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Articles 1 - 27 of 27
Full-Text Articles in Physics
Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel
Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel
Honors Scholar Theses
Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Chemistry: Faculty Publications and Other Works
Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …
Computational Studies Of Thermal Properties And Desalination Performance Of Low-Dimensional Materials, Yang Hong
Department of Chemistry: Dissertations, Theses, and Student Research
During the last 30 years, microelectronic devices have been continuously designed and developed with smaller size and yet more functionalities. Today, hundreds of millions of transistors and complementary metal-oxide-semiconductor cells can be designed and integrated on a single microchip through 3D packaging and chip stacking technology. A large amount of heat will be generated in a limited space during the operation of microchips. Moreover, there is a high possibility of hot spots due to non-uniform integrated circuit design patterns as some core parts of a microchip work harder than other memory parts. This issue becomes acute as stacked microchips get …
Real-Time Observation Of Molecular Spinning With Angular High-Harmonic Spectroscopy, Lixin He, Pengfei Lan, Anh-Thu Le, Baoning Wang, Bincheng Wang, Xiaosong Zhu, Peixiang Lu, C. D. Lin
Real-Time Observation Of Molecular Spinning With Angular High-Harmonic Spectroscopy, Lixin He, Pengfei Lan, Anh-Thu Le, Baoning Wang, Bincheng Wang, Xiaosong Zhu, Peixiang Lu, C. D. Lin
Physics Faculty Research & Creative Works
We demonstrate an angular high-harmonic spectroscopy method to probe the spinning dynamics of a molecular rotation wave packet in real time. With the excitation of two time-delayed, polarization-skewed pump pulses, the molecular ensemble is impulsively kicked to rotate unidirectionally, which is subsequently irradiated by another delayed probe pulse for high-order harmonic generation (HHG). The spatiotemporal evolution of the molecular rotation wave packet is visualized from the time-dependent angular distributions of the HHG yields and frequency shift measured at various polarization directions and time delays of the probe pulse. The observed frequency shift in HHG is demonstrated to arise from the …
Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru
Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru
University Scholar Projects
Though eradicated in most of the world, poliovirus remains a common model virus for a family of mammalian viruses known as Picornaviruses. Despite the development of a vaccination, little is understood about the infection process, particularly the mechanism of cell entry. Experimental studies have attempted to elucidate the dynamics of this process and have proposed pathways focused on VP4, the smallest of the four peptides which makes up the viral capsid, and its interaction with the pentameric interfaces of the five fold axes. This study utilizes coarse-grained molecular dynamics to supplement these proposed mechanisms with simplified simulations which reduce the …
Hard-Sphere-Like Dynamics In Highly Concentrated Alpha-Crystallin Suspensions, Preeti Vodnala, Laurence Lurio, Michael C. Vega, Elizabeth Gaillard
Hard-Sphere-Like Dynamics In Highly Concentrated Alpha-Crystallin Suspensions, Preeti Vodnala, Laurence Lurio, Michael C. Vega, Elizabeth Gaillard
Faculty Peer-Reviewed Publications
The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.
Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw
Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw
Physics Faculty Publications and Presentations
Patra et al. [Int. J. Bifurcat. Chaos 26, 1650089 (2016)] recently showed that the time-averaged rates of entropy production and phase-space volume contraction are equal for several different molecular dynamics methods used to simulate nonequilibrium steady states in Hamiltonian systems with thermostated temperature gradients. This equality is a plausible statistical analog of the second law of thermodynamics. Here we show that those two rates are identically equal in a wide class of methods in which the thermostat variables z are determined by ordinary differential equations of motion (i.e., methods of the Nosé-Hoover or integral feedback control type). This …
Scaling And Alpha-Helix Regulation Of Protein Relaxation In A Lipid Bilayer, Liming Qiu, Creighton Buie, Kwan H. Cheng, Mark W. Vaughn
Scaling And Alpha-Helix Regulation Of Protein Relaxation In A Lipid Bilayer, Liming Qiu, Creighton Buie, Kwan H. Cheng, Mark W. Vaughn
Physics and Astronomy Faculty Research
Protein conformation and orientation in the lipid membrane plays a key role in many cellular processes. Here we use molecular dynamics simulation to investigate the relaxation and C-terminus diffusion of a model helical peptide: beta-amyloid (Aβ) in a lipid membrane.We observed that after the helical peptide was initially half-embedded in the extracelluar leaflet of phosphatidylcholine (PC) or PC/cholesterol (PC/CHOL) membrane, the C-terminus diffused across the membrane and anchored to PC headgroups of the cytofacial lipid leaflet. In some cases, the membrane insertion domain of the Aβ was observed to partially unfold. Applying a sigmoidal fit to the process, we found …
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
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 …
Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi
Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi
FIU Electronic Theses and Dissertations
Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions …
Lattice Thermal Conductivity In Bulk And Nanosheet Naxcoo2, Denis Demchenko, David B. Ameen
Lattice Thermal Conductivity In Bulk And Nanosheet Naxcoo2, Denis Demchenko, David B. Ameen
Physics Publications
In this paper we present the results of calculations of the lattice thermal conductivity of layered complex metal oxide NaxCoO2 within the Green–Kubo theory. Using NaxCoO2 we identify the two competing mechanisms responsible for the favorable scaling properties of the Green–Kubo method for calculating the lattice thermal conductivity. The artificial correlations of the heat flux fluctuations due to the finite size of the supercells are partially cancelled by the missing long wavelength acoustic phonon modes. We compute the lattice thermoelectric properties of bulk NaxCoO2 with varying stoichiometry, structural defects, and temperature. …
Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell
Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell
Faculty Publications
We formulate low Mach number fluctuating hydrodynamic equations appropriate for modeling diffusive mixing in isothermal mixtures of fluids with different density and transport coefficients. These equations eliminate the fast isentropic fluctuations in pressure associated with the propagation of sound waves by replacing the equation of state with a local thermodynamic constraint. We demonstrate that the low Mach number model preserves the spatio-temporal spectrum of the slower diffusive fluctuations. We develop a strictly conservative finite-volume spatial discretization of the low Mach number fluctuating equations in both two and three dimensions. We construct several explicit Runge-Kutta temporal integrators that strictly maintain the …
Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier
Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier
Bioelectrics Publications
Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensively in biology, biotechnology, and medicine, its molecular mechanism is not well understood. This lack of knowledge limits the ability to control and fine-tune the process. In this article we propose a novel molecular mechanism for the electroporation of a lipid bilayer based on energetics analysis. Using molecular dynamics simulations we demonstrate that …
Molecular Dynamics Simulations Reveal The Protective Role Of Cholesterol In Β-Amyloid Protein-Induced Membrane Disruptions In Neuronal Membrane Mimics, Liming Qiu, Creighton Buie, Andrew Reay, Mark W. Vaughn, Kwan H. Cheng
Molecular Dynamics Simulations Reveal The Protective Role Of Cholesterol In Β-Amyloid Protein-Induced Membrane Disruptions In Neuronal Membrane Mimics, Liming Qiu, Creighton Buie, Andrew Reay, Mark W. Vaughn, Kwan H. Cheng
Physics and Astronomy Faculty Research
Interactions of β-amyloid (Aβ) peptides with neuronal membranes have been associated with the pathogenesis of Alzheimer's disease (AD); however, the molecular details remain unclear. We used atomistic molecular dynamics (MD) simulations to study the interactions of Aβ40 and Aβ42 with model neuronal membranes. The differences between cholesterol-enriched and depleted lipid domains were investigated by the use of model phosphatidylcholine (PC) lipid bilayers with and without 40 mol % cholesterol. A total of 16 independent 200 ns simulation replicates were investigated. The surface area per lipid, bilayer thickness, water permeability barrier, and lipid order parameter, which are sensitive indicators …
Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon
Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon
Chemistry and Biochemistry Faculty Research
We present a combined theoretical and experimental study of molecular field effects on molecular core levels. Polarization-dependent resonant inelastic x-ray scattering is observed experimentally after resonant K-shell excitation of CF3Cl and HCl. We explain the linear dichroism observed in spin-orbit level intensities as due to molecular field effects, including singlet-triplet exchange, and interpret this behavior in terms of population differences in the 2px,y,z inner-shell orbitals. We investigate theoretically the different factors that can affect the electronic populations and the dynamical R dependence of the spin-orbit ratio. Finally, the results obtained are used to interpret the L-shell …
Young-Type Interference In (E, 2e) Ionization Of H₂, D. S. Milne-Brownlie, Matthew S. Foster, Junfang Gao, B. Lohmann, Don H. Madison
Young-Type Interference In (E, 2e) Ionization Of H₂, D. S. Milne-Brownlie, Matthew S. Foster, Junfang Gao, B. Lohmann, Don H. Madison
Physics Faculty Research & Creative Works
We have investigated the electron impact single ionization of the hydrogen molecule, with fully determined kinematics. The experimental and theoretical results are compared with He ionization under the same conditions. The results indicate that the ejected electron angular distribution for H2 is modified due to Young-type interference between ionization amplitudes for scattering from the two centers in the hydrogen molecule. The observable result is a suppression of the backward scattering (recoil) peak compared with the binary peak.
Erratum: "Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes", Pavel Smejtek, Robert Campbell Word
Erratum: "Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes", Pavel Smejtek, Robert Campbell Word
Physics Faculty Publications and Presentations
Presents correction to an article related to configurational entropy in transfer of small molecules from water into alkanes, published in the 2005 issue of "The Journal Chemical Physics" and is available online at: http://archives.pdx.edu/ds/psu/8364
Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes, Pavel Smejtek, Robert Campbell Word
Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes, Pavel Smejtek, Robert Campbell Word
Physics Faculty Publications and Presentations
We studied the effect of segmented solvent molecules on the free energy of transfer of small molecules from water into alkanes (hexane, heptane, octane, decane, dodecane, tetradecane, and hexadecane). For these alkanes we measured partition coefficients of benzene, 3-methylindole (3MI), 2,3,4,6-tetrachlorophenol (TeCP), and 2,4,6-tribromophenol (TriBP) at 3, 11, 20, 3, and 47 °C. For 3MI, TeCP, and TriBP the dependence of free energy of transfer on length of alkane chains was found to be very different from that for benzene. In contrast to benzene, the energy of transfer for 3MI, TeCP, and TriBP was independent of the number of carbons …
Temperature Dependence Of Droplet Nucleation In A Yukawa Fluid, Jinsong Li, Gerald Wilemski
Temperature Dependence Of Droplet Nucleation In A Yukawa Fluid, Jinsong Li, Gerald Wilemski
Physics Faculty Research & Creative Works
We have studied the temperature dependence of gas-to-liquid nucleation in Yukawa fluids with gradient theory and density functional theory. Each of these nonclassical theories exhibits a weaker (i.e., better) temperature dependence than classical nucleation theory. At fixed temperature, the reversible work to form a critical nucleus found from gradient theory approaches the value given by density functional theory as the supersaturation increases. At high temperatures, the two theories remain quite close over a wide range of vapor densities. As the temperature is reduced, the difference between the two theories increases with decreasing vapor density. Compared to the classical theory we …
Local Versus Nonlocal Order-Parameter Field Theories For Quantum Phase Transitions, Dietrich Belitz, Theodore R. Kirkpatrick, Thomas Vojta
Local Versus Nonlocal Order-Parameter Field Theories For Quantum Phase Transitions, Dietrich Belitz, Theodore R. Kirkpatrick, Thomas Vojta
Physics Faculty Research & Creative Works
General conditions are formulated that allow us to determine which quantum phase transitions in itinerant electron systems can be described by a local Landau-Ginzburg-Wilson (LGW) theory solely in terms of the order parameter. A crucial question is the degree to which the order parameter fluctuations couple to other soft modes. Three general classes of zero-wave-number order parameters, in the particle-hole spin-singlet and spin-triplet channels and in the particle-particle channel, respectively, are considered. It is shown that the particle-hole spin-singlet class does allow for a local LGW theory, while the other two classes do not. The implications of this result for …
Short-Pulse Laser-Induced Stabilization Of Autoionizing States, Heider N. Ereifej, J. Greg Story
Short-Pulse Laser-Induced Stabilization Of Autoionizing States, Heider N. Ereifej, J. Greg Story
Physics Faculty Research & Creative Works
Atoms in doubly excited states above the first ionization limit can decay via autoionization in which an electron is emitted leaving an ion, or by photoemission which leaves the atom in a singly excited state. In this paper, it is demonstrated that interaction between the atoms and a laser pulse that is short compared to the autoionization lifetime can lead to large enhancement of the photoemission process by stimulating the atoms to emit a photon. Since the resultant singly excited atoms do not autoionize, this process can be viewed as an enhancement of the stabilization of the doubly excited atoms …
Decay Of Molecules At Spherical Surfaces: Nonlocal Effects, P.T. Leung
Decay Of Molecules At Spherical Surfaces: Nonlocal Effects, P.T. Leung
Physics Faculty Publications and Presentations
The decay rates for molecules in the vicinity of a metallic sphere are investigated in a phenomenological approach for very close molecule-surface distances d. The Fuchs-Claro model [Phys. Rev. B 35, 3722 (1987)] is adopted to describe the polarizability of the sphere with the nonlocal dielectric response being accounted for within the hydrodynamic description. The results show significant differences when compared with those obtained previously within a local description for dlsim50 Aring, with extra resonances observed in the high-frequency regime, a phenomenon similar to that noted previously by Ruppin (1982), in his calculation of the extinction cross section for such …
The Spectroscopy And Molecular Dynamics Of The High Frequency Ν1 6 Intermolecular Vibrations In Hcn‐‐‐Hf And Dcn‐‐‐Df, B. A. Wofford, M. W. Jackson, Shannon Lieb, J. W. Bevan
The Spectroscopy And Molecular Dynamics Of The High Frequency Ν1 6 Intermolecular Vibrations In Hcn‐‐‐Hf And Dcn‐‐‐Df, B. A. Wofford, M. W. Jackson, Shannon Lieb, J. W. Bevan
Scholarship and Professional Work - LAS
Gas phase rovibrational analysis of the high frequency intermolecular hydrogen bonded bending overtone 2ν0 6 [ν0=1132.4783(2) cm− 1] in HCN‐‐‐HF and its corresponding perdeuterated fundamental ν1 6 [ν0=409.1660(2) cm− 1] are reported. Evaluated rovibrational parameters provide the basis for quantitative modeling of the molecular dynamics associated with this vibration. A quantum mechanical calculation permits determination of the quadratic and quartic force constants K 6 6=537(17) and K 6 6 6 6=4.98(12) cm− 1 which in turn are used to estimate the pertinent cubic band stretching interaction constants …
Energy-Transfer Theory For The Classical Decay Rates Of Molecules At Rough Metallic Surfaces, P.T. Leung, Thomas F. George
Energy-Transfer Theory For The Classical Decay Rates Of Molecules At Rough Metallic Surfaces, P.T. Leung, Thomas F. George
Physics Faculty Publications and Presentations
The problem of the decay rates for molecules at rough metallic surfaces is considered, where the classical electromagnetic energy-transfer theory of Chance, Prock, and Silbey for a flat surface is generalized to the case of a rough boundary. A dynamical theory is constructed through the combination of the Sommerfeld antenna theory and the integral equation formalism of Maxwell's equations at rough boundaries established mainly by Maradudin, Mills, and Agarwal. Perturbative solutions are obtained and numerical results are given with reference to a shallow sinusoidal grating surface. The results, when compared with those obtained previously from the application of the image …
Molecular Dynamics In Hydrogen‐Bonded Interactions: A Preliminary Experimentally Determined Harmonic Stretching Force Field For Hcn‐‐‐Hf, B. A. Wofford, Shannon Lieb, J. W. Bevan
Molecular Dynamics In Hydrogen‐Bonded Interactions: A Preliminary Experimentally Determined Harmonic Stretching Force Field For Hcn‐‐‐Hf, B. A. Wofford, Shannon Lieb, J. W. Bevan
Scholarship and Professional Work - LAS
Observation of the 2ν1 overtone band in the hydrogen‐bonded complex HCN‐‐‐HF permits evaluation of the anharmonicity constant X 1 1=−116.9(1) cm− 1 and determination of the anharmonicity corrected fundamental frequency ω1. This information, and available data from previous rovibrational analyses in the common and perdeuterated isotopic species of HCN‐‐‐HF, offer an opportunity for calculation of an approximate stretching harmonic force field. With the assumptions f 1 2=f 2 4=0.0, the remaining force constants (in mdyn/Å) are evaluated as: f 1 1=8.600(20), f 2 2=6.228(9), f 3 3=19.115(40), f 4 …
An Approximate Variational Method For Improved Thermodynamics Of Molecular Fluids, M. S. Shaw, J. D. Johnson, John D. Ramshaw
An Approximate Variational Method For Improved Thermodynamics Of Molecular Fluids, M. S. Shaw, J. D. Johnson, John D. Ramshaw
Physics Faculty Publications and Presentations
For a certain class of thermodynamic perturbation theories, a generalization of the Gibbs-Bogoliubov inequality holds through second order of perturbation theory and for a subset of terms the inequality is true to infinite order. Using this approximate variational principle, a perturbation theory is chosen for which the Helmholtz free energy of the reference system is minimized under the constraint that the first order term is identically zero. We apply these ideas to the determination of effective spherical potentials that accurately reproduce the thermodynamics of nonspherical molecular potentials. For a diatomic-Lennard-Jones (DLJ) potential with l ∕σ = 0.793, the resulting spherical …
Brownian Motion In A Flowing Fluid, John D. Ramshaw
Brownian Motion In A Flowing Fluid, John D. Ramshaw
Physics Faculty Publications and Presentations
A phenomenological theory is developed for Brownian motion in a flowing incompressible fluid. The Brownian particles are regarded as an ideal gas subject to a position- and time-dependent force field that represents interactions with the host fluid. This approach immediately leads to deterministic partial differential equations of motion for the Brownian particles. These equations are then examined in the limit of large friction, in which they imply an expression for the diffusional mass flux of Brownian particles. This expression is a sum of terms representing concentration, forced, thermal, and pressure diffusion. Comparisons are made with earlier work, and with the …