Physics Commons^™

Pinning The Conformation Of A Protein (Cora) In A Solute Matrix With Selective Binding, Warin Rangubpit, Sunan Kitjaruwankul, Pornthep Sompornpisut, R. B. Pandey

Faculty Publications

Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute–residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach their targeted residue due to their unique interactions with the residues. Degree of slowing down of the protein depends on the interaction strength f. Unlike a predictable dependence of the radius of gyration of the same protein on interaction in an effective medium, it does not show a systematic dependence on interaction due to pinning caused by the solute binding. …

Disorder By Design: A Data-Driven Approach To Amorphous Semiconductors Without Total-Energy Functionals, Dil K. Limbu, Stephen R. Elliott, Raymond Atta-Fynn, Parthapratim Biswas

Faculty Publications

X-ray diffraction, Amorphous silicon, Multi-objective optimization, Monte Carlo methods. This paper addresses a difficult inverse problem that involves the reconstruction of a three-dimensional model of tetrahedral amorphous semiconductors via inversion of diffraction data. By posing the material-structure determination as a multiobjective optimization program, it has been shown that the problem can be solved accurately using a few structural constraints, but no total-energy functionals/forces, which describe the local chemistry of amorphous networks. The approach yields highly realistic models of amorphous silicon, with no or only a few coordination defects (≤1%), a narrow bond-angle distribution of width 9–11.5°, and an electronic gap …

Large And Realistic Models Of Amorphous Silicon, Dale Ingram, Bishal Bhattarai, Parthapratim Biswas, David A. Drabold

Faculty Publications

Amorphous silicon (a-Si) models are analyzed for structural, electronic and vibrational characteristics. Several models of various sizes have been computationally fabricated for this analysis. It is shown that a recently developed structural modeling algorithm known as force-enhanced atomic refinement (FEAR) provides results in agreement with experimental neutron and X-ray diffraction data while producing a total energy below conventional schemes. We also show that a large model (∼ 500 atoms) and a complete basis is necessary to properly describe vibrational and thermal properties. We compute the density for a-Si, and compare with experimental results.

A Selection Rule For Transitions In Pt-Symmetric Quantum Theory, Lawrence R. Mead, David Garfinkle

Faculty Publications

Carl Bender and collaborators have developed a quantum theory governed by Hamiltonians that are PT-symmetric rather than Hermitian. To implement this theory, the inner product was redefined to guarantee positive norms of eigenstates of the Hamiltonian. In the general case, which includes arbitrary time-dependence in the Hamiltonian, a modification of the Schrödinger equation is necessary as shown by Gong and Wang to conserve probability. In this paper, we derive the following selection rule: transitions induced by time dependence in a PT-symmetric Hamiltonian cannot occur between normalized states of differing PT-norm. We show three examples of this selection rule in action: …

Depth Perception, Christopher Sirola

Faculty Publications

In most disciplines, finding the distance from one object to the next is, at least in theory, a simple operation. Not so in astronomy. While the size of Earth itself was determined with a fair degree of accuracy in ancient times, the scale of the solar system wasn’t fully understood until just a few centuries ago, and the distances to even the closest of stars wasn’t reliably determined until Friedrich Bessel measured the distance to 61 Cygni in 1838.

I Love My Baffling, Backward, Counterintuitive, Overly Complicated Magnitudes, Christopher Sirola

Faculty Publications

All professions have their jargon. But astronomy goes the extra parsec. Here’s an example. Vega, one of the brighter stars in the night sky, has an apparent magnitude (i.e., an apparent brightness) of approximately zero. Polaris, the North Star, has an apparent magnitude of about +2. Despite this, Vega appears brighter than Polaris, and not by two, but by a factor of about six times.

Use Of Multiscale Zirconium Alloy Deformation Models In Nuclear Fuel Behavior Analysis, Robert Montgomery, Carlos Tomé, Wenfeng Liu, Alankar Alankar, Gopinath Subramanian, Christopher Stanek

Faculty Publications

Accurate prediction of cladding mechanical behavior is a key aspect of modeling nuclear fuel behavior, especially for conditions of pellet-cladding interaction (PCI), reactivity-initiated accidents (RIA), and loss of coolant accidents (LOCA). Current approaches to fuel performance modeling rely on empirical constitutive models for cladding creep, growth and plastic deformation, which are limited to the materials and conditions for which the models were developed. To improve upon this approach, a microstructurally-based zirconium alloy mechanical deformation analysis capability is being developed within the United States Department of Energy Consortium for Advanced Simulation of Light Water Reactors (CASL). Specifically, the viscoplastic self-consistent (VPSC) …

Inversion Of Diffraction Data For Amorphous Materials, Anup Pandey, Parthapratim Biswas, D.A. Drabold

Faculty Publications

The general and practical inversion of diffraction data–producing a computer model correctly representing the material explored–is an important unsolved problem for disordered materials. Such modeling should proceed by using our full knowledge base, both from experiment and theory. In this paper, we describe a robust method to jointly exploit the power of ab initio atomistic simulation along with the information carried by diffraction data. The method is applied to two very different systems: amorphous silicon and two compositions of a solid electrolyte memory material silver-doped GeSe₃. The technique is easy to implement, is faster and yields results much …

Force-Enhanced Atomic Refinement: Structural Modeling With Interatomic Forces In A Reverse Monte Carlo Approach Applied To Amorphous Si And Sio2, A. Pandey, Parthapratim Biswas, D. A. Drabold

Faculty Publications

We introduce a structural modeling technique, called force-enhanced atomic refinement (FEAR). The technique incorporates interatomic forces in reverse Monte Carlo (RMC) simulations for structural refinement by fitting experimental diffraction data using the conventional RMC algorithm, and minimizes the total energy and forces from an interatomic potential. We illustrate the usefulness of the approach by studying a−SiO₂ and a−Si. The structural and electronic properties of the FEAR models agree well with experimental neutron and x-ray diffraction data and the results obtained from previous molecular dynamics simulations of a−SiO₂ and a−Si. We have shown that the method is more efficient …

Sculpting The Band Gap: A Computational Approach, Kiran Prasai, Parthapratim Biswas, D.A. Drabold

Faculty Publications

Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations.

Relativistic Elastic Differential Cross Sections For Equal Mass Nuclei, Charles M. Werneth, Khin M. Maung, W.P. Ford

Faculty Publications

The effects of relativistic kinematics are studied for nuclear collisions of equal mass nuclei. It is found that the relativistic and non-relativistic elastic scattering amplitudes are nearly indistinguishable, and, hence, the relativistic and non-relativistic differential cross sections become indistinguishable. These results are explained by analyzing the Lippmann–Schwinger equation with the first order optical potential that was employed in the calculation.

A Generalized Force-Modified Potential Energy Surface For Mechanochemical Simulations, Gopinath Subramanian, Nithin Mathew, Jeff Leiding

Faculty Publications

We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G- level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules are blueshifted …

Structural Variation Of Alpha-Synuclein With Temperature By A Coarse-Grained Approach With Knowledge-Based Interactions, Peter Mirau, Barry L. Farmer, Ras B. Pandey

Faculty Publications

Despite enormous efforts, our understanding the structure and dynamics of α-synuclein (ASN), a disordered protein (that plays a key role in neurodegenerative disease) is far from complete. In order to better understand sequence-structure-property relationships in α-SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature (T) with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three …

Self-Assembly Dynamics For The Transition Of A Globular Aggregate To A Fibril Network Of Lysozyme Proteins Via A Coarse-Grained Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer, Bernard S. Gerstman

Faculty Publications

The self-organizing dynamics of lysozymes (an amyloid protein with 148 residues) with different numbers of protein chains, Nc = 1,5,10, and 15(concentration 0.004 – 0.063) is studied by a coarse-grained Monte Carlo simulation with knowledge-based residue-residue interactions. The dynamics of an isolated lysozyme (Nc = 1) is ultra-slow (quasi-static) at low temperatures and becomes diffusive asymptotically on raising the temperature. In contrast, the presence of interacting proteins leads to concentration induced protein diffusion at low temperatures and concentration-tempering sub-diffusion at high temperatures. Variation of the radius of gyration of the protein with temperature shows a …

Impact Of Homogeneous Strain On Uranium Vacancy Diffusion In Uranium Dioxide, Anuj Goyal, Simon R. Phillpot, Gopinath Subramanian, David A. Andersson, Chris R. Stanek, Blas P. Uberuaga

Faculty Publications

We present a detailed mechanism of, and the effect of homogeneous strains on, the migration of uranium vacancies in UO₂. Vacancy migration pathways and barriers are identified using density functional theory and the effect of uniform strain fields are accounted for using the dipole tensor approach. We report complex migration pathways and noncubic symmetry associated with the uranium vacancy in UO₂ and show that these complexities need to be carefully accounted for to predict the correct diffusion behavior of uranium vacancies. We show that under homogeneous strain fields, only the dipole tensor of the saddle with respect …

Lifetime Measurement Of The Cesium 6p3/2 Level Using Ultrafast Pump-Probe Laser Pulses, B. M. Patterson, J. F. Sell, T. Ehrenreich, M. A. Gearba, G. M. Brooke, J. Scoville, R. J. Knize

Faculty Publications

Using the inherent timing stability of pulses from a mode-locked laser, we measure the cesium 6P_3/2 excited-state lifetime. An initial pump pulse excites cesium atoms in two counterpropagating atomic beams to the 6P_3/2 level. A subsequent synchronized probe pulse ionizes atoms that remain in the excited state and the photoions are collected and counted. By selecting pump pulses that vary in time with respect to the probe pulses, we obtain a sampling of the excited-state population in time, resulting in a lifetime value of 30.462(46) ns. The measurement uncertainty (0.15%) is slightly larger than our previous report of …

Momentum Distributions For 2H (E, E' P), William P. Ford, Sabine Jeschonnek, J. W. Van Orden

Faculty Publications

Background: A primary goal of deuteron electrodisintegration is the possibility of extracting the deuteron momentum distribution. This extraction is inherently fraught with difficulty, as the momentum distribution is not an observable and the extraction relies on theoretical models dependent on other models as input.

Purpose: We present a new method for extracting the momentum distribution which takes into account a wide variety of model inputs thus providing a theoretical uncertainty due to the various model constituents. To test the extraction, pseudodata were generated, and the extracted “experimental” distribution, which has theoretical uncertainty accounted by this extraction method, can be compared …

Elastic Differential Cross Sections For Space Radiation Applications, Charles M. Werneth, Khin M. Maung, William P. Ford, John W. Norbury, Michael D. Vera

Faculty Publications

The eikonal, partial wave (PW) Lippmann-Schwinger, and three-dimensional Lippmann-Schwinger (LS3D) methods are compared for nuclear reactions that are relevant for space radiation applications. Numerical convergence of the eikonal method is readily achieved when exact formulas of the optical potential are used for light nuclei (>A≤>16), and the momentum-space representation of the optical potential is used for heavier nuclei. The PW solution method is known to be numerically unstable for systems that require a large number of partial waves, and, as a result, the LS3D method is employed. The effect of relativistic kinematics is studied with the PW and …

Binding Of Solvated Peptide (Eplqlkm) With A Graphene Sheet Via Simulated Coarse-Grained Approach, Somayyeh Sheikholeslami, R. B. Pandey, Nadiya Dragneva, Wely Floriano, Oleg Rubel, Stephen A. Barr, Zhifeng Kuang, Rajiv Berry, Rajesh Naik, Barry Farmer

Faculty Publications

Binding of a solvated peptide A1 (¹E ²P ³L ⁴Q ⁵L ⁶K ⁷M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and …

Conformational Response To Solvent Interaction And Temperature Of A Protein (Histone H3.1) By A Multi-Grained Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer

Faculty Publications

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low …

A Hierarchical Coarse-Grained (All-Atom-To-All-Residue) Computer Simulation Approach: Self-Assembly Of Peptides, Ras B. Pandey, Zhifeng Kuang, Barry L. Farmer

Faculty Publications

A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 (¹H ²S ³S ⁴Y ⁵W ⁶Y ⁷A ⁸F ⁹N ¹⁰N ¹¹K ¹²T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular …

Random Coil To Globular Thermal Response Of A Protein (H3.1) With Three Knowledge-Based Coarse-Grained Potentials, Ras B. Pandey, Barry L. Farmer

Faculty Publications

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (R_g) with the temperature (T) occurs, however, depends on the potential, i.e. ΔT_MJ ≈ 0.013–0.020, ΔT_BT ≈ 0.018–0.026 …

Conformational Temperature-Dependent Behavior Of A Histone H2ax: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials, Miriam Fritsche, Ras B. Pandey, Barry L. Farmer, Dieter W. Heerman

Faculty Publications

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input …

Conformation Of A Coarse-Grained Protein Chain (An Aspartic Acid Protease) Model In Effective Solvent By A Bond-Fluctuating Monte Carlo Simulation, Ras B. Pandey, B.L. Farmer

Faculty Publications

In a coarse-grained description of a protein chain, all of the 20 amino acid residues can be broadly divided into three groups: Hydrophobic (H), polar (P), and electrostatic (E). A protein can be described by nodes tethered in a chain with a node representing an amino acid group. Aspartic acid protease consists of 99 residues in a well-defined sequence of H, P, and E nodes tethered together by fluctuating bonds. The protein chain is placed on a cubic lattice where empty lattice sites constitute an effective solvent medium. The amino groups (nodes) interact with the solvent (S) sites with appropriate …

Real Space Information From Fluctuation Electron Microscopy: Applications To Amorphous Silicon, Parthapratim Biswas, Raymond Atta-Fynn, S. Chakraborty, D. A. Drabold

Faculty Publications

Ideal models of complex materials must satisfy all available information about the system. Generally, this information consists of experimental data, information implicit to sophisticated interatomic interactions and potentially other a priori information. By jointly imposing first-principles or tight-binding information in conjunction with experimental data, we have developed a method: experimentally constrained molecular relaxation (ECMR) that uses all of the information available. We apply the method to model medium range order in amorphous silicon using fluctuation electron microscopy (FEM) data as experimental information. The paracrystalline model of medium range order is examined, and a new model based on voids in amorphous …

Relativistic Multiple Scattering Theory And The Relativistic Impulse Approximation, Khin Maung Maung, John W. Norbury, Trina Coleman

Faculty Publications

It is shown that a relativistic multiple scattering theory for hadron - nucleus scattering can be consistently formulated in four dimensions in the context of meson exchange. We give a multiple scattering series for the optical potential and discuss the differences between the relativistic and non- relativistic versions. We develop the relativistic multiple scattering series by separating out the one-boson exchange term from the rest of the Feynman series. However, this particular separation is not absolutely necessary and we discuss how to include other terms. We then show how to make a three- dimensional reduction for hadron - nucleus scattering …

Experimentally Constrained Molecular Relaxation: The Case Of Hydrogenated Amorphous Silicon, Parthapratim Biswas, Raymond Atta-Fynn, D. A. Drabold

Faculty Publications

We have extended our experimentally constrained molecular relaxation technique [P. Biswas et al., Phys. Rev. B 71, 54204 (2005)] to hydrogenated amorphous silicon: a 540-atom model with 7.4% hydrogen and a 611-atom model with 22% hydrogen were constructed. Starting from a random configuration, using physically relevant constraints, ab initio interactions, and the experimental static structure factor, we construct realistic models of hydrogenated amorphous silicon. Our models confirm the presence of a high-frequency localized band in the vibrational density of states due to Si-H vibration that has been observed in recent vibrational transient grating measurements on plasma enhanced chemical …

Measurement Of Population Dynamics In Stimulated Raman Adiabatic Passage, Alina Gearba, H. A. Camp, M. L. Trachy, G. Veshapidze, M.H. Shah, H.U. Jang, B.D. Depaola

Faculty Publications

The temporal evolution of populations has been directly measured for a three-level ladder system undergoing coherent excitation by stimulated Raman adiabatic passage (STIRAP). The measurement technique makes use of charge transfer as diagnostic. The method is model independent and has a temporal resolution of a few nanoseconds. The temporal evolution is measured for several values of the delay between the pump and Stokes laser pulses that are part of the STIRAP excitation scheme. The corresponding quantum Liouville equations are solved and the results of the calculations are compared with experiment.

Multiscale Mode Dynamics Of A Tethered Membrane, Ras B. Pandey, Kelly L. Anderson, B. L. Farmer

Faculty Publications

Stochastic dynamics of a tethered membrane with a bond-fluctuating coarse-grained Monte Carlo simulation shows, in addition to diffusion, nondiffusive behavior sensitive to the type of membrane, its size, and quality of the solvent. Motion of the membrane’s center node is described by the variation of the mean-square displacement (R_2n) with time step (t), i.e., R_2n∝t2ν with the exponent ν≃1/8−1∕6 in the short time followed by subdiffusive power laws (i.e., ν∼1∕5, 1∕10) in the intermediate time regimes before reaching diffusion ν=1. The crossover between in-plane wrinkle modes is identified from the segmental (node) motion of the membrane.

Model-Independent Measurement Of The Excited Fraction In A Magneto-Optical Trap, M. H. Shah, H. A. Camp, M. L. Trachy, G. Veshapidze, M.A. Gearba, B.D. Depaola

Faculty Publications

In many experiments involving a magneto-optical trap (MOT) it is of great importance to know the fraction of atoms placed in an excited state due to the trapping process. Generally speaking, researchers have had to use overly simplistic and untested models to estimate this fraction. In this work, the excited fractions of ⁸⁷Rb atoms in a MOT are directly measured using a charge transfer technique, for a range of MOT parameters. Simple models are then fit to the measured fractions. Using the results of this work, the excited fraction of ⁸⁷Rb atoms trapped in a MOT can be …