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Full-Text Articles in Physics

Comparison Of S-Adsorption On (111) And (100) Facets Of Cu Nanoclusters, Jeffrey S. Boschen, Jiyoung Lee, Theresa L. Windus, James W. Evans, Patricia A. Thiel, Da-Jiang Liu Oct 2016

Comparison Of S-Adsorption On (111) And (100) Facets Of Cu Nanoclusters, Jeffrey S. Boschen, Jiyoung Lee, Theresa L. Windus, James W. Evans, Patricia A. Thiel, Da-Jiang Liu

Physics and Astronomy Publications

In order to gain insight into the nature of chemical bonding of sulfur atoms on coinage metal surfaces, we compare the adsorption energy and structural parameters for sulfur at four-fold hollow (4fh) sites on (100) facets and at three-fold hollow (3fh) sites on (111) facets of Cu nanoclusters. Consistent results are obtained from localized atomic orbital and plane-wave based density functional theory using the same functionals. PBE and its hybrid counterpart (PBE0 or HSE06) also give similar results. 4fh sites are preferred over 3fh sites with stronger bonding by ∼0.6 eV for nanocluster sizes above ∼280 atoms. However, for ...


Discontinuous Non-Equilibrium Phase Transition In A Threshold Schloegl Model For Autocatalysis: Generic Two-Phase Coexistence And Metastability, Chi-Jen Wang, Da-Jiang Liu, James W. Evans Apr 2015

Discontinuous Non-Equilibrium Phase Transition In A Threshold Schloegl Model For Autocatalysis: Generic Two-Phase Coexistence And Metastability, Chi-Jen Wang, Da-Jiang Liu, James W. Evans

Physics and Astronomy Publications

Threshold versions of Schloegl's model on a lattice, which involve autocatalytic creation and spontaneous annihilation of particles, can provide a simple prototype for discontinuous non-equilibrium phase transitions. These models are equivalent to so-called threshold contact processes. A discontinuous transition between populated and vacuum states can occur selecting a threshold of N ≥ 2 for the minimum number, N, of neighboring particles enabling autocatalytic creation at an empty site. Fundamental open questions remain given the lack of a thermodynamic framework for analysis. For a square lattice with N = 2, we show that phase coexistence occurs not at a unique value but ...


Crystal Structure Of The Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology, Jani Reddy Bolla, Chih-Chia Su, Jared A. Delmar, Pattathil Radhakrishnan, Nitin Kumar, Tsung-Han Chou, Feng Long, Kanagalaghatta R. Rajashankar, Edward Yu Jan 2015

Crystal Structure Of The Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology, Jani Reddy Bolla, Chih-Chia Su, Jared A. Delmar, Pattathil Radhakrishnan, Nitin Kumar, Tsung-Han Chou, Feng Long, Kanagalaghatta R. Rajashankar, Edward Yu

Physics and Astronomy Publications

The potential of the folic acid biosynthesis pathway as a target for the development of antibiotics has been clinically validated. However, many pathogens have developed resistance to these antibiotics, prompting a re-evaluation of potential drug targets within the pathway. The ydaH gene of Alcanivorax borkumensis encodes an integral membrane protein of the AbgT family of transporters for which no structural information was available. Here we report the crystal structure of A. borkumensis YdaH, revealing a dimeric molecule with an architecture distinct from other families of transporters. YdaH is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm to ...


Statistical Mechanical Models For Dissociative Adsorption Of O2 On Metal(100) Surfaces With Blocking, Steering, And Funneling, Da-Jiang Liu, James W. Evans May 2014

Statistical Mechanical Models For Dissociative Adsorption Of O2 On Metal(100) Surfaces With Blocking, Steering, And Funneling, Da-Jiang Liu, James W. Evans

Physics and Astronomy Publications

We develop statistical mechanical models amenable to analytic treatment for the dissociative adsorption of O2 at hollow sites on fcc(100) metal surfaces. The models incorporate exclusion of nearest-neighbor pairs of adsorbed O. However, corresponding simple site-blocking models, where adsorption requires a large ensemble of available sites, exhibit an anomalously fast initial decrease in sticking. Thus, in addition to blocking, our models also incorporate more facile adsorption via orientational steering and funneling dynamics (features supported by ab initio Molecular Dynamics studies). Behavior for equilibrated adlayers is distinct from those with finite adspecies mobility. We focus on the low-temperature limited-mobility regime ...


Controlling Reactivity Of Nanoporous Catalyst Materials By Tuning Reaction Product-Pore Interior Interactions: Statistical Mechanical Modeling, Jing Wang, David M. Ackerman, Victor S.-Y. Lin, Marek Pruski, James W. Evans Jan 2013

Controlling Reactivity Of Nanoporous Catalyst Materials By Tuning Reaction Product-Pore Interior Interactions: Statistical Mechanical Modeling, Jing Wang, David M. Ackerman, Victor S.-Y. Lin, Marek Pruski, James W. Evans

Physics and Astronomy Publications

Statistical mechanical modeling is performed of a catalytic conversion reaction within a functionalized nanoporous material to assess the effect of varying the reaction product-pore interior interaction from attractive to repulsive. A strong enhancement in reactivity is observed not just due to the shift in reaction equilibrium towards completion but also due to enhanced transport within the pore resulting from reduced loading. The latter effect is strongest for highly restricted transport (single-file diffusion), and applies even for irreversible reactions. The analysis is performed utilizing a generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction ...


Generalized Hydrodynamic Treatment Of The Interplay Between Restricted Transport And Catalytic Reactions In Nanoporous Materials, David M. Ackerman, Jing Wang, James W. Evans Jun 2012

Generalized Hydrodynamic Treatment Of The Interplay Between Restricted Transport And Catalytic Reactions In Nanoporous Materials, David M. Ackerman, Jing Wang, James W. Evans

Physics and Astronomy Publications

Behavior of catalytic reactions in narrow pores is controlled by a delicate interplay between fluctuations in adsorption-desorption at pore openings, restricted diffusion, and reaction. This behavior is captured by a generalized hydrodynamic formulation of appropriate reaction-diffusion equations (RDE). These RDE incorporate an unconventional description of chemical diffusion in mixed-component quasi-single-file systems based on a refined picture of tracer diffusion for finite-length pores. The RDE elucidate the nonexponential decay of the steady-state reactant concentration into the pore and the non-mean-field scaling of the reactant penetration depth.


Boundary Conditions For Burton–Cabrera–Frank Type Step-Flow Models: Coarse-Graining Of Discrete 2d Deposition-Diffusion Equations, David M. Ackerman, James W. Evans Jan 2011

Boundary Conditions For Burton–Cabrera–Frank Type Step-Flow Models: Coarse-Graining Of Discrete 2d Deposition-Diffusion Equations, David M. Ackerman, James W. Evans

Physics and Astronomy Publications

We analyze discrete two-dimensional (2D) deposition-diffusion equations for the density of adatoms deposited at a periodic array of adsorption sites on a vicinal crystalline surface with kinked steps. Our analysis provides insight into the appropriate boundary conditions (BC) at steps for a coarse-grained Burton-Cabrera-Frank (BCF) type treatment involving continuum 2D deposition-diffusion equations. Such a BCF type treatment should describe step flow on vicinal surfaces under nonequilibrium growth conditions. We focus on cases where there is no additional activation barrier inhibiting to attachment at steps beyond that for terrace diffusion. Then, the classical BCF treatment simply imposes a Dirichlet BC equating ...


Catalytic Conversion Reactions Mediated By Single-File Diffusion In Linear Nanopores: Hydrodynamic Versus Stochastic Behavior, David M. Ackerman, Jing Wang, Joseph H. Wendel, Da-Jiang Liu, Marek Pruski, James W. Evans Jan 2011

Catalytic Conversion Reactions Mediated By Single-File Diffusion In Linear Nanopores: Hydrodynamic Versus Stochastic Behavior, David M. Ackerman, Jing Wang, Joseph H. Wendel, Da-Jiang Liu, Marek Pruski, James W. Evans

Physics and Astronomy Publications

We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. Diffusion within the pores is subject to a strict single-file (no passing) constraint. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice–gas model for this reaction–diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction–diffusion type equations (mf-RDE). For slowly varying concentrations, we ...


Polymer Length Distributions For Catalytic Polymerization Within Mesoporous Materials: Non-Markovian Behavior Associated With Partial Extrusion, Da-Jiang Liu, Hung-Ting Chen, Victor S.-Y. Lin, James W. Evans Jan 2010

Polymer Length Distributions For Catalytic Polymerization Within Mesoporous Materials: Non-Markovian Behavior Associated With Partial Extrusion, Da-Jiang Liu, Hung-Ting Chen, Victor S.-Y. Lin, James W. Evans

Physics and Astronomy Publications

We analyze a model for polymerization at catalytic sites distributed within parallel linear pores of a mesoporous material. Polymerization occurs primarily by reaction of monomers diffusing into the pores with the ends of polymers near the pore openings. Monomers and polymers undergo single-file diffusion within the pores. Model behavior, including the polymer length distribution, is determined by kinetic Monte Carlo simulation of a suitable atomistic-level lattice model. While the polymers remain within the pore, their length distribution during growth can be described qualitatively by a Markovian rate equation treatment. However, once they become partially extruded, the distribution is shown to ...


Binding And Diffusion Of Al Adatoms And Dimers On The Si(100)-2 × 1 Reconstructed Surface: A Hybrid Qm/Mm Embedded Cluster Study, Deborah Zorn, Marvin Argulla Albao, James W. Evans, Mark S. Gordon Apr 2009

Binding And Diffusion Of Al Adatoms And Dimers On The Si(100)-2 × 1 Reconstructed Surface: A Hybrid Qm/Mm Embedded Cluster Study, Deborah Zorn, Marvin Argulla Albao, James W. Evans, Mark S. Gordon

Physics and Astronomy Publications

When group III metals are deposited onto the Si(100)-2 × 1 reconstructed surface they are observed to self-assemble into chains of atoms that are one atom high by one atom wide. To better understand this one-dimensional island growth, ab initio electronic structure calculations on the structures of Al atoms on silicon clusters have been performed. Natural orbital occupation numbers show that these systems display significant diradical character, suggesting that a multireference method is needed. A multiconfiguration self-consistent field (MCSCF) calculation with a 6-31G(d) basis set and effective core potentials was used to optimize geometries. The surface integrated molecular ...


Some Properties Of F And E-Aggregate Centers In Cesium Halides*, David W. Lynch, A. D. Brothers, D. A. Robinson Jul 1965

Some Properties Of F And E-Aggregate Centers In Cesium Halides*, David W. Lynch, A. D. Brothers, D. A. Robinson

Physics and Astronomy Publications

Measurements of the absorption spectrum of F centers in CsI reveal structure similar to that of the F band in CsBr. Bands like the L bands in other alkali halides have been observed in CsBr and CsI. In CsBr these L bands exhibit structure similar to that of the CsBr F band. The emission of F centers in CsCl, CsBr, and CsI has been measured. The emission spectra are double Gaussian, peaking at 1.255, 0.910, and 0.740 eV in CsCl, CsBr, and CsI, respectively. The full widths at half-maximum are 0.245, 0.184, and 0.140 ...


Linear Thermal Expansion Coefficient Of The Nacl Phase Of Cscl, J. M. Christian, David W. Lynch Jan 1964

Linear Thermal Expansion Coefficient Of The Nacl Phase Of Cscl, J. M. Christian, David W. Lynch

Physics and Astronomy Publications

Cesium chloride undergoes a phase change from the low-temperature CsCI structure to the high-temperature NaCI structure at about 469°C.l There is a volume increase of about 16% when the NaCI structure appears.1 The nature of the transition is of interest, as are the physical properties of the high-temperature phase. If sufficient high-temperature phase data are available for CsCI, calculations of the heat of transition can be made more accurately.