16,295 research outputs found
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
= 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
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