Predicting Binding Sites Of Hydrolase-Inhibitor Complexes By Combining Several Methods, 2017 Iowa State University
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
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.
In order to increase the power of predictive methods for protein-protein interaction sites, we have developed a consensus methodology ...
Competing Irreversible Cooperative Reactions On Polymer Chains, 2017 Iowa State University
Competing Irreversible Cooperative Reactions On Polymer Chains, James W. Evans, D. K. Hoffman, D. R. Burgess
James W. Evans
We analyze model processes involving competition between several irreversible reactions at the sites of a 1D, infinite, uniform polymer chain. These reactionscan be cooperative, i.e., the corresponding rates depend on the state of the surrounding sites. An infinite hierarchy of rate equations is readily derived for the probabilities of various subconfigurations. By exploiting a shielding property of suitable blocks of unreacted sites, we show how exact hierarchy truncation and solution is sometimes possible. The behavior of solutions is illustrated in several cases by plotting families of ‘‘reaction trajectories’’ for varying ratios of reactant concentrations ...
Energy Sudden Dissociative Collisions: Structure And Applications Of Factorization Relations, 2017 Iowa State University
Energy Sudden Dissociative Collisions: Structure And Applications Of Factorization Relations, D. K. Chan, David K. Hoffman, James W. Evans
James W. Evans
In the energy sudden (ES) approximation for nonreactive molecular collisions,there exist factorization relations by which an arbitrary T‐matrix element can be predicted as a spectroscopic linear combination of those out of some other, input state. These were first discovered for ground state input but this restriction was later removed. This general form of the spectroscopicfactorization relations is straightforwardly extended here to ES dissociativecollisions. One finds that in predicting dissociation amplitudes out of some state, it is necessary to use input data out of a higher (energy) bound state. Thus ground state factorization relations cannot be used. The structure ...
The Kinematic Apse And Jz‐Preserving Propensities For Nonreactive, Dissociative, And Reactive Polyatomic Collisions, D. K. Hoffman, James W. Evans, D. J. Kouri
James W. Evans
We consider the generalization of the kinematic apse to nonreactive polyatom–polyatom impulsive collisions, dissociative atom–molecule impulsive collisions,and (partially) impulsive reactive atom–diatom collisions. Appropriate generalizations of the kinematic apse are obtained along which there is a classical propensity for preserving the projection of the total intrinsic spin. In the case of reactive scattering, we discuss several different situations for which such a propensity occurs. For reactive systems in which no such propensity exists, the analysis may still provide a basis for classifying reactions.
Zgb Surface Reaction Model With High Diffusion Rates, 2017 Iowa State University
Zgb Surface Reaction Model With High Diffusion Rates, James W. Evans
James W. Evans
The diffusionless ZGB (monomer–dimer) surface reaction model exhibits a discontinuous transition to a monomer‐poisoned state when the fraction of monomer adsorption attempts exceeds 0.525. It has been claimed that this transition shifts to 2/3 with introduction of rapid diffusion of the monomerspecies, or of both species. We show this is not the case, 2/3 representing the spinodal rather than the transition point. For equal diffusion rates of both species, we find that the transition only shifts to 0.5951±0.0002.
The Reactive Quantum Boltzmann Equations: A Derivation From An Arrangement Channel Space Representation And Bbgky Hierarchy, James W. Evans, D. K. Hoffman, D. J. Kouri
James W. Evans
A rigorous derivation of the reactive quantum Boltzmann equations is presented for systems where breakup and recombination are excluded. The use of an arrangement channel space representation allows an exact decomposition of the N particle density matrix into components for different chemical compositions and an exact definition of reduced species density matrices (as opposed, e.g., to standard projection operator techniques). This necessitates the use of the combinatorially complex arrangement channel BBGKY hierarchy which, however, avoids the need for the usual heuristic specification of collision terms. Another advantage is that scattering equations generated for the reactive and nonreactive many body ...
Temperature Dependence Of Metal Film Growth Via Low‐Energy Electron Diffraction Intensity Oscillations: Pt/Pd(100), D. K. Flynn, James W. Evans, P. A. Thiel
James W. Evans
A commercial, conventional low‐energy electron diffraction apparatus is used to monitor Bragg intensity oscillations during the growth of Pt on Pd(100). The effect of substrate temperature between 80 and 400 K is investigated. Between 80 and 300 K, two to three Bragg oscillations are observed. The oscillation amplitude damps out quickly as film coverage increases at fixed temperature, but damp out less quickly at the higher substrate temperatures. Above ∼350 K, reconstruction of the Pt overlayer interferes with the oscillations. These data indicate that a kinetic barrier, most probably the barrier to surface diffusion,inhibits the system from ...
Cluster Diffusivity: Structure, Correlation, And Scaling, 2017 Iowa State University
Cluster Diffusivity: Structure, Correlation, And Scaling, H. C. Kang, P. A. Thiel, James W. Evans
James W. Evans
We have investigated the diffusion of clusters on a triangular lattice using Monte Carlo simulations. A cluster is defined as a two‐dimensional collection of particles which are connected to each other, either directly or indirectly through other particles in the cluster, by nearest‐neighbor bonds. Each particle is allowed to hop, with probability αδb/2/(α−δb/2+αδb/2), to a vacant nearest‐neighbor site with the constraint that the hop does not break the cluster. The change in the number of bonds is given by δb. The equilibrium clusters are correlated animals with structure controlled by the ...
Modeling Spatiotemporal Behavior Of The No+Co Reaction On Pt, 2017 Iowa State University
Modeling Spatiotemporal Behavior Of The No+Co Reaction On Pt, James W. Evans, H. H. Madden, R. Imbihl
James W. Evans
Various features of NO+CO reaction kinetics on Pt(100) surfaces, including temporal oscillations, are well described by a three‐variable model incorporating only the CO, NO, and O coverages. Here we analyze the corresponding reaction–diffusion equations demonstrating the existence of chemical waves where an ‘‘oscillating phase’’ displaces an unreactive NO/CO phase leaving a spatially periodic structure in its wake; pulses excited via inhomogeneities from an unreactive NO/CO background; and Turing structures for sufficiently unequal NO and CO diffusion rates.
Interface Propagation And Nucleation Phenomena For Discontinuous Poisoning Transitions In Surface-Reaction Models, James W. Evans, T. R. Ray
James W. Evans
Here, we consider discontinuous nonequilibrium phase transitions to poisoned or ‘‘adsorbing’’ states in lattice-gas models of surface reactions. Specifically, we examine the monomer or CO-poisoning transition in the Ziff-Gulari-Barshad monomer-dimer reaction model for CO oxidation, modified to include adspecies diffusion. For CO pressures below the poisoning transition, we first characterize the propagation of and fluctuations at an interface between reactive and CO-poisoned states. Here, we utilize ideas from spatial contact models, reaction-diffusion theory, and kinetic roughening theory. Evolution is described by the Kardar-Parisi-Zhang equation, but with the nonlinearity and kinetic surface tension vanishing on approaching the transition. Next, again for ...
Lattice‐Gas Model Mimicking The No+Co Reaction On Pt(100), 2017 University of California, Santa Barbara
Lattice‐Gas Model Mimicking The No+Co Reaction On Pt(100), Baoqi Meng, W. Henry Weinberg, James W. Evans
James W. Evans
Various NO‐reduction reactions on Pt(100) exhibit similar dynamical behavior, presumably due to an empty site requirement for NO dissociation. This motivates analysis of a lattice‐gas model which incorporates this feature, and which here is chosen to mimic the NO+CO reaction on Pt(100): both reactants adsorb at single empty sites, NO instantaneously dissociates given an adjacent empty site (and nitrogen adatoms thus formed are immediately removed), and adjacent CO and O instantaneously react. We also include desorption of adsorbed NO and CO, but no adspecies diffusion. At lower temperatures where desorption is absent, we show that ...
Kinetics Of The Monomer-Monomer Surface Reaction Model, 2017 Iowa State University
Kinetics Of The Monomer-Monomer Surface Reaction Model, James W. Evans, T. R. Ray
James W. Evans
The two-dimensional monomer-monomer (AB) surface reaction model without diffusion is considered for infinitesimal, finite, and infinite reaction rates k. For equal reactant adsorption rates, in all cases, simulations reveal the same form of slow poisoning, associated with clustering of reactants. This behavior is also the same as that found in simulations of the two-dimensional voter model studied in interacting-particle systems theory. The voter model can also be obtained from the dimer-dimer or monomer-dimer surface reaction models with infinitesimal reaction rate. We provide a detailed elucidation of the slow poisoning kinetics via an analytic treatment for the k=0+ AB reaction ...
Kinetics Of Restricted Solid-On-Solid Models Of Film Growth, 2017 Iowa State University
Kinetics Of Restricted Solid-On-Solid Models Of Film Growth, James W. Evans, M. C. Bartelt
James W. Evans
We consider the kinetics of irreversible film growth in solid-on-solid models with various restrictions on the adsorption (or growth) sites. We show how the master equations for the probabilities of subconfigurations of filled sites can be analyzed exactly to obtain coverages and spatial correlations for the first several layers. These provide an efficient framework for analysis of the early-stage growth kinetics, and indicate rapid attainment of asymptotic behavior. We illustrate the (1+1)- and (2+1)-dimensional cases for the simplest restricted solid-on-solid condition, and various modifications.
Collisional Transfer Of Population And Orientation In Nak, 2017 Providence College
Collisional Transfer Of Population And Orientation In Nak, Seth T. Ashman, C. M. Wolfe, J. Bai, B. Beser, E. H. Ahmed, A. M. Lyyra, J. Huennekens
Collisional satellite lines with |ΔJ| ≤ 58 have been identified in recent polarization spectroscopy V-type optical–optical double resonance (OODR) excitation spectra of the Rb2 molecule [H. Salami et al., Phys. Rev.A80, 022515 (2009)]. Observation of these satellite lines clearly requires a transfer of population from the rotational level directly excited by the pump laser to a neighboring level in a collision of the molecule with an atomic perturber. However to be observed in polarization spectroscopy, the collision must also partially preserve the angular momentum orientation, which is at least somewhat surprising given the extremely large values of ΔJ that ...
Experimental Studies Of The Nacs 53Π0 And A3Σ+ States, 2017 Providence College
Experimental Studies Of The Nacs 53Π0 And A3Σ+ States, Seth T. Ashman, B. Mcgeehan, C. M. Wolfe, C. Faust, K. Richter
We report high resolution measurements of 372 NaCs 53Π0(v, J) ro-vibrational level energies in the range 0 ≤ v ≤ 22. The data have been used to construct NaCs 53Π0 potential energy curves using the Rydberg–Klein-Rees and inverted perturbation approximation methods. Bound-free 53Π0(v, J) → 1(a)3Σ+ emission has also been measured, and is used to determine the repulsive wall of the 1(a)3Σ+ state and the 53Π0 → 1(a)3Σ+ relative transition dipole moment function. Hyperfine structure in the 53Π0 state has not been observed in this experiment. This null result is explained using a simple vector ...
Functional And Structural Studies Of Cytochromes P450 By Resonance Raman Spectroscopy, 2017 Marquette University
Functional And Structural Studies Of Cytochromes P450 By Resonance Raman Spectroscopy, Yilin Liu
Dissertations (2009 -)
Cytochrome P450 is a broad class of heme monooxygenase enzymes which catalyze various oxidative transformations. There are two main kinds of mammalian P450s: steroidogenic and drug metabolizing P450s. The first project involves a steroidogenic P450, CYP17A1, occupying a central role in the biosynthesis of steroid hormones. It catalyzes hydroxylation reaction on pregnenolone and progesterone, generating 17OH-pregnenolone and 17OH-progesterone, presumably utilizing a “Compound I” species. However, these hydroxylated products can be further processed in a second oxidative cycle to cleave the C17–C20 bond to form dehydroepiandrosterone or androstenedione, respectively, a crucial step in androgen production. Interestingly, it is well known ...
Enhancement Of The Superconducting Gap By Nesting In Cakfe4as4: A New High Temperature Superconductor, 2017 Iowa State University
Enhancement Of The Superconducting Gap By Nesting In Cakfe4as4: A New High Temperature Superconductor, Daixiang Mou, Tai Kong, William R. Meier, Felix Lochner, Lin-Lin Wang, Qisheng Lin, Yun Wu, S. L. Bud’Ko, Ilya Eremin, Duane D. Johnson, Paul C. Canfield, Adam Kaminski
Paul C. Canfield
We use high resolution angle resolved photoemission spectroscopy and density functional theory with measured crystal structure parameters to study the electronic properties of CaKFe4As4. In contrast to the related CaFe2As2 compounds, CaKFe4As4 has a high Tc of 35 K at stochiometric composition. This presents a unique opportunity to study the properties of high temperature superconductivity in the iron arsenides in the absence of doping or substitution. The Fermi surface consists of several hole and electron pockets that have a range of diameters. We find that the values of the superconducting gap are nearly isotropic (within the explored portions of the ...
Tracer Counterpermeation Analysis Of Diffusivity In Finite-Length Nanopores With And Without Single-File Dynamics, David Ackerman, James W. Evans
James W. Evans
We perform a tracer counterpermeation (TCP) analysis for a stochastic model of diffusive transport through a narrow linear pore where passing of species within the pore is inhibited or even excluded (single-file diffusion). TCP involves differently labeled but otherwise identical particles from two decoupled infinite reservoirs adsorbing into opposite ends of the pore, and desorbing from either end. In addition to transient behavior, we assess steady-state concentration profiles, spatial correlations, particle number fluctuations, and diffusion fluxes through the pore. From the profiles and fluxes, we determine a generalized tracer diffusion coefficient Dtr(x), at various positions x within the pore ...
Basic Vision Research With Clinical Applications And Science Education Assessments, 2017 The University of Maine
Basic Vision Research With Clinical Applications And Science Education Assessments, Andrew Wilson
Electronic Theses and Dissertations
Visual Acuity (VA) examinations are one of the most commonly conducted medical assessment throughout the world. Recent advances in computer technology allows for new forms of visual assessment to be conducted. In Part I of this thesis I demonstrate the capability of an automated computer program named VISION to assess human visual acuities. Different color combinations of an object against a background emitted from a computer screen are used to examine a variety of human color vision acuities. Results indicated a large difference in acuity scores between human subjects tested with these different color combinations. A single human subject exhibits ...
Thin Film Thermal Deposition At Various Pressures, 2017 Linfield College
Thin Film Thermal Deposition At Various Pressures, James Kela Yee Keen Grace
This research was to verify the hypothesis that resistivity of metal's thin film deposited in a low-pressure environment is the same as its solid material. Thermal Evaporation is a thin film deposition technique in which metal inside a vacuum is evaporated, then deposited onto a surface. Higher quality metal films are deposited when the vacuum pressure is lower. At higher pressures, more air molecules are trapped within the layers of metal, thus increasing scattering sites and increasing the resistance. However, reaching a lower pressure requires more time and effort. In this research, films were deposited at various pressures and ...