein-Plesset model for gas microparticle dissolution in aqueous media: effect of surface tension and gas undersaturation in solution. 
  • The H2O-NaCl-glycerol phase diagram and its application in cryobiology. 
  • The Haemophilus influenzae HMW1 adhesin is a glycoprotein with an unusual N-linked carbohydrate modification. 
  • The aqueous humor of rabbit contains high concentrations of pyrroline-5-carboxylate. 
  • The calmodulin binding domain of chicken smooth muscle myosin light chain kinase contains a pseudosubstrate sequence. 
  • The chiroptical signature of achiral metal clusters induced by dissymmetric adsorbates. 
  • The contribution of the exosite residues of plasminogen activator inhibitor-1 to proteinase inhibition. 
  • The cubic ternary complex receptor-occupancy model. III. resurrecting efficacy. 
  • The effect of a single boranophosphate substitution with defined configuration on the thermal stability and conformation of a DNA duplex. 
  • The effect of detergents on the reduction of tetrazolium salts. 
  • The effect of plasmin on the subunit structure of human fibrin. 
  • The effect of the degree of chitosan deacetylation on the efficiency of gene transfection. 
  • The energy landscape of a fast-folding protein mapped by Ala-->Gly substitutions. 
  • The extracellular nuclease of Staphylococcus aureus: structures of the native enzyme and an enzyme-inhibitor complex at 4 A resolution. 
  • The interaction of nitric oxide (NO) with the yeast transcription factor Ace1: A model system for NO-protein thiol interactions with implications to metal metabolism. 
  • The intracellular proteolytic processing of extracellular superoxide dismutase (EC-SOD) is a two-step event. 
  • The kinase Grk2 regulates Nedd4/Nedd4-2-dependent control of epithelial Na+ channels. 
  • The kinetic mechanism of EcoRI endonuclease. 
  • The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. 
  • The molecular basis for ligand specificity in a mouse olfactory receptor: a network of functionally important residues. 
  • The motion of a single molecule, the lambda-receptor, in the bacterial outer membrane. 
  • The nature of aqueous tunneling pathways between electron-transfer proteins. 
  • The oxyhemoglobin reaction of nitric oxide. 
  • The regulation and nature of the cyanide-resistant alternative oxidase of plant mitochondria. 
  • The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria. 
  • The role of cavitation in liposome formation. 
  • The role of thickness transitions in convective assembly. 
  • The role of tyrosine 343 in substrate binding and catalysis by human sulfite oxidase. 
  • The stoichiometry and kinetics of the inducible cysteine desulfhydrase from Salmonella typhimurium. 
  • The structural mechanism of GTP stabilized oligomerization and catalytic activation of the Toxoplasma gondii uracil phosphoribosyltransferase. 
  • The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding. 
  • The use of Bayesian networks for nanoparticle risk forecasting: model formulation and baseline evaluation. 
  • The use of magnetic resonance imaging to track controlled drug release and transport in the brain. 
  • Theoretical study of catalytic mechanism for single-site water oxidation process. 
  • Thermodynamic analysis of subunit interactions in Escherichia coli molybdopterin synthase. 
  • Thermodynamics of reactions catalyzed by PABA synthase. 
  • Thermodynamics, kinetics, and mechanism of the stepwise dissociation and formation of Tris(L-lysinehydroxamato)iron(III) in aqueous acid. 
  • Thermopower of molecular junctions: an ab initio study. 
  • Three-dimensional modeling, estimation, and fault diagnosis of spacecraft air contaminants. 
  • Total synthesis of (-)-hennoxazole A. 
  • Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network. 
  • Towards Raman optical activity calculations of large molecules. 
  • Transient kinetic approaches to enzyme mechanisms. 
  • Transition dynamics and magic-number-like behavior of frictional granular clusters. 
  • Transport properties of the calcium ionophore ETH-129. 
  • Treatment of mixtures of toluene and n-propanol vapours in a compost-woodchip-based biofilter. 
  • Troglitazone-induced intracellular oxidative stress in rat hepatoma cells: a flow cytometric assessment. 
  • Two-dimensional tracking of ncd motility by back focal plane interferometry. 
  • Ultrasonic absorption measurements in aqueous solutions of glycine, diglycine, and triglycine. 
  • Understanding the force-vs-distance profiles of terminally attached poly(N-isopropyl acrylamide) thin films. 
  • Using dynamic programming to create isotopic distribution maps from mass spectra. 
  • Validation challenge of density-functional theory for peptides-example of Ac-Phe-Ala5-LysH(+). 
  • Vibrational Properties of Metastable Polymorph Structures by Machine Learning. 
  • WRP/srGAP3 facilitates the initiation of spine development by an inverse F-BAR domain, and its loss impairs long-term memory. 
  • Why Are DNA and Protein Electron Transfer So Different? 
  • X-ray crystal structure and conformation of a spin-labeled acetylcholine, DL-4-[N,N-dimethyl-n-(ethan-2'-olacetate)amino]-2,2,6,6-tetramethylpiperidine-1-oxyliodide. 
  • X-ray diffraction indicates that active cross-bridges bind to actin target zones in insect flight muscle. 
  • YbiV from Escherichia coli K12 is a HAD phosphatase. 
• 

  Keywords of People

  • Blum, Volker, Associate Professor in the Department of Mechanical Engineering and Materials Science, Duke University Energy Initiative
  • Chitneni, Satish K., Associate Professor in Radiology, Radiology
  • Cohen-Wolkowiez, Michael, Professor of Pediatrics, Pediatrics, Infectious Diseases
  • Deshusses, Marc, Professor of Civil and Environmental Engineering, Duke University Energy Initiative
  • Erickson, Harold Paul, James B. Duke Distinguished Professor of Cell Biology, Cell Biology
  • Gottlin, Elizabeth B., Assistant Professor in Radiology, Radiology
  • Heffernan, James Brendan, Associate Professor of Ecosystem Ecology and Ecohydrology, Environmental Sciences and Policy
  • Hsu-Kim, Heileen, Sternberg Family Professor of Civil & Environmental Engineering, Civil and Environmental Engineering
  • Katz, David F., Nello L. Teer, Jr. Distinguished Professor of Biomedical Engineering, in the Edmund T. Pratt, Jr. School of Engineering, Biomedical Engineering
  • Oas, Terrence Gilbert, Professor of Biochemistry, Biochemistry
  • Palmer, Gregory M., Associate Professor of Radiation Oncology, Radiation Oncology
  • Shindell, Drew Todd, Nicholas Distinguished Professor of Earth Science, Earth and Ocean Sciences
  • Soderling, Scott Haydn, George Barth Geller Distinguished Professor of Molecular Biology, Cell Biology
  • Sullivan, Daniel Carl, Professor Emeritus of Radiology, Radiology
  • Yellen, Benjamin, Associate Professor in the Department of Mechanical Engineering and Materials Science, Mechanical Engineering and Materials Science