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Series

Biological and Chemical Physics

2006

Articles 1 - 19 of 19

Full-Text Articles in Physics

Structure Inhomogeneities, Shallow Defects, And Charge Transport In The Series Of Thermoelectric Materials K2bi8−Xsbxse13, Jeffrey S. Dyck, T. Kyratski, E. Hatzikraniotis, K. M. Paraskevopoulos, C. D. Malliakas, C. Uher, M. G. Kanatzidis Dec 2006

Structure Inhomogeneities, Shallow Defects, And Charge Transport In The Series Of Thermoelectric Materials K2bi8−Xsbxse13, Jeffrey S. Dyck, T. Kyratski, E. Hatzikraniotis, K. M. Paraskevopoulos, C. D. Malliakas, C. Uher, M. G. Kanatzidis

Physics

The charge transport properties of the low-dimensional thermoelectric materials K2Bi8-xSbxSe13 (02Bi8-xSbxSe13 was analyzed on the basis of the classical semiconductor theory and discussed in the context of recent band calculations. The results suggest that the K2Bi8-xSbxSe13 materials possess coexisting domains with semimetallic and semiconducting characters whose ratio is influenced by the value of x and by local defects. The extent and relative distribution of these domains control the charge transport properties. Electron diffraction experiments performed on samples of K2 ...


The Intermediate Filament Protein, Synemin, Is An Akap In The Heart, Mary Russell, Linda M. Lund, Roy Haber, Kathleen Mckeegan, Nicholas Cianciola, Meredith Bond Dec 2006

The Intermediate Filament Protein, Synemin, Is An Akap In The Heart, Mary Russell, Linda M. Lund, Roy Haber, Kathleen Mckeegan, Nicholas Cianciola, Meredith Bond

Biological Sciences Publications

Targeting of protein kinase A (PKA) by A-kinase anchoring proteins (AKAPs) contributes to high specificity of PKA signaling pathways. PKA phosphorylation of myofilament and cytoskeletal proteins may regulate myofibrillogenesis and myocyte remodeling during heart disease; however, known cardiac AKAPs do not localize to these regions. To identify novel AKAPs which target PKA to the cytoskeleton or myofilaments, a human heart cDNA library was screened and the intermediate filament (IF) protein, synemin, was identified as a putative RII (PKA regulatory subunit type II) binding protein. A predicted RII binding region was mutated and resulted in loss of RII binding. Furthermore, synemin ...


Predicting Residue Contacts Using Pragmatic Correlated Mutations Method: Reducing The False Positives, Petras J. Kundrotas, Emil Alexov Nov 2006

Predicting Residue Contacts Using Pragmatic Correlated Mutations Method: Reducing The False Positives, Petras J. Kundrotas, Emil Alexov

Publications

Background

Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins.

Results

Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal ...


Protcom: Searchable Database Of Protein Complexes Enhanced With Domain-Domain Structures, Petras Kundrotas, Emil Alexov Oct 2006

Protcom: Searchable Database Of Protein Complexes Enhanced With Domain-Domain Structures, Petras Kundrotas, Emil Alexov

Publications

The database of protein complexes (PROTCOM) is a compilation of known 3D structures of protein–protein complexes enriched with artificially created domain–domain structures using the available entries in the Protein Data Bank. The domain–domain structures are generated by parsing single chain structures into loosely connected domains and are important features of the database. The database (http://www.ces.clemson.edu/compbio/protcom) could be used for benchmarking purposes of the docking and other algorithms for predicting 3D structures of protein–protein complexes. The database can be utilized as a template database in the homology or threading methods for ...


Electrostatic Properties Of Protein-Protein Complexes, Petras J. Kundrotas, Emil Alexov Sep 2006

Electrostatic Properties Of Protein-Protein Complexes, Petras J. Kundrotas, Emil Alexov

Publications

Statistical electrostatic analysis of 37 protein-protein complexes extracted from the previously developed database of protein complexes (ProtCom, http://www.ces.clemson.edu/compbio/protcom) is presented. It is shown that small interfaces have a higher content of charged and polar groups compared to large interfaces. In a vast majority of the cases the average pKa shifts for acidic residues induced by the complex formation are negative, indicating that complex formation stabilizes their ionizable states, whereas the histidines are predicted to destabilize the complex. The individual pKa shifts show the same tendency since 80% of the interfacial acidic groups ...


Chemical Diffusion Of Co In Mixed Co+O Adlayers And Reaction-Front Propagation In Co Oxidation On Pd(100), Da-Jiang Liu, James W. Evans Aug 2006

Chemical Diffusion Of Co In Mixed Co+O Adlayers And Reaction-Front Propagation In Co Oxidation On Pd(100), Da-Jiang Liu, James W. Evans

Physics and Astronomy Publications

Within the framework of a realistic atomistic lattice-gas model, we present the theoretical formulation and simulation procedures for precise analysis of the chemical diffusion flux of highly mobile CO within a nonuniform interacting mixed CO+O adlayer on a Pd(100) surface. The approach applies in both regimes of relatively immobile unequilibrated and fairly mobile near-equilibrated O adlayer distributions. Spatiotemporal behavior in surface reactions is controlled by chemical diffusion in mixed adlayers. Thus, we naturally integrate the above analysis with a previously developed multiscale modeling strategy to describe mesoscale reaction front propagation in CO oxidation on Pd(100). This treatment ...


Atomistic Lattice-Gas Modeling Of Co Oxidation On Pd(100): Temperature-Programed Spectroscopy And Steady-State Behavior, Da-Jiang Liu, James W. Evans Apr 2006

Atomistic Lattice-Gas Modeling Of Co Oxidation On Pd(100): Temperature-Programed Spectroscopy And Steady-State Behavior, Da-Jiang Liu, James W. Evans

Physics and Astronomy Publications

We have developed an atomistic lattice-gas model for the catalytic oxidation of CO on single-crystal Pd(100) surfaces under ultrahigh vacuum conditions. This model necessarily incorporates an detailed description of adlayer ordering and adsorption-desorption kinetics both for CO on Pd(100), and for oxygen on Pd(100). Relevant energetic parameters are determined by comparing model predictions with experiment, together with some guidance from density functional theory calculations. The latter also facilitates description of the interaction and reaction of adsorbed CO and oxygen. Kinetic Monte Carlo simulations of this reaction model are performed to predict temperature- programed reaction spectra, as well ...


Measuring Inter-Dna Potentials In Solution, Xiangyun Qiu, Lisa W. Kwok, Hye Yoon Park, Jessica S. Lamb, Kurt Andresen, Lois Pollack Apr 2006

Measuring Inter-Dna Potentials In Solution, Xiangyun Qiu, Lisa W. Kwok, Hye Yoon Park, Jessica S. Lamb, Kurt Andresen, Lois Pollack

Physics and Astronomy Faculty Publications

Interactions between short strands of DNA can be tuned from repulsive to attractive by varying solution conditions and have been quantified using small angle x-ray scattering techniques. The effective DNA interaction charge was extracted by fitting the scattering profiles with the generalized one-component method and inter-DNA Yukawa pair potentials. A significant charge is measured at low to moderate monovalent counterion concentrations, resulting in strong inter-DNA repulsion. The charge and repulsion diminish rapidly upon the addition of divalent counterions. An intriguing short range attraction is observed at surprisingly low divalent cation concentrations, ~16 mM Mg2+. Quantitative measurements of inter- DNA potentials ...


Mound Slope And Shape Selection During Unstable Multilayer Growth: Analysis Of Step-Dynamics Models Including Downward Funneling, Maozhi Li, James W. Evans Mar 2006

Mound Slope And Shape Selection During Unstable Multilayer Growth: Analysis Of Step-Dynamics Models Including Downward Funneling, Maozhi Li, James W. Evans

Physics and Astronomy Publications

Step-dynamics models are developed for mound shape evolution during multilayer homoepitaxial growth in the presence of inhibited interlayer transport. Unconventionally, our models also incorporate downward funneling (DF) of atoms deposited at step edges. The extent of DF can be reduced continuously to zero where one recovers traditional step dynamics models. This allows direct comparison between the behavior of models with and without DF. We show that DF greatly enhances growth of the height of valleys at the mound bases to an extent compatible with slope selection. To elucidate the selected shapes of finite mounds, we consider a suitably defined net ...


Erratum: The Structure Of Alkali Halide Dimers: A Critical Test Of Ionic Models And New Ab Initio Results, T. Törring, S. Biermann, J. Hoeft, Richard J. Mawhorter, Robert J. Cave, C. Szemenyei Feb 2006

Erratum: The Structure Of Alkali Halide Dimers: A Critical Test Of Ionic Models And New Ab Initio Results, T. Törring, S. Biermann, J. Hoeft, Richard J. Mawhorter, Robert J. Cave, C. Szemenyei

All HMC Faculty Publications and Research

It has come to our attention that some of the ab initio results presented are incorrect due to errors in the Cs and C1 basis sets, and a small error in the binding energy of Rb2F2. The corrected results are presented below for the species that were affected, modifying the results in Table III of the original paper. Only those values which are different from the results of the original Table III are included. Note that some of these results are used for comparison with the ionic models in later tables. In addition, some HF data quoted in Tables V ...


Femtosecond Nuclear Motion Of Hcl Probed By Resonant X-Ray Raman Scattering In The Cl 1s Region, Marc Simon, Loic Journel, Stephane Carniato, Richard Taieb, I. Minkov, Faris Gel'mukhanov, P. Salek, H. Agren, Renaud Guillemin, Wayne C. Stolte, A. C. Hudson, Dennis W. Lindle Feb 2006

Femtosecond Nuclear Motion Of Hcl Probed By Resonant X-Ray Raman Scattering In The Cl 1s Region, Marc Simon, Loic Journel, Stephane Carniato, Richard Taieb, I. Minkov, Faris Gel'mukhanov, P. Salek, H. Agren, Renaud Guillemin, Wayne C. Stolte, A. C. Hudson, Dennis W. Lindle

Chemistry and Biochemistry Faculty Publications

Femtosecond dynamics are observed by resonant x-ray Raman scattering (RXS) after excitation along the dissociative Cl 1s→6ơ* resonance of gas-phase HCl. The short core-hole lifetime results in a complete breakdown of the common nondispersive behavior of soft-x-ray transitions between parallel potentials. We evidence a general phenomenon of RXS in the hard-x-ray region: a complete quenching of vibrational broadening. This opens up a unique opportunity for superhigh resolution x-ray spectroscopy beyond vibrational and lifetime limitations.


Thermal Desorption Of Hydrogen From Carbon Nanosheets., X Zhao, R A. Outlaw, J J. Wang, M Y. Zhu, Gregory D. Smith, B C. Holloway Jan 2006

Thermal Desorption Of Hydrogen From Carbon Nanosheets., X Zhao, R A. Outlaw, J J. Wang, M Y. Zhu, Gregory D. Smith, B C. Holloway

Applied Science Articles & Book Chapters

Carbon nanosheets are a unique nanostructure that, at their thinnest configuration, approach a single freestanding graphene sheet. Temperature desorption spectroscopy (TDS) has shown that the hydrogen adsorption and incorporation during growth of the nanosheets by radio frequency plasma-enhanced chemical vapor deposition are significant. A numerical peak fitting to the desorption spectra (300–1273 K) via the Polanyi-Wigner equation showed that desorption followed a second order process, presumably by the Langmuir-Hinshelwood mechanism. Six peaks provide the best fit to the TDS spectra. Surface desorption activation energies were determined to be 0.59, 0.63, and 0.65 eV for the external ...


Conformation Of The Acrb Multidrug Efflux Pump In Mutants Of The Putative Proton Relay Pathway, Chih-Chia Su, Ming Li, Ruoyu Gu, Yumiko Takatsuka, Gerry Mcdermott, Hiroshi Nikaido, Edward Yu Jan 2006

Conformation Of The Acrb Multidrug Efflux Pump In Mutants Of The Putative Proton Relay Pathway, Chih-Chia Su, Ming Li, Ruoyu Gu, Yumiko Takatsuka, Gerry Mcdermott, Hiroshi Nikaido, Edward Yu

Physics and Astronomy Publications

We previously reported the X-ray structures of wild-type Escherichia coli AcrB, a proton motive force-dependent multidrug efflux pump, and its N109A mutant. These structures presumably reflect the resting state of AcrB, which can bind drugs. After ligand binding, a proton may bind to an acidic residue(s) in the transmembrane domain, i.e., Asp407 or Asp408, within the putative network of electrostatically interacting residues, which also include Lys940 and Thr978, and this may initiate a series of conformational changes that result in drug expulsion. Herein we report the X-ray structures of four AcrB mutants, the D407A, D408A, K940A, and T978A ...


Cloning, Expression, Purification, Crystallization And Preliminary X-Ray Diffraction Analysis Of The Regulator Acrr From Escherichia Coli, Ming Li, Xi Qiu, Chih-Chia Su, Feng Long, Ruoyu Gu, Gerry Mcdermott, Edward Yu Jan 2006

Cloning, Expression, Purification, Crystallization And Preliminary X-Ray Diffraction Analysis Of The Regulator Acrr From Escherichia Coli, Ming Li, Xi Qiu, Chih-Chia Su, Feng Long, Ruoyu Gu, Gerry Mcdermott, Edward Yu

Physics and Astronomy Publications

This paper describes the cloning, expression, purification and preliminary X-ray data analysis of the AcrR regulatory protein. The Escherichia coli AcrR is a member of the TetR family of transcriptional regulators. It regulates the expression of the AcrAB multidrug transporter. Recombinant AcrR with a 6×His tag at the C-terminus was expressed in E. coli and purified by metal-affinity chromatography. The protein was crystallized using hanging-drop vapor diffusion. X-ray diffraction data were collected from cryocooled crystals at a synchrotron light source. The best crystal diffracted to 2.5 Å. The space group was determined to be P32, with ...


Interaction-Induced Dipole Moment Of The Ar–H2 Dimer: Dependence On The H2 Bond Length, Robert J. Hinde Jan 2006

Interaction-Induced Dipole Moment Of The Ar–H2 Dimer: Dependence On The H2 Bond Length, Robert J. Hinde

Chemistry Publications and Other Works

We present ab initio calculations of the interaction-induced dipole moment of the Ar–H2 van der Waals dimer. The primary focus of our calculations is on the H2 bond length dependence of the dipole moment, which determines the intensities of both the collision-induced H2 = 1 ← 0 fundamental band in gaseous Ar–H2 mixtures and the dopant-induced H2 = 1 ← 0 absorption feature in Ar-doped solid H2 matrices. Our calculations employ large atom-centered basis sets, diffuse bond functions positioned between the two monomers, and a coupled cluster treatment of valence electron correlation; core-valence correlation effects appear ...


Population Size Bias In Descendant-Weighted Diffusion Quantum Monte Carlo Simulations, G. Lee Warren, Robert J. Hinde Jan 2006

Population Size Bias In Descendant-Weighted Diffusion Quantum Monte Carlo Simulations, G. Lee Warren, Robert J. Hinde

Chemistry Publications and Other Works

We consider the influence of population size on the accuracy of diffusion quantum Monte Carlo simulations that employ descendant weighting or forward walking techniques to compute expectation values of observables that do not commute with the Hamiltonian. We show that for a simple model system, the d-dimensional isotropic harmonic oscillator, the population size must increase rapidly with d in order to ensure that the simulations produce accurate results. When the population size is too small, expectation values computed using descendant-weighted diffusion quantum Monte Carlo simulations exhibit significant systematic biases.


Polarizable Contributions To The Surface Tension Of Liquid Water, J. L. Rivera, Francis W. Starr, P. Paricaud, P. T. Cummings Jan 2006

Polarizable Contributions To The Surface Tension Of Liquid Water, J. L. Rivera, Francis W. Starr, P. Paricaud, P. T. Cummings

Division III Faculty Publications

No abstract provided.


Semiclassical Nonadiabatic Dynamics Based On Quantum Trajectories For The O(3P,1D) + H2 System, Sophya V. Garashchuk, V. A. Rassolov, G. C. Schatz Jan 2006

Semiclassical Nonadiabatic Dynamics Based On Quantum Trajectories For The O(3P,1D) + H2 System, Sophya V. Garashchuk, V. A. Rassolov, G. C. Schatz

Faculty Publications

The O(P3,D1)+H2→OH+Hreaction is studied using trajectory dynamics within the approximate quantum potential approach. Calculations of the wave-packet reaction probabilities are performed for four coupled electronic states for total angular momentum J=0 using a mixed coordinate/polar representation of the wave function. Semiclassical dynamics is based on a single set of trajectories evolving on an effective potential-energy surface and in the presence of the approximate quantum potential. Population functions associated with each trajectory are computed for each electronic state. The effective surface is a linear combination of the electronic states with the contributions of individual ...


Tribological Properties Of Quasicrystals: Effect Of Aperiodic Versus Periodic Surface Order, Jeong Young Park, D. F. Ogletree, M. Salmeron, R. A. Ribeiro, Paul C. Canfield, Cynthia J. Jenks, Patricia A. Thiel Jan 2006

Tribological Properties Of Quasicrystals: Effect Of Aperiodic Versus Periodic Surface Order, Jeong Young Park, D. F. Ogletree, M. Salmeron, R. A. Ribeiro, Paul C. Canfield, Cynthia J. Jenks, Patricia A. Thiel

Chemistry Publications

We investigated the nanoscale tribological properties of a decagonal quasicrystal using a combination of atomic force microscopy and scanning tunneling microscopy in ultrahigh vacuum. This combination permitted a variety of in situ measurements, including atomic-scale structure, friction and adhesion force, tip-sample current, and topography. We found that thiol-passivated tips can be used for reproducible studies of the tip-quasicrystal contact while nonpassivated probes adhere irreversibly to the clean quasicrystalline surface causing permanent modifications. The most remarkable results were obtained on the twofold surface of the Al-Ni-Co decagonal quasicrystal where atoms are arranged periodically along the tenfold axis and aperiodically in the ...