Statistical Geometry of Packing Defects of Lattice Chain Polymer from Enumeration and Sequential Monte Carlo Method

Voids exist in proteins as packing defects and are often associated with protein functions. We study the statistical geometry of voids in two-dimensional lattice chain polymers. We define voids as topological features and develop a simple algorithm for their detection. For short chains, void geometry is examined by enumerating all conformations. For long chains, the space of void geometry is explored using sequential Monte Carlo importance sampling and resampling techniques. We characterize the relationship of geometric properties of voids with chain length, including probability of void formation, expected number of voids, void size, and wall size of voids. We formalize the concept of packing density for lattice polymers, and further study the relationship between packing density and compactness, two parameters frequently used to describe protein packing. We find that both fully extended and maximally compact polymers have the highest packing density, but polymers with intermediate compactness have low packing density. To study the conformational entropic effects of void formation, we characterize the conformation reduction factor of void formation and found that there are strong end-effect. Voids are more likely to form at the chain end. The critical exponent of end-effect is twice as large as that of self-contacting loop formation when existence of voids is not required. We also briefly discuss the sequential Monte Carlo sampling and resampling techniques used in this study.Comment: 29 pages, including 12 figure

Testing Alternative Theories of the Property Price-Trading Volume Correlation

This article examines the correlation between the real housing price and trading volume. Contrary to the predictions of standard rational expectation models, a robust positive correlation between the two variables is identified. While no clear lead-lag relationship is found in the raw data, which is more consistent with the downpayment effect model, the medium-run component of the trading volume tends to lead (and Granger cause) the corresponding component of the property price, which is more consistent with the search theoretic model. An explanation for this difference in behavior is suggested and several future research directions are provided.

Thromboembolic complications of COVID-19

© 2020, American Society of Emergency Radiology. The symptomology of patients afflicted with novel 2019 coronavirus disease (SARS-CoV-2 or COVID-19) has varied greatly, ranging from the asymptomatic state to debilitating hypoxemic respiratory failure caused by severe atypical viral pneumonia. Patients may also develop a hyper-inflammatory state that can lead to multi-organ failure. It has become increasingly apparent that, as part of the hyper-inflammatory state, COVID-19 infection increases susceptibility to systemic thromboembolic complications that can contribute to rapid clinical deterioration or demise. This article aims to review imaging features of various systemic thrombotic complications in six patients with moderate to severe disease. This case series includes examples of pulmonary embolism, stroke, right ventricular thrombosis, renal vein thrombosis, and aortic thrombosis with leg ischemia

Electron interferometry with nano-gratings

We present an electron interferometer based on near-field diffraction from two nanostructure gratings. Lau fringes are observed with an imaging detector, and revivals in the fringe visibility occur as the separation between gratings is increased from 0 to 3 mm. This verifies that electron beams diffracted by nanostructures remain coherent after propagating farther than the Talbot length $z_T = 2d^2/\lambda$ = 1.2 mm, and hence is a proof of principle for the function of a Talbot-Lau interferometer for electrons. Distorted fringes due to a phase object demonstrates an application for this new type of electron interferometer.Comment: 4 pgs, 6 figure

A New Algorithm for Protein Design

We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach produces sequences that are likely to fold into desired structures. Our method is a significant improvement over previous attempts which used the energy function for designing sequences.Comment: 10 pages latex 2.09 no figures. Use uufiles to decod

Entanglement and the nonlinear elastic behavior of forests of coiled carbon nanotubes

Helical or coiled nanostructures have been object of intense experimental and theoretical studies due to their special electronic and mechanical properties. Recently, it was experimentally reported that the dynamical response of foamlike forest of coiled carbon nanotubes under mechanical impact exhibits a nonlinear, non-Hertzian behavior, with no trace of plastic deformation. The physical origin of this unusual behavior is not yet fully understood. In this work, based on analytical models, we show that the entanglement among neighboring coils in the superior part of the forest surface must be taken into account for a full description of the strongly nonlinear behavior of the impact response of a drop-ball onto a forest of coiled carbon nanotubes.Comment: 4 pages, 3 figure

Non-magnetic semiconductor spin transistor

We propose a spin transistor using only non-magnetic materials that exploits the characteristics of bulk inversion asymmetry (BIA) in (110) symmetric quantum wells. We show that extremely large spin splittings due to BIA are possible in (110) InAs/GaSb/AlSb heterostructures, which together with the enhanced spin decay times in (110) quantum wells demonstrates the potential for exploitation of BIA effects in semiconductor spintronics devices. Spin injection and detection is achieved using spin-dependent resonant interband tunneling and spin transistor action is realized through control of the electron spin lifetime in an InAs lateral transport channel using an applied electric field (Rashba effect). This device may also be used as a spin valve, or a magnetic field sensor. The electronic structure and spin relaxation times for the spin transistor proposed here are calculated using a nonperturbative 14-band k.p nanostructure model.Comment: Accepted for publication in Applied Physics Letter

A New Monte Carlo Algorithm for Protein Folding

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare to published Monte Carlo studies. In all cases our algorithms are faster than all previous ones, and in several cases we find new minimal energy states. In addition to ground states, our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett., revised version with changes in the tex

Regulatory networks and connected components of the neutral space

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory systems is neutrality - typically a large number of alternative network structures give rise to the necessary dynamics. Here we study the discretized regulatory dynamics of the yeast cell cycle [Li et al., PNAS, 2004] and the set of networks capable of reproducing it, which we call functional. Among these, the empirical yeast wildtype network is close to optimal with respect to sparse wiring. Under point mutations, which establish or delete single interactions, the neutral space of functional networks is fragmented into 4.7 * 10^8 components. One of the smaller ones contains the wildtype network. On average, functional networks reachable from the wildtype by mutations are sparser, have higher noise resilience and fewer fixed point attractors as compared with networks outside of this wildtype component.Comment: 6 pages, 5 figure