Biological and Chemical Physics Commons^™

Toward Improving Understanding Of The Structure And Biophysics Of Glycosaminoglycans, Elizabeth K. Whitmore

Electronic Theses and Dissertations

Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) that mediate PG bioactivities, including signal transduction, tissue morphogenesis, and matrix assembly. To understand GAG function, it is important to understand GAG structure and biophysics at atomic resolution. This is a challenge for existing experimental and computational methods because GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharides. Molecular dynamics (MD) simulations come close to overcoming this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies conformations from unbiased all-atom explicit-solvent MD simulations of short GAG polymers ...

Statistics Of Velocity Fluctuations In A Homogeneous Liquid Fluidized Bed, Elise Alméras, Frédéric Risso, Olivier Masbernat, Rodney O. Fox

Chemical and Biological Engineering Publications

This work reports an experimental investigation of a liquid-solid fluidized bed involving inertial particles at a large Reynolds number. Owing to optical techniques and index matching, the statistics of the velocity fluctuations of both the particles and the liquid are measured for a wide range of the particle volume fraction αp. The dynamics of the fluctuations suggests that the flow possesses the following three properties: (1) The liquid volume involves a wake region in which vertical fluctuations are negative and an interstitial region where they are positive. (2) The statistics of the horizontal fluctuations are similar to vertical ones, except ...

Determination Of The Rydberg Constant From The Emission Spectra Of H And He+, Kyle D. Shaffer

Ramifications

Abstract

In this experiment, the Rydberg constants for the hydrogen atom and He⁺ were determined by analysis of the emission spectra of Hand He, respectively, in comparison to the principal quantum numbers of each transition. Using both a hydrogen and then a helium atomic lamp attached to a 0.5 m grating spectrometer and a photomultiplier detector (PMT), a change in voltage detected by the PMT can be paired with a corresponding wavelength passing through the spectrometer from each emission peak in the visible to ultraviolet range. The peaks acquired from this change in voltage were analyzed to find their ...

Competitive Formation Of Intercalated Versus Supported Metal Nanoclusters During Deposition On Layered Materials With Surface Point Defects, Yong Han, Ann Lii-Rosales, Michael C. Tringides, James W. Evans

Ames Laboratory Accepted Manuscripts

Intercalated metal nanoclusters (NCs) can be formed under the surface of graphite after sputtering to generate surface “portal” defects that allow deposited atoms to reach the subsurface gallery. However, there is a competition between formation of supported NCs on top of the surface and intercalated NCs under the surface, the latter only dominating at sufficiently high temperature. A stochastic model incorporating appropriate system thermodynamics and kinetics is developed to capture this complex and competitive nucleation and growth process. Kinetic Monte Carlo simulation shows that the model captures experimental trends observed for Cu and other metals and reveals that higher temperatures ...

Shallow-Circuit Variational Quantum Eigensolver Based On Symmetry-Inspired Hilbert Space Partitioning For Quantum Chemical Calculations, Feng Zhang, Niladri Gomes, Noah F. Berthusen, Peter P. Orth, Cai-Zhuang Wang, Kai-Ming Ho, Yong-Xin Yao

Physics and Astronomy Publications

Development of resource-friendly quantum algorithms remains highly desirable for noisy intermediate-scale quantum computing. Based on the variational quantum eigensolver (VQE) with unitary coupled-cluster Ansatz, we demonstrate that partitioning of the Hilbert space made possible by the point-group symmetry of the molecular systems greatly reduces the number of variational operators by confining the variational search within a subspace. In addition, we found that instead of including all subterms for each excitation operator, a single-term representation suffices to reach required accuracy for various molecules tested, resulting in an additional shortening of the quantum circuit by a factor of 4–8. With these ...

Power Amplification Strategies Across Animals, Rayhan Asif

Williams Honors College, Honors Research Projects

Animals use muscles for movement, but some have evolved mechanisms to exceed maximum power used in a motion known as power amplification. In this literature review, I analyzed and compared the evolution of structures capable of power amplification between species. Structures capable of power amplification were broken down into the basic components of the engine, amplifier, and tool. The species analyzed were found to possess necessary structures for power amplification which were relatively similar to each other in morphology, but varied greatly in function. The ease with which these structures evolved was evaluated based on the amount of divergence which ...

Physical Models Of Living Systems 2nd Ed, New Chapter: Demographic Variation In Epidemic Spread, Philip C. Nelson

Department of Physics Papers

This chapter extends the first edition of Physical Models of Living Systems (WH Freeman 2015). This preliminary version is made freely available as-is in the hope that it will be useful.

Composite Network Of Actin And Microtubule Filaments, Self-Organization And Steady-State Dynamics, Leila Farhadi

Doctoral Dissertations

Actin and microtubule filaments, with their auxiliary proteins, enable the cytoskeleton to perform vital processes in the cell by tuning the organizational, mechanical properties and dynamics of the network. Despite their critical importance and interactions in cells, we are only beginning to uncover information about the composite network. Here, I use florescence microscopy to explore the role of filaments characteristics, interactions and activities in the self-organization and steady-state dynamics of the composite network of filaments. First, I discuss active self-organization of semiflexible actin and rigid microtubule filaments in the 2D composite network while myosin II and kinesin-1 motor proteins propel ...

Controlled Membrane Remodeling By Nanospheres And Nanorods: Experiments Targeting The Design Principles For Membrane-Based Materials, Sarah Zuraw-Weston

Doctoral Dissertations

In this thesis we explore two experimental systems probing the interactions of nanoparticles with lipid bilayer membranes. Inspired by the ability of cell membranes to alter their shape in response to bound particles, we report two experimental studies: one of nanospheres the other of long, slender nano-rods binding to lipid bilayer vesicles and altering the membrane shape. Our work illuminates the role of particle geometry, particle concentration, adhesion strength and membrane tension in how membrane morphology is determined. We combine giant unilamellar vesicles with oppositely charged nanoparticles, carefully tuning adhesion strength, membrane tension and particle concentration.

In the case of ...

Live Cell Super-Resolution Microscopy Quanitifies An Interaction Between Influenza Hemagglutinin And Phosphatidylinositol 4,5-Bisphosphate, Jaqulin N. Wallace

Electronic Theses and Dissertations

Influenza virus, colloquially known as the flu, is an acute respiratory disease that infects several millions of individuals each year in the U.S. and kills tens of thousands of those infected. Yearly viral vaccines are widely available, however, due to the virus’s high mutation rate, their efficacy varies greatly. Due to the variability in vaccine efficiency against seasonal influenza, and the potential for even more pathogenic versions of influenza to emerge at any time, there is a high demand for a universal treatment option.

Influenza virus hijacks a variety of host cell components in order to replicate. The ...

Physical Models Of Living Systems 2nd Ed, New Chapter: Random Walks On An Energy Landscape, Philip C. Nelson

Department of Physics Papers

This chapter extends the first edition of Physical Models of Living Systems (WH Freeman 2015). This preliminary version is made freely available as-is in the hope that it will be useful.

Physics 516: Electromagnetic Phenomena (Spring 2020), Philip C. Nelson

Department of Physics Papers

These course notes are made publicly available in the hope that they will be useful. All reports of errata will be gratefully received. I will also be glad to hear from anyone who reads them, whether or not you find errors: pcn@upenn.edu.

Stability Of Group Four Monochalcogenides In Water And Air, William Shattuck

Theses and Dissertations

Previously published works have simulated the behavior of monolayer group IV monochalcogenides and predicted them to have very useful electronic properties. These simulations have also predicted that monolayers of group IV monochalcogenides will degrade quickly when exposed to water, even in extremely low concentrations. We hypothesize that thin samples of these materials will show signs of degradation if left in air and in water for an extended period of time.

Samples of each of the four monochalcogenides (GeS, GeSe, SnS and SnSe) were exfoliated onto clean oxidized silicon substrates. Chemical analysis showed the SnSe samples were contaminated, so they were ...

Growth And Stability Of Pb Intercalated Phases Under Graphene On Sic, Shaojiang Chen, Patricia A. Thiel, E. Conrad, Michael C. Tringides

Chemistry Publications

Graphene intercalation is a novel way to control graphene's band structure and generate two-dimensional quantum materials with unusual spintronic and electronic properties. Despite its importance, information about the intercalation mechanism is lacking, especially the role of low density domain boundaries between regions of graphene of different thickness. With high resolution surface diffraction we have systematically studied Pb intercalation on epi-graphene grown on SiC, with domain boundaries between buffer and single layer graphene. By examining the evolution of different diffraction spots as a function of temperature, the location of Pb and stability of the intercalated phases underneath were determined.

Characterizing Childhood And Diet In Migration Period Hungary, Kirsten A. Verostick

Graduate Theses and Dissertations

This project investigates children, childhood and diet of two different Migration Period (4^th-8^th century AD) populations, the Gepids and the Avars, in the Great Hungarian Plain. The main goal was to assess whether there are differences in treatment of children and differences in breastfeeding and weaning practices in these distinct sites and populations. Secondarily, this research also focused on characterizing diet for the Gepids and the Avars at four different sites from the Migration Period, to understand how the migration and settling into the region and the assimilation of other groups into the two populations affected their ...

High Layer Uniformity Of Two-Dimensional Materials Demonstrated Surprisingly From Broad Features In Surface Electron Diffraction, Shen Chen, Michael Horn Von Hoegen, Patricia A. Thiel, Adam Kaminski, Benjamin Schrunk, Thanassis Speliotis, Edward Henry Conrad, Michael C. Tringides

Chemistry Publications

Paradoxically a very broad diffraction background, named the Bell-Shaped-Component (BSC), has been established as a feature of graphene growth. Although the BSC has been present in the earlier literature it has been ignored. Recent diffraction studies as a function of electron energy have shown that the BSC is not related to scattering interference. The BSC is a very strong effect, but its origin is still unclear. Here, additional experiments are carried out as a function of temperature while monitoring changes in the intensity of different spots over the range that single-layer-graphene (SLG) grows. Quantitative fitting of the profiles shows that ...

Protein Conformational Entropy Is Not Slaved To Water, Bryan S Marques, Matthew A Stetz, Christine Jorge, Kathleen G Valentine, A Joshua Wand, Nathaniel V Nucci

Faculty Scholarship for the College of Science & Mathematics

Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The "solvent slaving" model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side ...

Period Estimation And Noise In A Neutrally Stable Stochastic Oscillator, Kevin R. Sanft, Ben F. M. Intoy

Spora: A Journal of Biomathematics

The periods of the orbits for the well-mixed cyclic three-species Lotka-Volterra model far away from the fixed point are studied. For finite system sizes, a discrete stochastic approach is employed and periods are found via wavelet analysis. As the system size is increased, a hierarchy of approximations ranging from Poisson noise to Gaussian noise to deterministic models are utilized. Based on the deterministic equations, a mathematical relationship between a conserved quantity of the model and the period of the population oscillations is found. Exploiting this property we then study the deterministic conserved quantity and period noise in finite size systems.

Pressure-Stabilized Divalent Ozonide Cao3 And Its Impact On Earth’S Oxygen Cycles, Yanchao Wang, Meiling Xu, Liuxiang Yang, Bingmin Yan, Qin Qin, Xuecheng Shao, Yunwei Zhang, Dajian Huang, Xiaohuan Lin, Jian Lv, Dongzhou Zhang, Huiyang Gou, Ho-Kwang Mao, Changfeng Chen, Yanming Ma

Physics & Astronomy Faculty Publications

High pressure can drastically alter chemical bonding and produce exotic compounds that defy conventional wisdom. Especially significant are compounds pertaining to oxygen cycles inside Earth, which hold key to understanding major geological events that impact the environment essential to life on Earth. Here we report the discovery of pressure-stabilized divalent ozonide CaO3 crystal that exhibits intriguing bonding and oxidation states with profound geological implications. Our computational study identifies a crystalline phase of CaO3 by reaction of CaO and O2 at high pressure and high temperature conditions; ensuing experiments synthesize this rare compound under compression in a diamond anvil cell with ...

Pressure Driven Desalination Utilizing Nanomaterials, Fangyou Xie

Master's Theses

Nanomaterials such as graphene oxide and carbon nanotubes, have demonstrated excellent properties for membrane desalination, including decrease of maintenance, increase of flux rate, simple solution casting, and impressive chemical inertness. Here, two projects are studied to investigate nanocarbon based membrane desalination. The first project is to prepare hybrid membranes with amyloid fibrils intercalated with graphene oxide sheets. The addition of protein amyloid fibrils expands the interlayer spacing between graphene oxide nanosheets and introduces additional functional groups in the diffusion pathways, resulting in increase of flux rate and rejection rate for the organic dyes. Amyloid fibrils also provide structural assistance to ...