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Biological and Chemical Physics

2004

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Articles 1 - 19 of 19

Full-Text Articles in Physics

Spatial Distribution Of Competing Ions Around Dna In Solution, Kurt Andresen, R. Das, Hye Yoon Park, H. Smith, Lisa W. Kwok, Jessica S. Lamb, E. J. Kirkland, D. Herschlag, K. D. Finkelstein, Lois Pollack Dec 2004

Spatial Distribution Of Competing Ions Around Dna In Solution, Kurt Andresen, R. Das, Hye Yoon Park, H. Smith, Lisa W. Kwok, Jessica S. Lamb, E. J. Kirkland, D. Herschlag, K. D. Finkelstein, Lois Pollack

Physics and Astronomy Faculty Publications

The competition of monovalent and divalent cations for proximity to negatively charged DNA is of biological importance and can provide strong constraints for theoretical treatments of polyelectrolytes. Resonant x-ray scattering experiments have allowed us to monitor the number and distribution of each cation in a mixed ion cloud around DNA. These measurements provide experimental evidence to support a general theoretical prediction: the normalized distribution of each ion around polyelectrolytes remains constant when ions are mixed at different ratios. In addition, the amplitudes of the scattering signals throughout the competition provide a measurement of the surface concentration parameter that predicts the ...


From Atomic Scale Reactant Ordering To Mesoscale Reaction Front Propagation: Co Oxidation On Pd(100), Da-Jiang Liu, James W. Evans Nov 2004

From Atomic Scale Reactant Ordering To Mesoscale Reaction Front Propagation: Co Oxidation On Pd(100), Da-Jiang Liu, James W. Evans

Mathematics Publications

We utilize a heterogeneous coupled lattice-gas (HCLG) approach to connect the length scales from a realistic atomistic description of surface reactions to the associated mesoscale spatiotemporal behavior. This method is applied to describe reaction front structure in a model for CO oxidation on Pd(100) which incorporates complex ordering of CO and O adlayers, and a precise treatment of the chemical diffusion for interacting CO adlayers in an environment of coadsorbed O.


Probing Cation Antisite Disorder In Gd2ti2o7 Pyrochlore By Site-Specific Nexafs And Xps, Ponnusamy Nachimuthu, S. Thevuthasan, Mark H. Engelhard, W. J. Weber, D. K. Shuh, N. M. Hamdan, B. S. Mun, E. M. Adams, D. E. Mccready, V. Shutthanandan, Dennis W. Lindle, G. Balakrishnan, R. C. Ewing Sep 2004

Probing Cation Antisite Disorder In Gd2ti2o7 Pyrochlore By Site-Specific Nexafs And Xps, Ponnusamy Nachimuthu, S. Thevuthasan, Mark H. Engelhard, W. J. Weber, D. K. Shuh, N. M. Hamdan, B. S. Mun, E. M. Adams, D. E. Mccready, V. Shutthanandan, Dennis W. Lindle, G. Balakrishnan, R. C. Ewing

Chemistry and Biochemistry Faculty Publications

Disorder in Gd2Ti2O7 is investigated by near-edge x-ray-absorption fine structure (NEXAFS) and x-ray photoelectron spectroscopy (XPS). NEXAFS shows Ti4+ ions occupy octahedral sites with a tetragonal distortion induced by vacant oxygen sites. O 1s XPS spectra obtained with a charge neutralization system from Gd2Ti2O7(100) and the Gd2Ti2O7 pyrochlore used by Chen et al. [Phys. Rev. Lett. 88, 105901 (2002)], both yielded a single peak, unlike the previous result on the latter that found two peaks. The current results give no evidence for ...


Spectroscopic And Microscopic Investigation Of The Corrosion Of 316/316l Stainless Steel By Lead-Bismuth Eutectic (Lbe) At Elevated Temperatures: Importance Of Surface Preparation, Allen L. Johnson, Denise Parsons, Julia Manzerova, Dale L. Perry, Daniel Koury, Brian D. Hosterman, John Farley Jul 2004

Spectroscopic And Microscopic Investigation Of The Corrosion Of 316/316l Stainless Steel By Lead-Bismuth Eutectic (Lbe) At Elevated Temperatures: Importance Of Surface Preparation, Allen L. Johnson, Denise Parsons, Julia Manzerova, Dale L. Perry, Daniel Koury, Brian D. Hosterman, John Farley

Transmutation Sciences Materials (TRP)

The corrosion of steel by lead–bismuth eutectic (LBE) is an important issue in proposed nuclear transmutation schemes. Russian scientists at the IPPE exposed steel samples to oxygen-controlled LBE at temperatures up to 823 K and exposure times up to 3000 h. We have characterized these post-exposure steel samples and unexposed controls, using scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDAX) and X-ray photoelectron spectroscopy (XPS). Previous researchers have investigated the corrosion by LBE of steel of varying composition. In the present work, we compared two samples having the same composition (standard nuclear grade 316/316L) but different surface preparation ...


Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber May 2004

Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber

Faculty Publications

n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 µA/µm and 4.9 µA/V, respectively, with device yields of >85%.


Double Excitations Within Time-Dependent Density Functional Theory Linear Response, Neepa T. Maitra, Fan Zhang, Robert J. Cave, Kieron Burke Apr 2004

Double Excitations Within Time-Dependent Density Functional Theory Linear Response, Neepa T. Maitra, Fan Zhang, Robert J. Cave, Kieron Burke

All HMC Faculty Publications and Research

Within the adiabatic approximation, time-dependent density functional theory yields only single excitations. Near states of double excitation character, the exact exchange–correlation kernel has a strong dependence on frequency. We derive the exact frequency-dependent kernel when a double excitation mixes with a single excitation, well separated from the other excitations, in the limit that the electron–electron interaction is weak. Building on this, we construct a nonempirical approximation for the general case, and illustrate our results on a simple model.


Conduction Band Splitting And Transport Properties Of Bi2se3., J. Navrátil, J. Horák, T. Plecháček, S. Kamba, P. LošŤÁK, Jeffrey Dyck, W. Chen, C. Uher Mar 2004

Conduction Band Splitting And Transport Properties Of Bi2se3., J. Navrátil, J. Horák, T. Plecháček, S. Kamba, P. LošŤÁK, Jeffrey Dyck, W. Chen, C. Uher

Jeffrey Dyck

Detailed transport studies of single crystals of Bi2Se3 were made in the temperature range of 2–300K, and the data were analyzed in terms of a model consisting of two groups of electrons—a centrosymmetrical lower conduction band and an upper conduction band located away from the Γ-point. Very good agreement with the experimental data is obtained assuming the electrons are scattered on acoustic phonons and ionized impurities. A rather strong influence of the latter mechanism is attributed to a large number of charged selenium vacancies in Bi2Se3. The fitted transport parameters were used to calculate the electronic portion of ...


State-To-State Rotational Relaxation Rate Constants For Co+Ne From Ir-Ir Double-Resonance Experiments: Comparing Theory To Experiment, David A. Hostutler, Tony C. Smith, Gordon D. Hager, George C. Mcbane, Michael C. Heaven Jan 2004

State-To-State Rotational Relaxation Rate Constants For Co+Ne From Ir-Ir Double-Resonance Experiments: Comparing Theory To Experiment, David A. Hostutler, Tony C. Smith, Gordon D. Hager, George C. Mcbane, Michael C. Heaven

Peer Reviewed Articles

IR-IR double-resonance experiments were used to study the state-to-state rotational relaxation of CO with Ne as a collision partner. Rotational levels in the range Ji=2-9 were excited and collisional energy transfer of population to the levels Jf=2-8 was monitored. The resulting data set was analyzed by fitting to numerical solutions of the master equation. State-to-state rate constant matrices were generated using fitting law functions. Fitting laws based on the modifed exponential gap (MEG) and statistical power exponential gap (SPEG) models were used; the MEG model performed better than the SPEG model. A rate constant matrix was ...


Dynamic Heterogeneities In Supercooled Water, Nicolas Giovambattista, Marco Mazza, Sergey V. Buldyrev, Francis W. Starr, H. Eugene Stanley Jan 2004

Dynamic Heterogeneities In Supercooled Water, Nicolas Giovambattista, Marco Mazza, Sergey V. Buldyrev, Francis W. Starr, H. Eugene Stanley

Division III Faculty Publications

No abstract provided.


Energy Conserving Approximations To The Quantum Potential: Dynamics With Linearized Quantum Force, Sophya V. Garashchuk, V. A. Rassolov Jan 2004

Energy Conserving Approximations To The Quantum Potential: Dynamics With Linearized Quantum Force, Sophya V. Garashchuk, V. A. Rassolov

Faculty Publications

Solution of the Schrödinger equation within the de Broglie–Bohm formulation is based on propagation of trajectories in the presence of a nonlocal quantum potential. We present a new strategy for defining approximate quantum potentials within a restricted trial function by performing the optimal fit to the log-derivatives of the wave function density. This procedure results in the energy-conserving dynamics for a closed system. For one particular form of the trial function leading to the linear quantum force, the optimization problem is solved analytically in terms of the first and second moments of the weighted trajectory distribution. This approach gives ...


Modified Quantum Trajectory Dynamics Using A Mixed Wave Function Representation, Sophya V. Garashchuk, V. A. Rassolov Jan 2004

Modified Quantum Trajectory Dynamics Using A Mixed Wave Function Representation, Sophya V. Garashchuk, V. A. Rassolov

Faculty Publications

Dynamics of quantum trajectories provides an efficient framework for description of various quantum effects in large systems, but it is unstable near the wave function density nodes where the quantum potential becomes singular. A mixed coordinate space/polar representation of the wave function is used to circumvent this problem. The resulting modified trajectory dynamics associated with the polar representation is nonsingular and smooth. The interference structure and the nodes of the wave function density are described, in principle, exactly in the coordinate representation. The approximate version of this approach is consistent with the semiclassical linearized quantum force method [S. Garashchuk ...


Bohmian Dynamics On Subspaces Using Linearized Quantum Force, V. A. Rassolov, Sophya V. Garashchuk Jan 2004

Bohmian Dynamics On Subspaces Using Linearized Quantum Force, V. A. Rassolov, Sophya V. Garashchuk

Faculty Publications

In the de Broglie–Bohm formulation of quantum mechanics the time-dependent Schrödinger equation is solved in terms of quantum trajectories evolving under the influence of quantum and classical potentials. For a practical implementation that scales favorably with system size and is accurate for semiclassical systems, we use approximate quantum potentials. Recently, we have shown that optimization of the nonclassical component of the momentum operator in terms of fitting functions leads to the energy-conserving approximate quantum potential. In particular, linear fitting functions give the exact time evolution of a Gaussian wave packet in a locally quadratic potential and can describe the ...


Geminal Model Chemistry Ii. Perturbative Corrections, V. A. Rassolov, F. Xu, Sophya V. Garashchuk Jan 2004

Geminal Model Chemistry Ii. Perturbative Corrections, V. A. Rassolov, F. Xu, Sophya V. Garashchuk

Faculty Publications

We introduce and investigate a chemical model based on perturbative corrections to the product of singlet-type strongly orthogonal geminals wave function. Two specific points are addressed (i) Overall chemical accuracy of such a model with perturbative corrections at a leading order; (ii) Quality of strong orthogonality approximation of geminals in diverse chemical systems. We use the Epstein–Nesbet form of perturbation theory and show that its known shortcomings disappear when it is used with the reference Hamiltonian based on strongly orthogonal geminals. Application of this model to various chemical systems reveals that strongly orthogonal geminals are well suited for chemical ...


Crystallographic, Electronic, And Magnetic Studies Of Ζ2-Gam (M = Cr, Mn Or Fe):  Trends In Itinerant Magnetism, Olivier Gourdon, Sergey L. Bud'ko, Darrick Williams, Gordon J. Miller Jan 2004

Crystallographic, Electronic, And Magnetic Studies Of Ζ2-Gam (M = Cr, Mn Or Fe):  Trends In Itinerant Magnetism, Olivier Gourdon, Sergey L. Bud'ko, Darrick Williams, Gordon J. Miller

Chemistry Publications

This study of the crystal structure, electronic structure, and magnetic properties of the ζ2-GaM (M = Cr, Mn or Fe) alloys is motivated by the recent reinvestigation of the crystallographic Al8Cr5 structure type of ζ2-GaMn. The isostructural compounds ζ2-GaFe and ζ2-GaCr have been refined using X-ray powder diffraction as well as neutron powder diffraction for ζ2-GaFe. Their structures have been refined using the space group Rm, with cell parameters a = 12.625(8) Å and c = 7.785(10) Å for ζ2-GaCr and a ...


Performance Characteristics Of Beamline 6.3.1 From 200 Ev To 2000 Ev At The Advanced Light Source, Ponnusamy Nachimuthu, J. H. Underwood, C. D. Kemp, Eric M. Gullikson, Dennis W. Lindle, David K. Shuh, Rupert C. Perera Jan 2004

Performance Characteristics Of Beamline 6.3.1 From 200 Ev To 2000 Ev At The Advanced Light Source, Ponnusamy Nachimuthu, J. H. Underwood, C. D. Kemp, Eric M. Gullikson, Dennis W. Lindle, David K. Shuh, Rupert C. Perera

Chemistry and Biochemistry Faculty Publications

Bend magnet beamline 6.3.1 at the Advanced Light Source operates from 200 eV to 2000 eV, primarily used for x-ray absorption fine structure investigations. The beamline optics consist of a compact, entrance-slitless, Hettrick-Underwood type variable-line-spacing plane-grating monochromator and refocusing mirrors to provide a 25 μm × 500 μm spot at the focal point in the reflectometer end station. Wavelength is scanned by the simple rotation of the grating and illuminates a fixed exit slit. The LabView based beamline control and data acquisition computer code has been implemented to provide a convenient interface to the user. The dedicated end station ...


Predicting Binding Sites Of Hydrolase-Inhibitor Complexes By Combining Several Methods, Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant Honovar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs Jan 2004

Predicting Binding Sites Of Hydrolase-Inhibitor Complexes By Combining Several Methods, Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant Honovar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs

Genetics, Development and Cell Biology Publications

Background

Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major efforts to identify interacting protein pairs experimentally in order to decipher the networks of interacting, coordinated-in-action proteins. Identification of protein-protein interaction sites and detection of specific amino acids that contribute to the specificity and the strength of protein interactions is an important problem with broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks.

Results

In order to increase the power of predictive methods for protein-protein interaction sites, we have developed a consensus methodology ...


Anomalous Temperature-Dependent Transport In Ybni2b2c And Its Correlation To Microstructural Features, M.A. Avila, Y.Q. Wu, C.L. Condron, Sergey L. Bud'ko, M. J. Kramer, Gordon J. Miller, Paul C. Canfield Jan 2004

Anomalous Temperature-Dependent Transport In Ybni2b2c And Its Correlation To Microstructural Features, M.A. Avila, Y.Q. Wu, C.L. Condron, Sergey L. Bud'ko, M. J. Kramer, Gordon J. Miller, Paul C. Canfield

Chemistry Publications

We address the nature of the ligandal disorder leading to local redistributions of Kondo temperatures, manifested as annealing-induced changes in the transport behavior of the heavy fermion system YbNi2B2C. The anomalous transport behavior was fully characterized by temperature dependent resistivity measurements in an extended range of 0.4


Studies In Cardiac Defribrillation, Eamonn Mckenna Jan 2004

Studies In Cardiac Defribrillation, Eamonn Mckenna

Masters

Cardiac disease resulting in cardiac arrest is one of the most common fatal diseases in the developed world. Defibrillation is the medical procedure used to correct the irregular cardiac rhythm (ventricular fibrillation (VF)) which is very often detected in patients suffering cardiac arrest. In the work reported in this thesis, two aspects of the defibrillation of patients in VF were examined. The first area of investigation concentrated on the use of multiple defibrillation electrodes to be used during closed chest (transthoracic) defibrillation. This study was carried out in a saline bath and centred on “focusing” electric fields from perimeter electrodes ...


Dynamic Heterogeneities In Supercooled Water, Nicolas Giovambattista, Marco Mazza, Sergey V. Buldyrev, Francis W. Starr, H. Eugene Stanley Dec 2003

Dynamic Heterogeneities In Supercooled Water, Nicolas Giovambattista, Marco Mazza, Sergey V. Buldyrev, Francis W. Starr, H. Eugene Stanley

Francis Starr

No abstract provided.