Dept. of Physics
http://hdl.handle.net/2142/8858
Tue, 26 Sep 2017 07:29:07 GMT2017-09-26T07:29:07ZModification and regulation of biomolecules in vitro and in silico
http://hdl.handle.net/2142/95604
Modification and regulation of biomolecules in vitro and in silico
Chao, Shu-Han
The focus in functional and dynamics studies of biomolecules, such as protein or DNA, has been very much on their own structures and energy landscapes. However, in real biological systems, biomolecules are usually modified or regulated by several external factors, including surface coating, hydration condition, and local environment. For example, by covalently coupling a Poly(ethylene glycol) (PEG) on a protein surface, the stability of the host protein could be largely enhanced. This method, called PEGylation, has been widely used in pharmaceutical industry to protect protein drugs and increase their circulation life-time since the 1990s. However, the mechanism of protein-PEG interaction is yet to be understood.
On the other hand, in developing one of the advanced DNA sequencing techniques --- nanopore sequencing, different mechanisms have been introduced to the nanopore system to regulate the conformation and motion of DNA molecules, attempting to achieve a better signal-to-noise ratio in reading DNA sequence.
This dissertation aims to study the above two topics from both experiments and molecular dynamics simulations. The first part focuses on developing nanopore sequencing techniques. We have developed a method combining continuum modeling results of a nano-scale system and a coarse-grained DNA model to study the DNA translocation through a nanopore in a device scale. We use this method to develop advanced DNA sequencing techniques, including plasmonic nanopore and double nanopores. Both of them show great potential as novel approaches for DNA sequencing. The protein-PEG interaction is addressed in the second part. We show that the conjugated PEG affects the thermodynamic stability and local structure of the host protein WW domain, but not that of Lambda repressor. A reoccurring and cooperative folding of a PEG molecule onto the protein surface is revealed by molecular dynamics simulations. Specific PEG-binding motifs on the protein surface are identified.
DNA sequencing; molecular dynamics; nanopore; coarsed-grained model; double-nanopore; protein folding; PEGylation; thermal denaturation; Temperature Jump
Thu, 01 Dec 2016 00:00:00 GMThttp://hdl.handle.net/2142/956042016-12-01T00:00:00ZChao, Shu-HanElectromagnetic response of time-reversal breaking metallic phases in two dimensions
http://hdl.handle.net/2142/95602
Electromagnetic response of time-reversal breaking metallic phases in two dimensions
Assawasunthonnet, Wathid
We explore two phases in two-dimensional electron fluids in which the time-reversal symmetry is broken spontaneously by using the method of higher dimensional bosonization. Mean-field calculations show that the order parameter is two two-component real vectors [Sun and Fradkin 2008]. There are two phases: the beta phase in which the two order parameters are perpendicular and the alpha phase in which they are parallel. This beta phase exhibits nonvanishing un-quantized anomalous Hall effect in the absence of external magnetic fields, which corresponds to the Berry curvature on the Fermi surface. The alpha phase does not have that property. To go beyond the mean-field, we introduce the machinery of higher dimensional bosonization. Our preliminary results show that in the mean field limit of the bosonized theory, the fluid spontaneously transforms into the time-reversal broken phase. It is evident from the result that the critical point we have is similar to that of Pomeranchuk instability. The quartic term in the dispersion expansion needed to be introduced to stabilize the theory. The correction coming from the higher order terms introduces the coupling to the curvature of the Fermi surfaces. The beta phase in the bosonized picture is not correct so we go back to the fermionic theory and integrate out the fermions in the symmetric phase directly to achieve an effective action. Finally, the full response polarization tensor is derived and its Ward identity is shown to be obeyed.
Anomalous Hall Effect; Non-Fermi liquid; Condensed matter
Fri, 02 Dec 2016 00:00:00 GMThttp://hdl.handle.net/2142/956022016-12-02T00:00:00ZAssawasunthonnet, WathidMultiscale dynamics in honeybee societies
http://hdl.handle.net/2142/95563
Multiscale dynamics in honeybee societies
Deviprasad Rao, Vikyath
In this dissertation, I examine the social organization of a model organism, the honeybee, at multiple scales. I begin in Part I at the microbial scale, by studying the relationship between the social caste of individuals and the microbes they harbour in their gastrointestinal tracts. Using 16S rRNA sequence data, I reconstruct the gut microbiomes of honeybees of different castes. I find that the microbiomes of two previously-uncharacterized social castes -- drones and queens -- contain the same bacteria as those in the guts of worker bees. However, despite this similarity, I show that the compositions of these bacteria in drones and queens are sufficiently different that their microbiomes can be distinguished from those of workers.
In Part II, I study the honeybee society at the level of its individual constituents, in particular, the set of foragers. I characterize the distribution of foraging activity across these individuals in the society, and find that this is highly skewed, with some individuals contributing much more to the activity of the colony than others. I establish these results in the framework used to describe the wealth of individuals in human society, and also characterize the temporal variation and resilience of foraging activity.
In Part III, I describe a system to track individual honeybees and their interactions inside a two-dimensional observation hive with high spatiotemporal resolution. At the level of individual honeybees, I study the temporal statistics of trophallaxis, an important social interaction that occurs in honeybee societies, and find that the distribution of trophallaxis durations is similar to the distribution of face-to-face interactions among humans. I propose a scaling argument to explain the scaling exponent of these distributions, and test the argument in simple random-walk models of proximity interactions. I then study the honeybee society at the collective scale of the trophallaxis interaction network, and find that although bees exhibit bursty patterns of trophallaxis just as humans do in communication, the dynamics of simulated spreading on the trophallaxis networks is fast relative to randomized reference models, unlike in human temporal networks.
complex systems; biological physics; honey bee; social networks; microbiome; metagenomics
Thu, 10 Nov 2016 00:00:00 GMThttp://hdl.handle.net/2142/955632016-11-10T00:00:00ZDeviprasad Rao, VikyathSpectroscopic studies of high-temperature superconductors on planar tunnel junction devices and nanofabricated point contact junctions
http://hdl.handle.net/2142/95494
Spectroscopic studies of high-temperature superconductors on planar tunnel junction devices and nanofabricated point contact junctions
Zhao, Han
Since the discovery of high-temperature superconductors (HTS), there has been lots of effort to study their physical properties. Two powerful methods for this investigation are tunneling spectroscopy and point contact spectroscopy. The tunneling spectroscopy directly probes the density of states whereas the point contact spectroscopy detects the sample properties via quasiparticle scattering.
Two new approaches to fabricate devices for spectroscopic studies are presented in the thesis. The first one is atomic layer deposition (ALD) to grow ultra-thin and low-defect Al2O3 tunnel junction barriers, developed on sputter-deposited Nb thin films. The conductance characteristics at low temperature show the clear density of states signature of superconducting Nb. The junction resistance times area product increases exponentially with barrier thickness, further supporting the high quality of the junctions, in which single-step elastic tunneling predominates.
The second new approach is the focused ion beam (FIB) nanofabrication technique which can achieve precise control of the geometry of point contact junctions. Two different types of PCS devices (vertical and in-plane) have been studied, and the application of vertical junctions on niobium thin films shows consistent data insensitive to thermal cycling, which opens the possibility to perform PCS on materials while varying external variables, such as temperature, directional-dependent magnetic field, and stress. We also use this new method of FIB-fabricated PCS junctions to probe the strongly correlated election system FeTe0.55Se0.45, whose normal state spectra show a conductance enhancement around zero bias, which, through comparison with previous experiments, we associate with electronic nematicity.
Finally, preliminary results of planar tunnel junction devices on FeSeTe thin films and crystals to test the superconducting gap order parameter symmetry using the proximity effect are also presented.
Planar tunnel junction; Point contact spectroscopy; Superconductor; Nanofabrication
Tue, 29 Nov 2016 00:00:00 GMThttp://hdl.handle.net/2142/954942016-11-29T00:00:00ZZhao, HanChern-Simons theory of magnetization plateaus on the kagome lattice
http://hdl.handle.net/2142/95483
Chern-Simons theory of magnetization plateaus on the kagome lattice
Krishnakumar, Ponnuraj
Frustrated spin systems on Kagome lattices have long been considered to be a promising candidate for realizing exotic spin liquid phases. Recently, there has been a lot of renewed interest in these systems with the discovery of experimental materials such as Volborthite and Herbertsmithite that have Kagome like structures. In this thesis I will focus on studying frustrated spin systems on the Kagome lattice using a spin-1/2 antiferromagnetic XXZ Heisenberg model in the presence of an external magnetic field as well as other perturbations. Such a system is expected to give rise to magnetization platueaus which can exhibit topological characteristics in certain regimes.
We will first develop a flux-attachment transformation that maps the Heisenberg spins (hard-core bosons) onto a problem of fermions coupled to a Chern-Simons gauge field. This mapping relies on being able to define a consistent Chern-Simons term on the lattice. Using this newly developed mapping we analyse the phases/magnetization plateaus that arise at the mean-field level and also consider the effects of adding fluctuations to various mean-fi eld states. Along the way, we show how to discretize an abelian Chern-Simons gauge theory on generic 2D planar lattices that satisfy certain conditions. We find that as long as there exists a one-to-one correspondence between the vertices and plaquettes defined on the graph, one can write down a discretized lattice version of the abelian Chern-Simons gauge theory.
Using the newly developed flux attachment transformation, we show the existence of chiral spin liquid
states for various magnetization plateaus for certain range of parameters in the XXZ Heisenberg model in the presence of an external magnetic field. Speci cally, in the regime of XY anisotropy the ground states at the 1/3 and 2/3 plateau are equivalent to a bosonic fractional quantum Hall Laughlin state with filling fraction 1/2 and that the 5/9 plateau is equivalent to the first bosonic Jain daughter state at filling fraction 2/3.
Next, we also consider the effects of several perturbations: a) a chirality term, b) a Dzyaloshinskii-Moriya term, and c) a ring-exchange type term on the bowties of the kagome lattice, and inquire if they can also support chiral spin liquids as ground states. We find that the chirality term leads to a chiral spin liquid even in the absence of an uniform magnetic field, with an effective spin Hall conductance of 1/2 in the regime of XY anisotropy. The Dzyaloshinkii-Moriya term also leads a similar chiral spin liquid but only when this term is not too strong. An external magnetic field when combined with some of the above perturbations also has the possibility of giving rise to additional plateaus which also behave like chiral spin liquids in the XY regime. Under the in influence of a ring-exchange term we find that provided its coupling constant is large enough, it may trigger a phase transition into a chiral spin liquid by the spontaneous breaking of time-reversal invariance.
Finally, we also present some numerical results based on some exact diagonalization studies. Here, we specifically focus on the 2/3-magnetization plateau which we previously argued should be a chiral spin liquid with a spin hall conductance of 1/2 . Such a topological state has a non-trivial ground state degeneracy and it excitations are described by semionic quasiparticles. In the numerical analysis, we analyse the ground state degeneracy structure on various Kagome clusters of different sizes. We compute modular matrices from the resultant minimally entangled states as well as the Chern numbers of various eigenstates all of which provide strong evidence that the 2/3-magnetization plateau very closely resembles a chiral spin liquid state with the expected characteristics.
Magnetization plateaus; lattice chern-simons theory; discretized abelian gauge theoies; kagome lattice; Heisenberg model; chiral spin liquid
Tue, 29 Nov 2016 00:00:00 GMThttp://hdl.handle.net/2142/954832016-11-29T00:00:00ZKrishnakumar, PonnurajAb initio investigations of low Z materials under extreme conditions
http://hdl.handle.net/2142/95454
Ab initio investigations of low Z materials under extreme conditions
Clay, Raymond C
Low Z elements, particularly hydrogen and helium, make up the vast majority of matter in the universe. These elements are observed to exist over the widest known ranges of pressures and temperatures, from interstellar plasmas to the cores of stars. In modeling Jovian planets or inertial confinement fusion, the pressures and temperatures of hydrogen and helium can even vary by orders of magnitude within a single system. Thus, understanding these systems requires an accurate phase diagram over a large range of thermodynamic conditions, particularly at high pressures.
Attaining this level of accuracy has been an ongoing challenge for experimentalists and theorists since the phase diagrams of low Z elements exhibit surprising complexity. Experimentally, static compression experiments are frustrated by the high reactivity of lithium and hydrogen, which greatly limits the pressure ranges that can be accurately characterized. Additionally, determining the relevant crystal structures of interesting phases can be very difficult for various reasons. Theoretically, most \textit{ab initio} based methods that can treat bulk systems have to treat electron correlation and nuclear quantum effects approximately. In hydrogen and lithium, the errors introduced by these approximations are comparable to the enthalpy differences between competing phases, giving inaccurate phase boundaries.
We believe that several outstanding questions in low Z phase diagrams can be resolved through a careful and systematic application of ab initio methods, particularly quantum Monte Carlo. Quantum Monte Carlo is well suited for the study of high-pressure low Z elements, as it is possible to treat all electrons quantum mechanically and with few uncontrolled approximations. This level of accuracy is suitable not only for direct applications of QMC to problems of interest, but also to benchmark and establish confidence in widely used density functional theory (DFT) calculations.
The purpose of my thesis will be two-fold: to use ab initio methods like quantum Monte Carlo to shed light on the phase diagram of bulk low Z elements, and to use these systems as a test bed for new QMC methods which make use of forces. The first part of this thesis will cover the necessary theoretical background, including our work on force and stress estimators. Then we will discuss our QMC based benchmarking method in both hydrogen and helium. The results of these benchmarking studies are then used in an attempt to resolve some major issues in the phase diagrams of hydrogen and hydrogen-helium mixtures. Lastly, we will present our results for the melting line and solid phase diagram for dense lithium.
Physics; Chemistry; Condensed matter; High pressure; Extreme conditions; Hydrogen; Lithium; Hydrogen-helium mixtures; Quantum Monte Carlo (QMC); Density functional theory (DFT); Benchmarking; Forces
Mon, 19 Sep 2016 00:00:00 GMThttp://hdl.handle.net/2142/954542016-09-19T00:00:00ZClay, Raymond CDelocalization phenomena in strongly disordered systems
http://hdl.handle.net/2142/95432
Delocalization phenomena in strongly disordered systems
Mondragon Shem, Ian
In this dissertation, we study delocalization mechanisms in strongly disordered systems. We focus on one-dimensional systems where the localizing effects of disorder are strongest. Our explorations of delocalization mechanisms will reveal new insights into the nature of Anderson transitions in the context of the entanglement, topology and interactions. We begin by proposing momentum entanglement as an efficient tool for detecting delocalized states in a broad class of disordered systems that undergo metal-insulator transitions. We find that the signatures of delocalized states in the momentum entanglement are remarkably clear. We explain this structure in the momentum entanglement by elucidating the underlying mechanism for delocalization in these disordered models. We will afterwards discuss a different type of delocalized state that arises at disorder-induced topological phase transitions. Anderson transitions in this case occur between insulating phases, with the emergence of critical states at the transition point. Through a mapping to a disordered spin chain, we provide a real-space description of the topology of the ground state and the delocalized state that emerges at the critical point. In this case, the mechanism that leads to delocalization reveals an unconventional type of disorder-induced topological phase transition that is fundamentally different, for example, from quantum Hall transitions. Finally, we examine delocalization processes in strongly interacting many-body localized phases. We find that strong interactions and the presence of symmetry constraints lead to an important spectral asymmetry in the localization transition. This asymmetry arises from the different dynamical properties of short-ranged correlated states that form due to having strong interactions. We explain how this asymmetry presents advantages in the numerical as well as experimental study of many-body localization transitions.
Anderson localization; Disordered systems; Entanglement; Topological phases; Quantum phase transitions; Many-body localization
Mon, 01 Aug 2016 00:00:00 GMThttp://hdl.handle.net/2142/954322016-08-01T00:00:00ZMondragon Shem, IanNonperturbative renormalization in classical φ4 theory
http://hdl.handle.net/2142/95295
Nonperturbative renormalization in classical φ4 theory
Hegg, Anthony C
This is an in-depth study of two analytic nonperturbative renormalization group methods used to study nonrelativistic quartic interacting systems. The model studied is that of classical real scalar φ4 theory. A variety of techniques are used including a rescaling of a nonlinear complete basis, a limit of finite periodic systems, and an analytic calculation of RG equations using a limit of finite systems. Assuming that the truncated forms of the action employed do not change the physics and that standard scaling techniques can be transcribed from more conventional RG approaches to these truncated forms, key results are a new fixed point at strong coupling with exponents ν=2/d and η=2 - d/2 as well as a nonperturbative generation of RG equations and subsequent solution to reduced φ4 theory. A nontrivial critical point for d=3 is identified in this reduced model with ν=4/(1+√41) ≈ 0.540 and η=0.
renormalization; nonperturbative; phi-4; elliptic; basis; critical point; strong coupling; strongly coupled
Fri, 14 Oct 2016 00:00:00 GMThttp://hdl.handle.net/2142/952952016-10-14T00:00:00ZHegg, Anthony CMethods for increasing model accuracy and simulation time scales of biological processes with molecular dynamics
http://hdl.handle.net/2142/95286
Methods for increasing model accuracy and simulation time scales of biological processes with molecular dynamics
Teo, Koon Heng Ivan
This dissertation presents three research projects on novel methods in computational bio- physics. Each of these projects introduces methodologies to extend the capabilities of molecular dynamics simulations in one way or another. In the first chapter, molecular dynamics simulations and the central role they play in the field of structural biology is introduced to give the reader some background on the common basis of the projects. The second chapter describes the first of these projects, where the molecular dynamics flexible fitting method for refining molecular structures of macromolecules using experimental electron density data is extended to be able to handle high-resolution density data, which are becoming increasingly commonplace. The third chapter focuses on adaptive multilevel splitting, a replica-based sampling technique that was employed in molecular dynamics simulations to measure the rate of drug molecule dissociation, a process that occurs on the order of milliseconds and above, which is out of the reach of typical molecular dynamics simulations. In the final chapter, a kinetic model of diffusion is introduced. This model allows simulation of the diffusion of small molecules in arbitrary potentials, for example, those that characterize the space around and within a membrane protein channel. The adaptive discretization scheme allows simulations between the micro- to millisecond time scales, which are typical of diffusive processes. This collection of projects is a snapshot of the diversity and versatility of current problems in structural biology that can be addressed by molecular dynamics simulations. I hope to instill in the reader a sense of how method development in molecular dynamics will expand the contributions of the field to both scientific and practical pursuits in biology.
molecular dynamics; cryo-electron microscopy; flexible fitting; adaptive multilevel splitting; rare event; kinetic model; benzamidine; trypsin; diffusion; Smoluchowski equation; self-organizing map; structure refinement
Wed, 28 Sep 2016 00:00:00 GMThttp://hdl.handle.net/2142/952862016-09-28T00:00:00ZTeo, Koon Heng IvanThe proton's longitudinal spin structure studied through the weak interaction in pp collisions
http://hdl.handle.net/2142/95285
The proton's longitudinal spin structure studied through the weak interaction in pp collisions
Jumper, Daniel S
For many years there has been limited knowledge of the spin structure of the proton. The degree to which the antiquarks and gluons of radiative origin inside the proton contribute to the total spin is particularly not well confined. The PHENIX experiment at RHIC has made measurements that have, and will, better confine these spin contributions. One of these measurements, made possible by a series of experimental upgrades, is a study of the single spin asymmetry in W boson production ($A_L^W$) in polarized proton-proton collisions. In this measurement, the parity violating weak interaction serves, compared to than previously used techniques, as a cleaner and more direct probe of flavor separated quark and antiquark spin-dependent momentum distributions. This is most significant in the case of the antiquark distributions, which are currently not well constrained. PHENIX has taken data toward this measurement in 2013, analysis of the data was performed, and preliminary $A_L^W$ results have been released. Work is currently underway to finalize these results for forthcoming publication. Once finalized, these results will be included in a global fit along with data from other experiments to reduce the uncertainty of the antiquarks' contribution to proton spin. This dissertation will detail the theoretical basis for this measurement and describe the experimental and analytic procedures used to obtain the result, with special emphasis on contributions from the author.
PHENIX; proton; nucleon; structure; polarized; spin; collider; longitudinal; Relativistic heavy ion collider (RHIC); W Boson; Asymmetry; Single spin; sea; antiquark
Thu, 22 Sep 2016 00:00:00 GMThttp://hdl.handle.net/2142/952852016-09-22T00:00:00ZJumper, Daniel S