Department of Physics Articles

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Coset Group Construction of Multidimensional Number Systems
(2014-07) Petrache, Horia I
Extensions of real numbers in more than two dimensions, in particular quaternions and octonions, are finding applications in physics due to the fact that they naturally capture symmetries of physical systems. However, in the conventional mathematical construction of complex and multicomplex numbers multiplication rules are postulated instead of being derived from a general principle. A more transparent and systematic approach is proposed here based on the concept of coset product from group theory. It is shown that extensions of real numbers in two or more dimensions follow naturally from the closure property of finite coset groups adding insight into the utility of multidimensional number systems in describing symmetries in nature.
Current Induced Vortex Wall Dynamics in Helical Magnetic Systems
(Elsevier, 2015-03) Roostaei, Bahman; Department of Physics, School of Science
Nontrivial topology of interfaces separating phases with opposite chirality in helical magnetic metals result in new effects as they interact with spin polarized current. These interfaces or vortex walls consist of a one dimensional array of vortex lines. We predict that adiabatic transfer of angular momentum between vortex array and spin polarized current will result in topological Hall effect in multi-domain samples. Also we predict that the motion of the vortex array will result in a new damping mechanism for magnetic moments based on Lenz’s law. We study the dynamics of these walls interacting with electric current and use fundamental electromagnetic laws to quantify those predictions. On the other hand discrete nature of vortex walls affects their pinning and results in low depinning current density. We predict the value of this current using collective pinning theory.
A data-driven alternative to the fractional Fokker–Planck equation
(IOP, 2015-07) Pressé, Steve; Department of Physics, School of Science
Anomalous diffusion processes are ubiquitous in biology and arise in the transport of proteins, vesicles and other particles. Such anomalously diffusive behavior is attributed to a number of factors within the cell including heterogeneous environments, active transport processes and local trapping/binding. There are a number of microscopic principles?such as power law jump size and/or waiting time distributions?from which the fractional Fokker?Planck equation (FFPE) can be derived and used to provide mechanistic insight into the origins of anomalous diffusion. On the other hand, it is fair to ask if other microscopic principles could also have given rise to the evolution of an observed density profile that appears to be well fit by an FFPE. Here we discuss another possible mechanistic alternative that can give rise to densities like those generated by FFPEs. Rather than to fit a density (or concentration profile) using a solution to the spatial FFPE, we reconstruct the profile generated by an FFPE using a regular FPE with a spatial and time-dependent force. We focus on the special case of the spatial FFPE for superdiffusive processes. This special case is relevant to, for example, active transport in a biological context. We devise a prescription for extracting such forces on synthetically generated data and provide an interpretation to the forces extracted. In particular, the time-dependence of forces could tell us about ATP depletion or changes in the cell's metabolic activity. Modeling anomalous behavior with normal diffusion driven by these effective forces yields an alternative mechanistic picture that, ultimately, could help motivate future experiments.
Survivals of mouse oocytes approach 100% after vitrification in 3-fold diluted media and ultra-rapid warming by an IR laser pulse
(Elsevier, 2014-06) Jin, Bo; Kleinhans, F.W.; Mazur, Peter; Department of Physics, School of Science
Vitrification is the most sought after route to the cryopreservation of animal embryos and oocytes and other cells of medical, genetic, and agricultural importance. Current thinking is that successful vitrification requires that cells be suspended in and permeated by high concentrations of protective solutes and that they be cooled at very high rates to below − 100°C. We report here that neither of these beliefs holds for mouse oocytes. Rather, we find that if mouse oocytes are suspended in media that produce considerable osmotic dehydration before vitrification and are subsequently warmed at ultra high rates (10,000,000°C/min) achieved by a laser pulse, nearly 100% will survive even when cooled rather slowly and when the concentration of solutes in the medium is only 1/3rd of standard.
Monte Carlo Simulations of HIV Capsid Protein Homodimer
(ACS, 2015-06) Zhu, Fangqiang; Chen, Bo; Department of Physics, School of Science
Capsid protein (CA) is the building block of virus coats. To help understand how the HIV CA proteins self-organize into large assemblies of various shapes, we aim to computationally evaluate the binding affinity and interfaces in a CA homodimer. We model the N- and C-terminal domains (NTD and CTD) of the CA as rigid bodies and treat the five-residue loop between the two domains as a flexible linker. We adopt a transferrable residue-level coarse-grained energy function to describe the interactions between the protein domains. In seven extensive Monte Carlo simulations with different volumes, a large number of binding/unbinding transitions between the two CA proteins are observed, thus allowing a reliable estimation of the equilibrium probabilities for the dimeric vs monomeric forms. The obtained dissociation constant for the CA homodimer from our simulations, 20–25 μM, is in reasonable agreement with experimental measurement. A wide range of binding interfaces, primarily between the NTDs, are identified in the simulations. Although some observed bound structures here closely resemble the major binding interfaces in the capsid assembly, they are statistically insignificant in our simulation trajectories. Our results suggest that although the general purpose energy functions adopted here could reasonably reproduce the overall binding affinity for the CA homodimer, further adjustment would be needed to accurately represent the relative strength of individual binding interfaces.
Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin
(American Chemical Society, 2014-06-19) Pressé, Steve; Peterson, Jack; Lee, Julian; Elms, Phillip; MacCallum, Justin L.; Marqusee, Susan; Bustamante, Carlos; Dill, Ken; Department of Physics, School of Science
Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others.
Stochastic approach to the molecular counting problem in superresolution microscopy.
(PNAS, 2015-01-13) Rollins, Geoffrey C.; Yen Shin, Jae; Bustamante, Carlos; Pressé, Steve; Department of Physics, School of Science
Superresolution imaging methods--now widely used to characterize biological structures below the diffraction limit--are poised to reveal in quantitative detail the stoichiometry of protein complexes in living cells. In practice, the photophysical properties of the fluorophores used as tags in superresolution methods have posed a severe theoretical challenge toward achieving this goal. Here we develop a stochastic approach to enumerate fluorophores in a diffraction-limited area measured by superresolution microscopy. The method is a generalization of aggregated Markov methods developed in the ion channel literature for studying gating dynamics. We show that the method accurately and precisely enumerates fluorophores in simulated data while simultaneously determining the kinetic rates that govern the stochastic photophysics of the fluorophores to improve the prediction's accuracy. This stochastic method overcomes several critical limitations of temporal thresholding methods.
Effects of Lipid Interactions on Model Vesicle Engulfment by Alveolar Macrophages
(Elsevier B.V., 2014-02-04) Justice, Matthew J.; Petrusca, Daniela N.; Rogozea, Adriana L.; Williams, Justin A.; Schweitzer, Kelly S.; Petrache, Irina; Wassall, Stephen R.; Petrache, Horia I.; Department of Physics, School of Science
The engulfment function of macrophages relies on complex molecular interactions involving both lipids and proteins. In particular, the clearance of apoptotic bodies (efferocytosis) is enabled by externalization on the cell target of phosphatidylserine lipids, which activate receptors on macrophages, suggesting that (local) specific lipid-protein interactions are required at least for the initiation of efferocytosis. However, in addition to apoptotic cells, macrophages can engulf foreign bodies that vary substantially in size from a few nanometers to microns, suggesting that nonspecific interactions over a wide range of length scales could be relevant. Here, we use model lipid membranes (made of phosphatidylcholine, phosphatidylserine, and ceramide) and rat alveolar macrophages to show how lipid bilayer properties probed by small-angle x-ray scattering and solid-state 2H NMR correlate with engulfment rates measured by flow cytometry. We find that engulfment of protein-free model lipid vesicles is promoted by the presence of phosphatidylserine lipids but inhibited by ceramide, in accord with a previous study of apoptotic cells. We conclude that the roles of phosphatidylserine and ceramide in phagocytosis is based, at least in part, on lipid-mediated modification of membrane physical properties, including interactions at large length scales as well as local lipid ordering and possible domain formation.
How does Water Pass through a Sugar Transporter?
(Elsevier B.V., 2014-03-18) Zhu, Fangqiang; Department of Physics, School of Science
Atom-Light Hybrid Interferometer
(APS, 2015-07) Chen, Bing; Qiu, Shuying; Guo, Jinxian; Chen, L. Q.; Ou, Z. Y.; Zhang, Weiping; Department of Physics, School of Science
A new type of hybrid atom-light interferometer is demonstrated with atomic Raman amplification processes replacing the beam splitting elements in a traditional interferometer. This nonconventional interferometer involves correlated optical and atomic waves in the two arms. The correlation between atoms and light developed with the Raman process makes this interferometer different from conventional interferometers with linear beam splitters. It is observed that the high-contrast interference fringes are sensitive to the optical phase via a path change as well as the atomic phase via a magnetic field change. This new atom-light correlated hybrid interferometer is a sensitive probe of the atomic internal state and should find wide applications in precision measurement and quantum control with atoms and photons.

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