Current Search: Berg, Bernd A. (x)
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 Title
 A Brief History Of The Introduction Of Generalized Ensembles To Markov Chain Monte Carlo Simulations.
 Creator

Berg, Bernd A.
 Abstract/Description

The most efficient weights for Markov chain Monte Carlo calculations of physical observables are not necessarily those of the canonical ensemble. Generalized ensembles, which do not exist in nature but can be simulated on computers, lead often to a much faster convergence. In particular, they have been used for simulations of first order phase transitions and for simulations of complex systems in which conflicting constraints lead to a rugged free energy landscape. Starting off with the...
Show moreThe most efficient weights for Markov chain Monte Carlo calculations of physical observables are not necessarily those of the canonical ensemble. Generalized ensembles, which do not exist in nature but can be simulated on computers, lead often to a much faster convergence. In particular, they have been used for simulations of first order phase transitions and for simulations of complex systems in which conflicting constraints lead to a rugged free energy landscape. Starting off with the Metropolis algorithm and Hastings' extension, I present a minireview which focuses on the explosive use of generalized ensembles in the early 1990s. Illustrations are given, which range from spin models to peptides.
Show less  Date Issued
 201704
 Identifier
 FSU_libsubv1_wos_000399440100003, 10.1140/epjst/e2016602362
 Format
 Citation
 Title
 Topological Charge And Cooling Scales In Pure Su(2) Lattice Gauge Theory.
 Creator

Berg, Bernd A., Clarke, David A.
 Abstract/Description

Using Monte Carlo simulations with overrelaxation, we have equilibrated lattices up to beta = 2.928, size 60(4), for pure SU(2) lattice gauge theory with the Wilson action. We calculate topological charges with the standard cooling method and find that they become more reliable with increasing beta values and lattice sizes. Continuum limit estimates of the topological susceptibility chi are obtained of which we favor chi(1/4)/Tc = 0.643(12), where Tc is the SU(2) deconfinement temperature....
Show moreUsing Monte Carlo simulations with overrelaxation, we have equilibrated lattices up to beta = 2.928, size 60(4), for pure SU(2) lattice gauge theory with the Wilson action. We calculate topological charges with the standard cooling method and find that they become more reliable with increasing beta values and lattice sizes. Continuum limit estimates of the topological susceptibility chi are obtained of which we favor chi(1/4)/Tc = 0.643(12), where Tc is the SU(2) deconfinement temperature. Differences between cooling length scales in different topological sectors turn out to be too small to be detectable within our statistical errors.
Show less  Date Issued
 20180315
 Identifier
 FSU_libsubv1_wos_000427603400006, 10.1103/PhysRevD.97.054506
 Format
 Citation
 Title
 ZSum Approach to Loop Integrals.
 Creator

Rottmann, Paulo A., Reina, Laura, Aluﬃ, Paolo, Berg, Bernd A., Wahl, Horst D., Rikvold, Per Arne, Department of Physics, Florida State University
 Abstract/Description

We study the applicability of the ZSum approach to multiloop calculations with massive particles in perturbative quantum field theory. We systematically analyze the case of oneloop scalar integrals, which represent the building blocks of any higherloop calculation. We focus in particular on triangle oneloop integrals and identify strengths and limitations of the ZSum approach, extending our results to the case of oneloop box integrals when appropriate. We conclude with the calculation...
Show moreWe study the applicability of the ZSum approach to multiloop calculations with massive particles in perturbative quantum field theory. We systematically analyze the case of oneloop scalar integrals, which represent the building blocks of any higherloop calculation. We focus in particular on triangle oneloop integrals and identify strengths and limitations of the ZSum approach, extending our results to the case of oneloop box integrals when appropriate. We conclude with the calculation of a specific physical example: the calculation of heavy flavor corrections to the renormalized scattering amplitude for deep inelastic scattering.
Show less  Date Issued
 2011
 Identifier
 FSU_migr_etd1784
 Format
 Thesis
 Title
 A Model Study of the Deconfining Phase Transition.
 Creator

Velytsky, Alexander, Berg, Bernd A., Riccardi, Gregory A., Heller, Urs M., Hagopian, Vasken, Rikvold, Per Arne, Department of Physics, Florida State University
 Abstract/Description

The study of the deconfining phase transition or crossover is important for the understanding of properties of nuclear matter and the quark gluon plasma. Heavy ion collisions experiments are capable of creating conditions necessary for deconfinement. The dynamics of this process and not only its equilibrium properties are of interest. In this dissertation nonequilibrium aspects of rapid heating and cooling of the QCD vacuum are studied in a model framework. The 3D Potts model with an...
Show moreThe study of the deconfining phase transition or crossover is important for the understanding of properties of nuclear matter and the quark gluon plasma. Heavy ion collisions experiments are capable of creating conditions necessary for deconfinement. The dynamics of this process and not only its equilibrium properties are of interest. In this dissertation nonequilibrium aspects of rapid heating and cooling of the QCD vacuum are studied in a model framework. The 3D Potts model with an external magnetic field is an effective model of QCD (of pure SU(3) gauge theory, when the magnetic field is set to zero), which we study by means of Monte Carlo simulations. Other models are used to understand the influence of the strength of the phase transition. In our investigations these systems are temperature driven through a phase transition or a rapid crossover using updating procedures in the Glauber universality class. We study hysteresis cycles with different updating speeds and simulations of a quench. Qualitatively this should reveal the physics of nonequilibrium configurations. A number of observables are measured during the simulations: thermodynamical quantities such as the internal energy and the magnetization, properties of FortuinKasteleyn clusters and structure functions. Comparing with equilibrium data we conclude that the Monte Carlo dynamics is capable of creating a spinodal decomposition, which dominates the statistical properties of configurations. A slowing down of the equilibration in the ordered phase due to the competition of different magnetization domains is observed. This could lead to a situation where the system does not fully equilibrate in the available time. Spinodal decomposition of the Polyakov loops may lead to an enhancement of low momentum degrees of freedom. If this scenario is realized by Nature, this may be observed in experiments as an increase in the low energy gluon production.
Show less  Date Issued
 2004
 Identifier
 FSU_migr_etd4574
 Format
 Thesis
 Title
 Dynamics of Biomolecules, Ligand Binding & Biological Functions.
 Creator

Yi, Myunggi, Zhou, Huanxiang, Logan, Timothy M., Berg, Bernd A., Xiong, Peng, Nymeyer, Hugh, Department of Physics, Florida State University
 Abstract/Description

Proteins are flexible and dynamic. One static structure alone does not often completely explain biological functions of the protein, and some proteins do not even have high resolution structures. In order to provide better understanding to the biological functions of nicotinic acetylcholine receptor, Diphtheria toxin repressor and M2 proton channel, the dynamics of these proteins are investigated using molecular modeling and molecular dynamics (MD) simulations. With absence of high resolution...
Show moreProteins are flexible and dynamic. One static structure alone does not often completely explain biological functions of the protein, and some proteins do not even have high resolution structures. In order to provide better understanding to the biological functions of nicotinic acetylcholine receptor, Diphtheria toxin repressor and M2 proton channel, the dynamics of these proteins are investigated using molecular modeling and molecular dynamics (MD) simulations. With absence of high resolution structure of alpha 7 receptor, the homology models of apo and cobra toxin bound forms have been built. From the MD simulations of these model structures, we observed one subunit of apo simulation moved away from other four subunits. With local movement of flexible loop regions, the whole subunit tilted clockwise. These conformational changes occurred spontaneously, and were strongly correlated with the conformational change when the channel is activated by agonists. Unlike other computational studies, we directly compared our model of open conformation with the experimental data. However, the subunits of toxin bound form were stable, and conformational change is restricted by the bound cobra toxin. These results provide activation and inhibition mechanisms of alpha 7 receptors and a possible explanation for intermediate conductance of the channel. Intramolecular complex of SH3like domain with a prolinerich (Pr) peptide segment in Diphtheria toxin repressor (DtxR) is stabilized in inactive state. Upon activation of DtxR by transition metal binding, this intramolecular complex should be dissociated. The dynamics of this intramolecular complex is investigated using MD simulations and NMR spectroscopy. We observed spontaneous opening and closing motions of the Pr segment binding pockets in both PrSH3 and SH3 simulations. The MD simulation results and NMR relaxation data suggest that the Pr segment exhibits a binding ¡ê unbinding equilibrium. Despite a wealth of experimental validation of GouyChapman (GC) theory to charged lipid membranes, a test of GC theory by MD simulations has been elusive. Here we demonstrate that the ion distributions at different salt concentrations in anionic lipid bilayer systems agree well with GC predictions using MD simulations. Na+ ions are adsorbed to the bilayer through favorable interactions with carbonyls and hydroxyls, reducing the surface charge density by 72.5%. The interactions of amantadine, an antiinfluenza A drug, with DMPC bilayers are investigated by an MD simulation and by solidstate NMR. The MD simulation results and NMR data demonstrate that amantadine is located within the interfacial region with upward orientation and interacts with the lipid headgroup and glycerol backbone, while the adamantane group of amantadine interacts with the glycerol backbone and much of fatty acyl chain, as it wraps underneath of the drug. The lipid headgroup orientation is influenced by the drug as well. The recent prevalence of amantadineresistant mutants makes a development of new drug urgent. The mechanism of inhibition of M2 proton channel in influenza virus A by amantadine is investigated. In the absence of high resolution structure, we model the apo and drug bound forms based on NMR structures. MD simulations demonstrate that channel pore is blocked by a primary gate formed by Trp41 helped by His37 and a secondary gate formed by Val27. The blockage by the secondary gate is extended by the drug bound just below the gate, resulting in a broken water wire throughout the simulation, suggesting a novel role of Val27 in the inhibition by amantadine. Recent Xray structure validates the simulation results.
Show less  Date Issued
 2008
 Identifier
 FSU_migr_etd0661
 Format
 Thesis
 Title
 The Deconfining Phase Transition in and out of Equilibrium.
 Creator

Bazavov, Oleksiy, Berg, Bernd A., Mascagni, Michael, Capstick, Simon, Frawley, Anthony, Reina, Laura, Department of Physics, Florida State University
 Abstract/Description

Recent experiments carried out at the Relativistic Heavy Ion Collider at the Brookhaven National Laboratory provide strong evidence that a matter can be driven from a confined, lowtemperature phase, observed in our every day world into a deconfined hightemperature phase of liberated quarks and gluons. The equilibrium and dynamical properties of the deconfining phase transition are thus of great theoretical interest, since they also provide an information about the first femtoseconds of the...
Show moreRecent experiments carried out at the Relativistic Heavy Ion Collider at the Brookhaven National Laboratory provide strong evidence that a matter can be driven from a confined, lowtemperature phase, observed in our every day world into a deconfined hightemperature phase of liberated quarks and gluons. The equilibrium and dynamical properties of the deconfining phase transition are thus of great theoretical interest, since they also provide an information about the first femtoseconds of the evolution of our Universe, when the hot primordial soup while cooling has undergone a chain of phase transitions. The aspects of the deconfining phase transition studied in this work include: the dynamics of the SU(3) gauge theory after the heating quench (which models rapid heating in the heavyion collisions), equilibrium properties of the phase transition in the SU(3) gauge theory with boundaries at low temperature (small volumes at RHIC suggest that boundary effects cannot be neglected and periodic boundary conditions normally used in lattice simulations do not correspond to the experimental situation), and a study of the order of the transition in U(1) gauge theory.
Show less  Date Issued
 2007
 Identifier
 FSU_migr_etd1166
 Format
 Thesis
 Title
 Modeling Electrostatic Contributions to Protein Folding and Binding.
 Creator

Tjong, Harianto, Zhou, Huan‐Xiang, Nymeyer, Hugh, Berg, Bernd A., Rikvold, Per Arne, Xiong, Peng, Department of Physics, Florida State University
 Abstract/Description

Protein binding and folding stability are important properties, not only for fundamental reasons but also for biological functions. Mutations on proteins, even at a single residue level, can significantly affect binding specificity and folding stability. A major goal of this dissertation work is to model contributions, especially those from electrostatic interactions, to binding and folding stability. The PoissonBoltzmann (PB) equation has long been held as the benchmark for modeling...
Show moreProtein binding and folding stability are important properties, not only for fundamental reasons but also for biological functions. Mutations on proteins, even at a single residue level, can significantly affect binding specificity and folding stability. A major goal of this dissertation work is to model contributions, especially those from electrostatic interactions, to binding and folding stability. The PoissonBoltzmann (PB) equation has long been held as the benchmark for modeling electrostatic interactions in biomolecules. However, the computational cost of solving the PB equation has restricted its applications largely to singleconformation calculations. We have developed a highly efficient method based on the generalized Born (GB) model that is able to reproduce PB results with higher accuracy than current GB methods. However, even our GB method is inadequate to model small effects due to point mutations on binding and folding stability. To meet this challenge, we have designed a simple scaling scheme based on the PB results for a small number of conformations out of a large ensemble. We show that the scaled GB method is able to reproduce PB results extremely well for the whole ensemble in a variety of applications, including binding, folding, and transfer free energy. The scaling method makes it possible to thoroughly sample the transientcomplex ensemble in predicting protein binding rate constants and to incorporate conformational sampling in electrostatic modeling without loss of accuracy. The body of work presented in this dissertation may serve as both tools and inspirations for research in protein design and drug design.
Show less  Date Issued
 2008
 Identifier
 FSU_migr_etd1415
 Format
 Thesis
 Title
 Deconfinement Transition in Equilibrium Lattice Gauge Theory with Realistic Boundary Conditions.
 Creator

Wu, Hao, Berg, Bernd A., Brüschweiler, Rafael, Adams, Todd, Piekarewicz, Jorge, Reina, Laura, Department of Physics, Florida State University
 Abstract/Description

Heavyion collision experiments carried out at the Brookhaven National Laboratory, or BNL, and at the European Organization for Nuclear Research, or CERN, provide evidence that matter can be driven from a confined, lowtemperature phase into a deconfined high temperature phase of liberated quarks and gluons. Understanding of the deconfinement transition can bring our knowledge of stronglyinteracting matter to a deeper level. Ab initio equilibrium studies of the thermodynamic equation of...
Show moreHeavyion collision experiments carried out at the Brookhaven National Laboratory, or BNL, and at the European Organization for Nuclear Research, or CERN, provide evidence that matter can be driven from a confined, lowtemperature phase into a deconfined high temperature phase of liberated quarks and gluons. Understanding of the deconfinement transition can bring our knowledge of stronglyinteracting matter to a deeper level. Ab initio equilibrium studies of the thermodynamic equation of state in the deconfined phase are possible in the framework of lattice gauge theory. It is often desired in such studies to approach the infinite volume thermodynamic limit. To accomplish it quickly, most studies have implemented lattices with periodic boundary conditions. However, the physical volumes created at the Brookhaven National Laboratory are small and exploratory work for pure SU(3) lattice gauge theory suggests that boundary effects cannot be neglected. In this work we study the SU(3) deconfined equilibrium phase in small volumes with inside and outside temperatures in the SU(3) scaling region, using a lattice geometry of the doublelayered torus. Our results show substantial finite size effects on the deconfining transition temperature under realistic boundary conditions.
Show less  Date Issued
 2012
 Identifier
 FSU_migr_etd5461
 Format
 Thesis
 Title
 Comparing the PoissonBoltzmann Equation to Alternative Electrostatic Theories and Improving Stochastic Techniques for Implicit Solvent Models.
 Creator

Harris, Robert C., Fenley, Marcia O., Blaber, Michael, Berg, Bernd A., Van Winkle, David, Dobrosavljevic, Vladimir, Department of Physics, Florida State University
 Abstract/Description

The PoissonBoltzmann equation, PBE, the linearized PBE, LPBE, and generalized Born, GB, model are implicit solvent methods that accelerate biophysical calculations by eliminating the need to integrate across the solvent's degrees of freedom. This thesis compares the predictions of the PoissonBoltzmann equation, PBE, to those of another electrostatic theory, the counterion condensation theory, CCT. It demonstrates that the CCT's predictions of the salt dependence of the electrostatic binding...
Show moreThe PoissonBoltzmann equation, PBE, the linearized PBE, LPBE, and generalized Born, GB, model are implicit solvent methods that accelerate biophysical calculations by eliminating the need to integrate across the solvent's degrees of freedom. This thesis compares the predictions of the PoissonBoltzmann equation, PBE, to those of another electrostatic theory, the counterion condensation theory, CCT. It demonstrates that the CCT's predictions of the salt dependence of the electrostatic binding free energy agree with those of the PBE, but its predictions of the electrostatic binding free energy itself do not. This observation is explained by deriving a simple analytical expression for the salt dependence of the electrostatic binding free energy from the GB model. This expression indicates that essentially any electrostatic theory with the same longdistance predictions will predict the same salt dependence, it explains the observed correlations between this salt dependence and various empirical quantities, and it provides a rapid method for predicting its change upon mutation of the charged residues of the binding partners. Implicit solvent models do include several approximations whose validity should be evaluated to determine the reliability of their estimates of experimental quantities. In this thesis the effect of finite ion sizes upon PBE solutions is examined with the sizemodified PBE, SMPBE. These findings show that the SMPBE predicts different dependences of electrostatic energies upon ion size than the PBE, but whether these changes lead to different predictions for observable quantities is not clear. Additionally, the ionexclusion layer does not match the dependences on ion size given by the SMPBE, and combined with the superior physical basis of the SMPBE, the use of the ionexclusion layer is called into question. Additionally, this thesis improves stochastic solvers of the LPBE and presents a new stochastic solver of the GB model. By optimizing the biasgenerating parameters in a walkonspheres, WOS, LPBE solver, dividing the variance evenly across the atoms of the molecule, and using an approximate nearestneighbor solver, WOS solvers can solve the LPBE in times comparable to deterministic solvers. The stochastic GB solver has the advantage over traditional analytical solvers of the GB in that analytical solutions to the GB model must approximate a set of parameters called the Born radii, and the error due to this approximation cannot usually be evaluated. The stochastic solver, on the other hand quantifies this error and converges to the exact GB model with additional computation time. This behavior allows the validity of the Born approximation itself to be evaluated, and the results presented here indicate that the GB model gives different estimates of the electrostatic binding free energy than the LPBE. More research will be required to refine the GB approximation to better compute the electrostatic binding free energy, and that the radii in the stochastic method are arbitrarily precise indicates that the stochastic solver will be useful in this endeavor.
Show less  Date Issued
 2012
 Identifier
 FSU_migr_etd5687
 Format
 Thesis
 Title
 Coulomb Liquids: from Electron to Biology Systems.
 Creator

Pramudya, Yohanes H. R., Dobrosavljevic, Vladimir, Dalal, Naresh, Manousakis, Efstratios, Berg, Bernd A., Engel, Lloyd, Department of Physics, Florida State University
 Abstract/Description

We study the unusual transport behavior driven mostly by the correlations between the charge carriers in lattice and continuum systems. The strongly correlated systems are studied in the classical limit where the Coulomb interaction dominates the systems and brings the systems into the nearly frozen state that we call Coulomb Liquids. Theoretical description of the materials with the strongly interacting electron systems in the lattice or solid state physics and ions in biological systems or...
Show moreWe study the unusual transport behavior driven mostly by the correlations between the charge carriers in lattice and continuum systems. The strongly correlated systems are studied in the classical limit where the Coulomb interaction dominates the systems and brings the systems into the nearly frozen state that we call Coulomb Liquids. Theoretical description of the materials with the strongly interacting electron systems in the lattice or solid state physics and ions in biological systems or solutions are constantly challenging problems in condensed matter physics and biophysics. First we investigate the nonactivated behavior of transport that observed near Wigner crystallization in two dimensions electron gas (2DEG) that is observed experimentally. The effect of Coulomb interaction in the system is studied with Monte Carlo (MC) simulation and extended dynamical mean field theory (EDMFT) in hypercubic lattice and pseudogap phase is found as a robust feature driven by longrange interaction. In the second part of the thesis we study the effect of geometrical frustration in pyrochlore lattice which competes with the interactiondriven frustration. The MC and EDMFT methods give pseudogap phase as found in cubic lattice that has no geometrical frustration and agree with the unusual transport property of ancient magnet/magnetite above the Verwey transition. The third part discusses the effect of stronglycorrelated liquid (SCL) model by Shklovskii and the meanfield approach of PoissonBoltzmann equation (PBE) describing the screening of macroions in solution or biological system. We compare those approximations with MC simulation and explain which approximation is good at different limit of temperature or ion density. And the last part describes the visualization for different type of interactions and the effect of filling, disordered, etc. from the study of Coulomb liquids.
Show less  Date Issued
 2013
 Identifier
 FSU_migr_etd8715
 Format
 Thesis
 Title
 Theoretical Studies of ProteinProtein and ProteinDNA Binding Rates.
 Creator

Alsallaq, Ramzi A., Zhou, HuanXiang, Blaber, Michael, Berg, Bernd, Rikvold, Per Arne, Xiong, Peng, Department of Physics, Florida State University
 Abstract/Description

Proteins are folded chains of amino acids. Some of the amino acids (e.g. Lys, Arg, His, Asp, and Glu) carry charges under physiological conditions. Proteins almost always function through binding to other proteins or ligands, for example barnase is a ribonuclease protein, found in the bacterium Bacil lus amyloliquefaceus. Barnase degrades RNA by hydrolysis. For the bacterium to inhibit the potentially lethal action of Barnase within its own cell it coproduces another protein called barstar...
Show moreProteins are folded chains of amino acids. Some of the amino acids (e.g. Lys, Arg, His, Asp, and Glu) carry charges under physiological conditions. Proteins almost always function through binding to other proteins or ligands, for example barnase is a ribonuclease protein, found in the bacterium Bacil lus amyloliquefaceus. Barnase degrades RNA by hydrolysis. For the bacterium to inhibit the potentially lethal action of Barnase within its own cell it coproduces another protein called barstar which binds quickly, and tightly, to barnase. The biological function of this binding is to block the active site of barnase. The speeds (rates) at which proteins associate are vital to many biological processes. They span a wide range (from less than 103 to 108 M1 s1 ). Rates greater than ~106 M 1s1 are typically found to be manifestations of enhancements by longrange electrostatic interactions between the associating proteins. A different paradigm appears in the case of protein binding to DNA. The rate in this case is enhanced through attractive surface potential that effectively reduces the dimensionality of the available search space for the diffusing protein. This thesis presents computational and theoretical models on the rate of association of ligands/proteins to other proteins or DNA. For proteinprotein association we present a general strategy for computing proteinprotein rates of association. The main achievements of this strategy is the ability to obtain a stringent reaction criteria based on the landscape of shortrange interactions between the associating proteins, and the ability to compute the effect of the electrostatic interactions on the rates of association accurately using the best known solvers for PoissonBoltzmann equation presently available. For proteinDNA association we present a mathematical model for proteins targeting specific sites on a circular DNA topology. The main achievements are the realization that a linear DNA with reflecting ends and specific site in the middle of the chain is kinetically indistinguishable from its circularized topology, and the ability to predict the effect of the dissociation via the ends of linear DNA on the rate of association which is to reduce the rate.
Show less  Date Issued
 2007
 Identifier
 FSU_migr_etd0182
 Format
 Set of related objects
 Title
 Topological Materials and Their Interfaces.
 Creator

Aryal, Niraj, Manousakis, Efstratios, Dalal, Naresh S., Bonesteel, N. E., Berg, Bernd A., Balicas, Luis, Florida State University, College of Arts and Sciences, Department of...
Show moreAryal, Niraj, Manousakis, Efstratios, Dalal, Naresh S., Bonesteel, N. E., Berg, Bernd A., Balicas, Luis, Florida State University, College of Arts and Sciences, Department of Physics
Show less  Abstract/Description

This dissertation is a theoretical and computational examination of electronic properties of topological materials, such as topological insulators and Weyl semimetals. Our work is motivated by various experimental observations and theoretical predictions about the presence of exotic electronic properties and transport phenomena in different topological materials. These materials have been a subject of intense research since last decade because their lowenergy dispersion can be described by...
Show moreThis dissertation is a theoretical and computational examination of electronic properties of topological materials, such as topological insulators and Weyl semimetals. Our work is motivated by various experimental observations and theoretical predictions about the presence of exotic electronic properties and transport phenomena in different topological materials. These materials have been a subject of intense research since last decade because their lowenergy dispersion can be described by Dirac and Weyl equations and they are predicted to have many exciting properties of both fundamental and practical significance. In this dissertation, we examine theoretical predictions and experimental measurements using density functional theory (DFT) based methods and using calculations based on a model Hamiltonian. In the first half of this dissertation, we present our detailed results for the Weyl semimetal candidate T[subscript d]MoTe₂ using DFT and DFT+U methods while making careful comparison to different experiments in order to validate our results. We also address the fate of the Weyl fermions as a function of the Hubbard U using both DFT and a model Hamiltonian approach. Moreover, from our calculations, we predict that the system could be in close vicinity of a Lifshitz transition. Such a prediction can be experimentally verified by means of doping or electrostatic gating. In the second half of this dissertation, we present our results for the surface and interface states of the prototypical topological insulator material Bi₂Se₃. We study interfaces of the topological insulator with different conventional insulators using both DFT and model Hamiltonian calculations and examine the fate of the topological states at the interface. Moreover, we predict the occurrence of a topological phase transition in the interface geometry from our calculations and point towards a few directions where some of these predictions could be verified experimentally. We conclude by presenting implications for further work.
Show less  Date Issued
 2019
 Identifier
 2019_Summer_Aryal_fsu_0071E_15363
 Format
 Thesis
 Title
 Search for the Dark Matter Signature in the Lepton Jet Final State √(S) = 7 TeV.
 Creator

Gleyzer, Sergei V., Hagopian, Vasken, Safron, Sanford A., Prosper, Harrison B., Berg, Bernd, Rogachev, Grigory, Department of Physics, Florida State University
 Abstract/Description

The Large Hadron Collider is pushing high energy physics in to a brand new territory. This extraordinary era may bring discoveries of unprecedented magnitude, delivering validation or extreme dissappointment to the physics theories of the previous decades. By colliding particles at more than 3.5 times the center of mass energy of the Tevatron accelerator at the Fermilab National Accelerator Laboratory, the CERN Large Hadron Collider aims to produce particles in the mass range above those that...
Show moreThe Large Hadron Collider is pushing high energy physics in to a brand new territory. This extraordinary era may bring discoveries of unprecedented magnitude, delivering validation or extreme dissappointment to the physics theories of the previous decades. By colliding particles at more than 3.5 times the center of mass energy of the Tevatron accelerator at the Fermilab National Accelerator Laboratory, the CERN Large Hadron Collider aims to produce particles in the mass range above those that are already known. At the same time, there are exciting possibilities for new physics in the lowmass range that may have gone unnoticed until now. An example of this is a GeVscale dark sector with a colorful spectrum of new particles. This physics model produces unique signatures of collimated leptons at the Large Hadron Collider energies. In the first part of this work, we describe the interesting astrophysical evidence that motivates a search for lepton jets and focus our attention on a minimal supersymmetric standard model with a GeVscale dark sector that produces this exciting signature. In the next part of the thesis, we describe a search using the Compact Muon Solenoid (CMS) detector for evidence of dark matter in events containing muonic leptonjets produced in 7 TeV protonproton collisions at the Large Hadron Collider. We employ a novel lepton jet algorithm and find no evidence of an excess of such events with respect to the rate predicted by the Standard Model and interpret the null result in terms of a recently developed supersymmetric theory of dark matter. In doing so, we severely constrain the theoretical model and its parameters with the actual data from the Large Hadron Collider. In addition, we report the first observation of double J/ψ production, a new physical process discovery at the next energy frontier.
Show less  Date Issued
 2011
 Identifier
 FSU_migr_etd4240
 Format
 Thesis
 Title
 PhotoExcited Multiple Excitons in Strongly Correlated Insulators.
 Creator

Coulter, John E., Manousakis, Efstratios, Siegrist, Theo M., Berg, Bernd A., Schlottmann, P., Beekman, Christianne, Florida State University, College of Arts and Sciences,...
Show moreCoulter, John E., Manousakis, Efstratios, Siegrist, Theo M., Berg, Bernd A., Schlottmann, P., Beekman, Christianne, Florida State University, College of Arts and Sciences, Department of Physics
Show less  Abstract/Description

This dissertation examines the theoretical and computational methods needed to calcu late optoelectronic multiplecarrier excitation rates in strongly correlated insulators (SCI). Through several studies, we find that we are able to calculate the excitonexciton decay rate, also called impact ionization rate (IIR) in real materials, and describe the the methods required to do so accurately. In the course of our search for a useful method, we investigate several levels of approximation, from...
Show moreThis dissertation examines the theoretical and computational methods needed to calcu late optoelectronic multiplecarrier excitation rates in strongly correlated insulators (SCI). Through several studies, we find that we are able to calculate the excitonexciton decay rate, also called impact ionization rate (IIR) in real materials, and describe the the methods required to do so accurately. In the course of our search for a useful method, we investigate several levels of approximation, from simple densityfunctional theory (DFT), to socalled hy brid functionals, and finally we add manybody corrections to the DFT scheme. We present results for the materials vanadium dioxide (VO 2 ), nickel oxide (NiO), lanthanum vanadate (LaVO 3 ) and yttrium titanate (YTIO 3 ) along the way. The first two have been used as sim ple test materials, while we have chosen the latter two as interesting and complex strongly correlated insulators. We present conclusions on the results, and discuss the implications for further experimental work.
Show less  Date Issued
 2015
 Identifier
 FSU_migr_etd9315
 Format
 Thesis
 Title
 Scale Setting and Topological Observables in Pure SU(2) LGT.
 Creator

Clarke, David A. (David Anthony), Berg, Bernd A., Reina, Laura, AlbrechtSchmitt, Thomas E., Yohay, Rachel, Höflich, Peter, Florida State University, College of Arts and...
Show moreClarke, David A. (David Anthony), Berg, Bernd A., Reina, Laura, AlbrechtSchmitt, Thomas E., Yohay, Rachel, Höflich, Peter, Florida State University, College of Arts and Sciences, Department of Physics
Show less  Abstract/Description

In this dissertation, we investigate the approach of pure SU(2) lattice gauge theory to its continuum limit using the deconfinement temperature, six gradient scales, and six cooling scales. We find that cooling scales exhibit similarly good scaling behavior as gradient scales, while being computationally more efficient. In addition, we estimate systematic error in continuum limit extrapolations of scale ratios by comparing standard scaling to asymptotic scaling. Finally we study topological...
Show moreIn this dissertation, we investigate the approach of pure SU(2) lattice gauge theory to its continuum limit using the deconfinement temperature, six gradient scales, and six cooling scales. We find that cooling scales exhibit similarly good scaling behavior as gradient scales, while being computationally more efficient. In addition, we estimate systematic error in continuum limit extrapolations of scale ratios by comparing standard scaling to asymptotic scaling. Finally we study topological observables in pure SU(2) using cooling to smooth the gauge fields, and investigate the sensitivity of cooling scales to topological charge. We find that large numbers of cooling sweeps lead to metastable charge sectors, without destroying physical instantons, provided the lattice spacing is fine enough and the volume is large enough. Continuum limit estimates of the topological susceptibility are obtained, of which we favor χ 1/4 /T c = 0.643(12). Differences between cooling scales in different topological sectors turn out to be too small to be detectable within our statistical error.
Show less  Date Issued
 2018
 Identifier
 2018_Fall_Clarke_fsu_0071E_14832
 Format
 Thesis
 Title
 Redefining the Actinide Series.
 Creator

Cary, Samantha K. (Samantha Kim), AlbrechtSchmitt, Thomas E., Berg, Bernd A., Dorsey, John G., Stiegman, Albert E., Dalal, Naresh S., Florida State University, College of Arts...
Show moreCary, Samantha K. (Samantha Kim), AlbrechtSchmitt, Thomas E., Berg, Bernd A., Dorsey, John G., Stiegman, Albert E., Dalal, Naresh S., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less  Abstract/Description

This dissertation focuses on probing the fundamental chemistry of the actinide series, specifically the structure and bonding in complexes of transuranium elements. The actinides consist of the elements from actinium to lawrencium in the periodic table, best known for uranium and plutonium, which were used to develop nuclear weapons and power. Today, nuclear power is used to generate over 17% of the electricity across the world.[1, 2] Although an effective means of generating electricity, the...
Show moreThis dissertation focuses on probing the fundamental chemistry of the actinide series, specifically the structure and bonding in complexes of transuranium elements. The actinides consist of the elements from actinium to lawrencium in the periodic table, best known for uranium and plutonium, which were used to develop nuclear weapons and power. Today, nuclear power is used to generate over 17% of the electricity across the world.[1, 2] Although an effective means of generating electricity, the waste generated from nuclear reactors is a major issue with relatively little progress being made to reduce the amount and radiotoxicity of the waste. Overall, this problem stems from the chemical complexity and highly radioactive nature of the actinides. Because of this the actinides are understudied, particularly beyond uranium, and as a result much of the fundamental chemistry is poorly understood. The goal of this work is to prepare coordination complexes that can be used as probes for elucidating changes in structure and bonding across the actinide series. Over the past couple decades, neutral nitrogen donating ligands have shown to have a greater affinity towards the actinides over the lanthanides.[1] The work discussed in this dissertation has focused on using nitrogencontaining carboxylates to explore periodic trends through the lanthanide and actinide series. The first step of this project was to explore structure and bonding differences between the lanthanide (4f) and actinide (5f) series. The early lanthanides, such as Ce and Nd are often used as surrogates for the actinides because they possess f orbitals and are relatively similar in size to that of their actinide analogs.[3] Depending on the coordinating ligand, the structure and bonding between the 4fs and 5fs can either mimic each other or diverge greatly. In some cases the structure of the actinides and lanthanides are very similar, but the electronic properties are vastly different. In chapters 3 and 4, unique structures and electronic properties of Pu and Ce complexes are explored. The second portion of this research was to investigate the differences in structure and bonding between of the transplutonium actinides, americium through californium (AmCf). Traditionally these later actinides were believed to mimic the lanthanides in both their structure and bonding characteristics, but as we explore the actinides more we find this might not be true. Our approach used a pyridine dicarboxylate derivative to make an isomorphous series of both the trivalent actinides and lanthanides. It was found that the late actinides, starting at Cf, have different electronic properties that are not paralleled by any of the lanthanides or early actinides. Much to our surprise, it seems that Cf represents a second transition in the actinide series, which is discussed in chapters 5 through 7. Overall, this dissertation focuses on exploring the structure and bonding of the f elements through solidstate chemistry utilizing a variety of characterization techniques.
Show less  Date Issued
 2015
 Identifier
 FSU_2015fall_Cary_fsu_0071E_12680
 Format
 Thesis