Physics Commons^™

In Silico Identification Of Vaccine Candidates Against Viral Infections, Prabin Baral

FIU Electronic Theses and Dissertations

There are many viral diseases without effective treatments or vaccines. These viruses can cause catastrophic epidemics such as the Lassa, Ebola, and Marburg viruses. Similarly, the recent coronavirus pandemic is of great concern as new variants are continuously emerging with decreased susceptibility to antibodies and vaccines that were developed for earlier strains. A critical step in the immune system’s fight against viruses involves an immunological protein molecule binding to a viral protein molecule. I investigate the atomic and molecular details of binding site recognition and binding interactions and dynamics for three important viruses.

Antigens are molecules, such as viral proteins, …

12 C(E,E'Pn) Measurements Of Short Range Correlations In The Tensor-To-Scalar Interaction Transition Region, I. Korover, J. R. Pybus, A. Schmidt, F. Hauenstein, M. Duer, O. Hen, E. Piasetzky, L. B. Weinstein, D. W. Higinbotham, S. Adhikari, K. Adhikari, M. J. Amaryan, Giovanni Angelini, H. Atac, L. Barion, M. Battaglieri, A. Beck, I. Bedlinkskiy, Fatiha Benmokhtar, Steffen Strauch, Ralf W. Gothe, Krishna Chandra Neupane, Et. Al.

Faculty Publications

High-momentum configurations of nucleon pairs at short-distance are probed using measurements of the C-12(e, e' p) and C-12(e, e' pN) reactions (where N is either n or p), at high-Q(2) and x(B) > 1.1. The data span a missing-momentum range of 300-1000 MeV/c and are predominantly sensitive to the transition region of the strong nuclear interaction from a Tensor to Scalar interaction. The data are well reproduced by theoretical calculations using the Generalized Contact Formalism with both chiral and phenomenological nucleon-nucleon (NN) interaction models. This agreement suggests that the measured high missing-momentum protons up to 1000 MeV/c predominantly belong to short-ranged …

¹² C(E,E'Pn) Measurements Of Short Range Correlations In The Tensor-To-Scalar Interaction Transition Region, I. Korover, J. R. Pybus, A. Schmidt, F. Hauenstein, M. Duer, L. B. Weinstein, M. J. Amaryan, D. Bullumulla, M. Hattawy, X. Zheng, Et Al., The Clas Collaboration

Physics Faculty Publications

High-momentum configurations of nucleon pairs at short-distance are probed using measurements of the ¹²C(e,'p) and ¹²C (e,e'pN) reactions (where N is either n or p), at high Q² and 𝒙_B > 1.1. The data span a missing-momentum range of 300-1000 MeV/c and are predominantly sensitive to the transition region of the strong nuclear interaction from a tensor to scalar interaction. The data are well reproduced by theoretical calculations using the generalized contact formalism with both chiral and phenomenological nucleon-nucleon (NN) interaction models. This agreement suggests that the measured high missing-momentum protons up to 1000 MeV/c predominantly …

Characterizing Complexity In A Semiconductor With Optical Feedback From Two Mirrors, Layla M. Abrams

2020 Symposium Posters

Lasers are stable devices with a broad spectrum of applications. They can be perturbed to induce complex dynamics in their output intensity. One interesting regime in semiconductor lasers is that the output intensity of the laser emits a sequence of non-regular optical spikes. This behavior resembles that of neurons. We use a semiconductor laser with optical feedback from two mirrors to characterize the behavior of the laser's power output. The data is then analyzed by transforming the intensity time series into a sequence of patterns or words. By doing this we want to explore how the laser changes its preferred …

Comparing Proton Momentum Distributions In A = 2 And 3 Nuclei Via 2H 3H And 3He (E,E′P) Measurements, R. Cruz-Torres, F. Hauenstein, A. Schmidt, D. Nguyen, D. Abrams, H. Albataineh, S. Alsalmi, D. Androic, K. Aniol, W. Armstrong, J. Arrington, H. Atac, D. Bulumulla, C. E. Hyde, V. Khachatryan, M. N.H. Rashad, L. B. Weinstein, Z. Y. Ye, J. Zhang, Jefferson Lab Hall A Tritium Collaboration

Physics Faculty Publications

We report the first measurement of the (e, e' p) reaction cross-section ratios for Helium-3 (³He), Tritium (³H), and Deuterium (d). The measurement covered a missing momentum range of 40 ≤ p_miss ≤ 550 MeV/c, at large momentum transfer ({Q²} ≈ 1.9 (GeV/c)²) and x_B > 1, which minimized contributions from non quasi-elastic (QE) reaction mechanisms. The data is compared with planewave impulse approximation (PWIA) calculations using realistic spectral functions and momentum distributions. The measured and PWIA-calculated cross-section ratios for ³He/d and ³H/d extend to just above the typical …

Muon Capture In Nuclei: An Ab Initio Approach Based On Green's Function Monte Carlo Methods, A. Lovato, N. Rocco, Rocco Schiavilla

Physics Faculty Publications

An ab initio Green’s function Monte Carlo (GFMC) method is introduced for calculating total rates of muon weak capture in light nuclei with mass number A ≤ 12. As a first application of the method, we perform a calculation of the rate in ³H and ⁴He in a dynamical framework based on realistic two- and three-nucleon interactions and realistic nuclear charge-changing weak currents. The currents include one- and two-body terms induced by π-and ρ-meson exchange, and N-to-Δ excitation, and are constrained to reproduce the empirical value of the Gamow-Teller matrix element in tritium. We investigate the sensitivity of …

Water Entry Of Spheres At Various Contact Angles, Nathan B. Spiers, Mohammad M. Mansoor, Jesse Belden, Tadd T. Truscott

Mechanical and Aerospace Engineering Faculty Publications

It is well known that the water entry of a sphere causes cavity formation above a critical impact velocity as a function of the solid-liquid contact angle (Duez et al. 2007). Using a rough sphere with a contact angle of 120^◦, Aristoff & Bush (2009) showed that there are four different cavity shapes dependent on the Bond and Weber numbers (i.e., quasi-static, shallow, deep and surface). We experimentally alter the Bond number, Weber number and contact angle of smooth spheres and find two key additions to the literature: 1) Cavity shape also depends on the contact angle; 2) …

Instability Of Flux Flow And Production Of Vortex-Antivortex Pairs By Current-Driven Josephson Vortices In Layered Superconductors, Ahmad Sheikhzada, Alex Gurevich

Physics Faculty Publications

We report numerical simulations of the nonlinear dynamics of Josephson vortices driven by strong dc currents in layered superconductors. Dynamic equations for interlayer phase differences in a stack of coupled superconducting layers were solved to calculate a drag coefficient η(J) of the vortex as a function of the perpendicular dc current density J. It is shown that Cherenkov radiation produced by a moving vortex causes significant radiation drag increasing η(v) at high vortex velocities v and striking instabilities of driven Josephson vortices moving faster than a terminal v_c. The steady-state flux flow breaks down at ν > v …

Current-Driven Production Of Vortex-Antivortex Pairs In Planar Josephson Junction Arrays And Phase Cracks In Long-Range Order, Francisco Estellés-Duart, Miguel Ortuño, Andrés M. Somoza, Valerii M. Vinokur, Alex Gurevich

Physics Faculty Publications

Proliferation of topological defects like vortices and dislocations plays a key role in the physics of systems with long-range order, particularly, superconductivity and superfluidity in thin films, plasticity of solids, and melting of atomic monolayers. Topological defects are characterized by their topological charge reflecting fundamental symmetries and conservation laws of the system. Conservation of topological charge manifests itself in extreme stability of static topological defects because destruction of a single defect requires overcoming a huge energy barrier proportional to the system size. However, the stability of driven topological defects remains largely unexplored. Here we address this issue and investigate numerically …

Catalysis Of Stark-Tuned Interactions Between Ultracold Rydberg Atoms, A. L. Win, W. D. Williams, T. J. Carroll, C. I. Sukenik

Physics Faculty Publications

We have experimentally investigated a catalysis effect in the resonant energy transfer between ultracold ⁸⁵Rb Rydberg atoms. We studied the time dependence of the process, 34p + 34p → 34s + 35s, and observed an enhancement of 34s state population when 34d state atoms are added. We have also performed numerical model simulations, which are in qualitative agreement with experiment and indicate that the enhancement arises from a redistribution of p-state atoms due to the presence of the d-state atoms.

Random Field Disorder At An Absorbing State Transition In One And Two Dimensions, Hatem Barghathi, Thomas Vojta

Physics Faculty Research & Creative Works

We investigate the behavior of nonequilibrium phase transitions under the influence of disorder that locally breaks the symmetry between two symmetrical macroscopic absorbing states. In equilibrium systems such "random-field" disorder destroys the phase transition in low dimensions by preventing spontaneous symmetry breaking. In contrast, we show here that random-field disorder fails to destroy the nonequilibrium phase transition of the one- and two-dimensional generalized contact process. Instead, it modifies the dynamics in the symmetry-broken phase. Specifically, the dynamics in the one-dimensional case is described by a Sinai walk of the domain walls between two different absorbing states. In the two-dimensional case, …

Yoyo Lab (Prelab), David Abbott

Handouts

No abstract provided.

Yoyo Lab (In-Lab), David Abbott

Handouts

No abstract provided.

Rate Kinetics And Molecular Dynamics Of The Structural Transitions In Amyloidogenic Proteins, Timothy Michael Steckmann

FIU Electronic Theses and Dissertations

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer’s, Creutzfeld-Jacob, diabetes, Parkinson’s and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous α-helix or random-coil structure. The α-helices convert their structure to β-strands that aggregate into β-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis …

Fragmentation Of Fast Josephson Vortices And Breakdown Of Ordered States By Moving Topological Defects, Ahmad Sheikhzada, Alex Gurevich

Physics Faculty Publications

Topological defects such as vortices, dislocations or domain walls define many important effects in superconductivity, superfluidity, magnetism, liquid crystals, and plasticity of solids. Here we address the breakdown of the topologically-protected stability of such defects driven by strong external forces. We focus on Josephson vortices that appear at planar weak links of suppressed superconductivity which have attracted much attention for electronic applications, new sources of THz radiation, and low-dissipative computing. Our numerical simulations show that a rapidly moving vortex driven by a constant current becomes unstable with respect to generation of vortex-antivortex pairs caused by Cherenkov radiation. As a result, …

Significant Impacts Of Radiation Physics In The Wrf Model On The Precipitation And Dynamics Of The West African Monsoon, R. Li, J. Jin, Shih-Yu (Simon) Wang, R. R. Gillies

Plants, Soils, and Climate Faculty Publications

Precipitation from the West African Monsoon (WAM) provides food security and supports the economy in the region. As a consequence of the intrinsic complexities of the WAM’s evolution, accurate simulations of the WAM and its precipitation regime, through the application of regional climate models, are challenging. We used the coupled Weather Research and Forecasting (WRF) and Community Land Model (CLM) to explore impacts of radiation physics on the precipitation and dynamics of the WAM. Our results indicate that the radiation physics schemes not only produce biases in radiation fluxes impacting radiative forcing, but more importantly, result in large bias in …

Ion-Lithium Collision Dynamics Studied With A Laser-Cooled In-Ring Target, Daniel Fischer, Dominik Globig, Johannes Goullon, Manfred Grieser, Renate Hubele, Vitor L B D De Jesus, Aditya H. Kelkar, Aaron C. Laforge, H. Lindenblatt, Deepankar S. Misra, B. Najjari, Katharina R. Schneider, Michael Schulz, Martin Sell, Xincheng Wang

Physics Faculty Research & Creative Works

We present a novel experimental tool allowing for kinematically complete studies of break-up processes of laser-cooled atoms. This apparatus, the 'MOTReMi,' is a combination of a magneto-optical trap (MOT) and a reaction microscope (ReMi). Operated in an ion-storage ring, the new setup enables us to study the dynamics in swift ion-atom collisions on an unprecedented level of precision and detail. In the inaugural experiment on collisions with 1.5MeV/amu O8 ⁺-Li the pure ionization of the valence electron as well as the ionization-excitation of the lithium target was investigated.

Ultrafast Intense-Field Photoionization And Photofragmentation Of Systematic Series Of Substituted Organic Molecules, Timothy D. Scarborough

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

The abundance and relevance of organic molecules similar to benzene makes their study important. Studying the interactions of such molecules with intense light fields has implications for the generation of short-wavelength radiation, attosecond science, high-harmonic generation, and many other fields. However, the computing power necessary to complete fully ab initio calculations describing molecules of this size does not exist; this leaves theoretical studies to rely on assumptions and approximations just to calculate the energies of the ground state. Including any sort of dynamics in these calculations is prohibitively complicated, and this makes experimental observations important. Since many organic molecules are …

The Inexorable Resistance Of Inertia Determines The Initial Regime Of Drop Coalescence, Joseph Paulsen, Justin C. Burton, Sidney R. Nagel, Santosh Appathurai, Michael T. Harris, Osman A. Basaran

Physics - All Scholarship

Drop coalescence is central to diverse processes involving dispersions of drops in industrial, engineering, and scientific realms. During coalescence, two drops first touch and then merge as the liquid neck connecting them grows from initially microscopic scales to a size comparable to the drop diameters. The curvature of the interface is infinite at the point where the drops first make contact, and the flows that ensue as the two drops coalesce are intimately coupled to this singularity in the dynamics. Conventionally, this process has been thought to have just two dynamical regimes: a viscous and an inertial regime with a …

The Role Of The Bow Shock In Solar Wind-Magnetosphere Coupling, R E. Lopez, V G. Merkin, J G. Lyon

Dartmouth Scholarship

No abstract provided.

Charge Dynamics In Highly Insulating Space Craft Materials, Alec Sim, John R. Dennison

All Physics Faculty Publications

We present a preliminary report on the theoretical and experimental study of transport models in highly insulating materials. The report is developed in four sections; first we give background on the nature of the problems in space craft charging, the contributions and connections made by the Utah State material physics group. Second we discuss the density of states to explore the connections between material composition and the microscopic and macroscopic transport equations. Third from Maxwell’s equations we present an overview of the transport equations. Finally we present preliminary results using experimental data on KaptonTM, the transport equations and relevant expressions …

Field Line Distribution Of Density At L=4.8 Inferred From Observations By Cluster, R E. Denton, P Décréau, M J. Engebretson, F Darrouzet

Dartmouth Scholarship

For two events observed by the CLUSTER space- craft, the field line distribution of mass density ρ was inferred from Alfve ́n wave harmonic frequencies and compared to the electron density ne from plasma wave data and the oxy- gen density nO+ from the ion composition experiment. In one case, the average ion mass M≡ρ/ne was about 5amu (28 October 2002), while in the other it was about 3 amu (10 September 2002). Both events occurred when the CLUSTER 1 (C1) spacecraft was in the plasmatrough. Nevertheless, the electron density ne was significantly lower for the first event (ne =8 …

Retrieving Photorecombination Cross Sections Of Atoms From High-Order Harmonic Spectra, Shinichiro Minemoto, Toshihito Umegaki, Yuichiro Oguchi, Toru Morishita, Anh-Thu Le, Shinichi Watanabe, Hirofumi Sakai

Physics Faculty Research & Creative Works

We observe high-order harmonic spectra generated from a thin atomic medium, Ar, Kr, and Xe, by intense 800-nm and 1300-nm femtosecond pulses. A clear signature of a single-atom response is observed in the harmonic spectra. Especially in the case of Ar, a Cooper minimum, reflecting the electronic structure of the atom, is observed in the harmonic spectra. We successfully extract the photorecombination cross sections of the atoms in the field-free condition with the help of an accurate recolliding electron wave packet. The present protocol paves the way for exploring ultrafast imaging of molecular dynamics with attosecond resolution.

Toy Blocks And Rotational Physics, Gabriele U. Varieschi, Isabel R. Jully

Physics Faculty Works

Have you ever observed a child playing with toy blocks? A favorite game is to build towers and then make them topple like falling trees. To the eye of a trained physicist this should immediately look like an example of the physics of “falling chimneys,” when tall structures bend and break in mid-air while falling to the ground. The game played with toy blocks can actually reproduce well what is usually seen in photographs of falling towers, such as the one that appeared on the cover of the September 1976 issue of The Physics Teacher.1 In this paper we describe …

Relativistic And Radiative Corrections To The Mollow Spectrum, Jorg Evers, Ulrich D. Jentschura, Christoph H. Keitel

Physics Faculty Research & Creative Works

The incoherent inelastic part of the resonance fluorescence spectrum of a laser-driven atom is known as the Mollow spectrum [B. R. Mollow, Phys. Rev. 188, 1969 (1969)]. Starting from this level of description, we discuss theoretical foundations of high-precision spectroscopy using the resonance fluorescence light of strongly laser-driven atoms. Specifically, we evaluate the leading relativistic and radiative corrections to the Mollow spectrum, up to the relative orders of ( Z α )² and α ( Z α )² , respectively, and Bloch-Siegert shifts as well as stimulated radiative corrections involving off-resonant virtual states. Complete results are provided for …

Simulations Of Resonant Alfvén Waves Generated By Artificial Hf Heating Of The Auroral Ionosphere, D Pokhotelov, W Lotko, A V. Streltsov

Dartmouth Scholarship

Numerical two-dimensional two-fluid MHD sim- ulations of dynamic magnetosphere-ionosphere (MI) cou- pling have been performed to model the effects imposed on the auroral ionosphere by a powerful HF radio wave trans- mitter. The simulations demonstrate that modifications of the ionospheric plasma temperature and recombination due to artificial heating may trigger the ionospheric feedback in- stability when the coupled MI system is close to the state of marginal stability. The linear dispersion analysis of MI coupling has been performed to find the favorable conditions for marginal stability of the system. The development of the ionospheric feedback instability leads to the generation …

High-Latitude Propagation Studies Using A Meridional Chain Of Lf/Mf/Hf Receivers, J Labelle

Dartmouth Scholarship

For over a decade, Dartmouth College has oper- ated programmable radio receivers at multiple high-latitude sites covering the frequency range 100–5000 kHz with about a 1-s resolution. Besides detecting radio emissions of auro- ral origin, these receivers record characteristics of the iono- spheric propagation of natural and man-made signals, docu- menting well-known effects, such as the diurnal variation in the propagation characteristics of short and long waves, and also revealing more subtle effects. For example, at auroral zone sites in equinoctial conditions, the amplitudes of dis- tant transmissions on MF/HF frequencies are often enhanced by a few dB just before …

Limits To Performance Improvement Provided By Balanced Interferometers And Balanced Detection In Oct/Ocm Instruments, David Liao, Adam E. Pivonka, Brendan R. Haberle, Daniel C. Petersen, Barbara M. Hoeling, Richard C. Haskell

All HMC Faculty Publications and Research

We compare the dynamic range of OCT/OCM instruments configured with unbalanced interferometers, e.g., Michelson interferometers, with that of instruments utilizing balanced interferometers and balanced photodetection. We define the dynamic range (DR) as the ratio of the maximum fringe amplitude achieved with a highly reflecting surface to the root-mean-square (rms) noise. Balanced systems achieve a dynamic range 2.5 times higher than that of a Michelson interferometer, enabling an image acquisition speed roughly 6 times faster. This maximum improvement occurs at light source powers of a few milliwatts. At light source powers higher than 30 mW, the advantage in acquisition speed of …

Superferromagnetic Domain State Dynamics In Discontinuous Cofe/Al2o3, Christian Binek

Christian Binek Publications

Magnetization hysteresis and AC susceptibility measurements were performed on the discontinuous metal–insulator multilayer [Co80Fe20(1.4 nm)/Al2O3(3 nm)]10. CoFe forms ferromagnetic single-previous domain term particles being embedded in the Al2O3 matrix. Due to strong dipolar inter-particle interactions a “previous superferromagnetic term” correlation of particle moments was previously stated. The dynamical magnetic properties of the superferromagnet can be understood in the framework of previous domain term wall motion in an impure ferromagnet. Kinetic simulations are employed, which are based on field and temperature-dependent previous domain term wall velocities. The magnetization hysteresis as well as the AC susceptibility, χ′−iχ′′, are calculated and compared to …

A Study Of Pc-5 Ulf Oscillations, M K. Hudson, R E. Denton, M R. Lessard, E G. Miftakhova, R R. Anderson

Dartmouth Scholarship

A study of Pc-5 magnetic pulsations using data from the Combined Release and Radiation Effects Satellite (CRRES) was carried out. Three-component dynamic mag- netic field spectrograms have been used to survey ULF pul- sation activity for the approximate fourteen month lifetime of CRRES. Two-hour panels of dynamic spectra were exam- ined to find events which fall into two basic categories: 1) toroidal modes (fundamental and harmonic resonances) and 2) poloidal modes, which include compressional oscillations. The occurence rates were determined as a function of L value and local time. The main result is a comparable probabil- ity of occurence of …