Physics Commons^™

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 K₂Bi_8-xSb_xSe₁₃ (02Bi_8-xSb_xSe₁₃ was analyzed on the basis of the classical semiconductor theory and discussed in the context of recent band calculations. The results suggest that the K₂Bi_8-xSb_xSe₁₃ 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 K_{2 …}

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

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 modeling the 3D structures of unknown protein–protein complexes. …

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 pK_a 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 pK_a shifts show the same tendency since 80% of the interfacial acidic groups were found to lower their …

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 …

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

Chemistry and Biochemistry Faculty Research

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.

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.

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 …