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The Kinematic Apse And Jz‐Preserving Propensities For Nonreactive, Dissociative, And Reactive Polyatomic Collisions, D. K. Hoffman, James W. Evans, D. J. Kouri 2017 Iowa State University

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, James W. Evans 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 2017 Iowa State University

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 2017 Iowa State University

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, H. C. Kang, P. A. Thiel, James W. Evans 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, James W. Evans, H. H. Madden, R. Imbihl 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 2017 Iowa State University

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), Baoqi Meng, W. Henry Weinberg, James W. Evans 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, James W. Evans, T. R. Ray 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, James W. Evans, M. C. Bartelt 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, Seth T. Ashman, C. M. Wolfe, J. BaI, B. Beser, E. H. Ahmed, A. M. Lyyra, J. Huennekens 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

Seth Ashman

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, Seth T. Ashman, B. McGeehan, C. M. Wolfe, C. Faust, K. Richter 2017 Providence College

Experimental Studies Of The Nacs 53Π0 And A3Σ+ States, Seth T. Ashman, B. Mcgeehan, C. M. Wolfe, C. Faust, K. Richter

Seth Ashman

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, Yilin Liu 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 ...


Preliminary Structural Studies Of The Transcriptional Regulator Cmer From Campylobacter Jejuni, Chih-chia Su, Feng Shi, Ruoyu Gu, Ming Li, Gerry McDermott, Edward Yu, Qijing Zhang 2017 Iowa State University

Preliminary Structural Studies Of The Transcriptional Regulator Cmer From Campylobacter Jejuni, Chih-Chia Su, Feng Shi, Ruoyu Gu, Ming Li, Gerry Mcdermott, Edward Yu, Qijing Zhang

Qijing Zhang

In Campylobacter jejuni, a Gram-negative bacterial pathogen causing gastroenteritis in humans, the CmeR regulatory protein controls transcription of the multidrug transporter gene operon cmeABC. CmeR belongs to the TetR family of transcriptional regulators. The 210-residue CmeR consists of two functional motifs: an N-terminal DNA-binding domain and a C-terminal ligand-binding domain. It is predicted that the DNA-binding domain interacts directly with target promoters, while the C-terminal motif interacts with inducing ligands (such as bile salts). As an initial step towards confirming this structural model, recombinant CmeR protein containing a 6×His tag at the N-terminus was crystallized. Crystals of ligand-free CmeR ...


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 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 2017 Iowa State University

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, Andrew Wilson 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 ...


Optimization Of Cardiac Pacing Stimulation By Current Configuration –A Theoretical, Numerical And Experimental Study., Flavio H. Fenton, Hila Dvir, Neil Hardy 2017 Georgia Institute of Technology

Optimization Of Cardiac Pacing Stimulation By Current Configuration –A Theoretical, Numerical And Experimental Study., Flavio H. Fenton, Hila Dvir, Neil Hardy

Biology and Medicine Through Mathematics Conference

No abstract provided.


Building And Validating A Model For Investigating The Dynamics Of Isolated Water Molecules, Grant Cates 2017 Linfield College

Building And Validating A Model For Investigating The Dynamics Of Isolated Water Molecules, Grant Cates

Senior Theses

Understanding how water molecules behave in isolation is vital to understand many fundamental processes in nature. To that end, scientists have begun studying crystals in which single water molecules become trapped in regularly occurring cavities in the crystal structure. As part of that investigation, numerical models used to investigate the dynamics of isolated water molecules are sought to help bolster our fundamental understanding of how these systems behave. To that end, the efficacy of three computational methods—the Euler Method, the Euler-Aspel Method and the Beeman Method—is compared using a newly defined parameter, called the predictive stability coefficient ρ ...


A Study In Cross-Beam Polarization Fluorescence Photoactivation Localization Microscopy On Dendra2-Hemagluttinin In Fixed Nih3t3 Cells, Matthew M. Valles 2017 University of Maine

A Study In Cross-Beam Polarization Fluorescence Photoactivation Localization Microscopy On Dendra2-Hemagluttinin In Fixed Nih3t3 Cells, Matthew M. Valles

Electronic Theses and Dissertations

Fluorescence microscopy is popular for its noninvasive properties and its use in imaging multiple species, simultaneously. Furthermore, superresolution fluorescence microscopy (SRFLM) utilizes photoswitchable proteins to improve the lateral resolution of conventional fluorescence microscopy by an order of magnitude. There is little work conducted on the study of excitation laser polarizations and their effect on the number of localizations as well as the brightness of molecules. This thesis attempts to study the effect of excitation wavelength polarization on the number of localizations and the brightness of molecules by comparing two orientations of circularly-polarized, excitation lasers. The first type of orientation involves ...


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