Study of a model for the folding of a small protein

We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the self-avoiding energy. In particular we find an improved free-energy profile. We also compare the efficiency of the multidimensional replica exchange method with the widely used parallel tempering.Comment: typos corrected, one figure adde

DNA double helices for single molecule electronics

The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of the DNA strands provides a possibility to drive the electric current through the DNA by the perpendicular electric (gating) field. The transistor effect in the poly(G)-poly(C) synthetic DNA is demonstrated within a simple model approach. We put forward experimental setups to observe the predicted effect and discuss possible device applications of DNA. In particular, we propose a design of the single molecule analog of the Esaki diode.Comment: 4 pages, 4 figur

An Analysis of Airline Quality Rating Components Using Bayesian Methods

The Airline Quality Rating, a unique metric that is of interval scale and is comparable across carriers and time periods, is a quantitative evaluation of the quality of U.S. domestic air carriers based on data that is collected and published by the U.S. Bureau of Transportation Statistics. One may gain insight into the relationship of the AQR metric to the carriers to which it is applied by grouping those carriers and examining the effects of the resulting groupings on the four individual factors that comprise the AQR. This study used Bayesian hierarchical modeling techniques to examine the differences between three carrier groupings (legacy, low-cost, and regional) on a longitudinal basis over a period of six years. Based on the results of a Bayesian two-way analysis of variance (BANOVA), results showed significant differences between the mishandled baggage, denied boardings, and customer complaints of the data sets. Thus, sufficient evidence was found to support the premise that different econometric models are needed to broaden stride ins air carrier service quality improvements. Based on the results of the Bayesian two-way analysis of variance, credible differences in on-time arrivals, mishandled baggage, and customer complaints were indicated. These results imply a rejection of the null hypothesis, Ho, for those data sets. There were no credible differences indicated between legacy, regional, and low-cost carriers regarding the denied boarding data set, implying a failure to reject the null hypothesis in that particular case

Some Fundamental Properties of a Multivariate von Mises Distribution

In application areas like bioinformatics multivariate distributions on angles are encountered which show significant clustering. One approach to statistical modelling of such situations is to use mixtures of unimodal distributions. In the literature (Mardia et al., 2011), the multivariate von Mises distribution, also known as the multivariate sine distribution, has been suggested for components of such models, but work in the area has been hampered by the fact that no good criteria for the von Mises distribution to be unimodal were available. In this article we study the question about when a multivariate von Mises distribution is unimodal. We give sufficient criteria for this to be the case and show examples of distributions with multiple modes when these criteria are violated. In addition, we propose a method to generate samples from the von Mises distribution in the case of high concentration.Comment: fixed a typo in the article title, minor fixes throughou

Elastic energy of proteins and the stages of protein folding

We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable parameters are fitted to data from the computer simulation of the folding of a set of proteins using the CSAW (conditioned self-avoiding walk) model. The elastic energy gives rise to scaling relations of the form $R_{g}\sim N^{\nu}$ in different regions. It shows three folding stages characterized by the progression with exponents $\nu = 3/5, 3/7, 2/5$, which we identify as the unfolded stage, pre-globule, and molten globule, respectively. The pre-globule goes over to the molten globule via a break in behavior akin to a first-order phase transition, which is initiated by a sudden acceleration of hydrogen bonding

Helical states of nonlocally interacting molecules and their linear stability: geometric approach

The equations for strands of rigid charge configurations interacting nonlocally are formulated on the special Euclidean group, SE(3), which naturally generates helical conformations. Helical stationary shapes are found by minimizing the energy for rigid charge configurations positioned along an infinitely long molecule with charges that are off-axis. The classical energy landscape for such a molecule is complex with a large number of energy minima, even when limited to helical shapes. The question of linear stability and selection of stationary shapes is studied using an SE(3) method that naturally accounts for the helical geometry. We investigate the linear stability of a general helical polymer that possesses torque-inducing non-local self-interactions and find the exact dispersion relation for the stability of the helical shapes with an arbitrary interaction potential. We explicitly determine the linearization operators and compute the numerical stability for the particular example of a linear polymer comprising a flexible rod with a repeated configuration of two equal and opposite off-axis charges, thereby showing that even in this simple case the non-local terms can induce instability that leads to the rod assuming helical shapes.Comment: 34 pages, 9 figure

LSST Classifier

The LSST (Large Synoptic Survey Telescope) Space Image Classifier Team built an application that uses crowd sourcing and machine learning to classify space objects in LSST image data. This project aims to work towards LSST science outreach goals.https://pilotscholars.up.edu/egr_project/1003/thumbnail.jp

Hierarchical Chain Model of Spider Capture Silk Elasticity

Spider capture silk is a biomaterial with both high strength and high elasticity, but the structural design principle underlying these remarkable properties is still unknown. It was revealed recently by atomic force microscopy that, an exponential force--extension relationship holds both for capture silk mesostructures and for intact capture silk fibers [N. Becker et al., Nature Materials 2, 278 (2003)]. In this Letter a simple hierarchical chain model was proposed to understand and reproduce this striking observation. In the hierarchical chain model, a polymer is composed of many structural motifs which organize into structural modules and supra-modules in a hierarchical manner. Each module in this hierarchy has its own characteristic force. The repetitive patterns in the amino acid sequence of the major flagelliform protein of spider capture silk is in support of this model.Comment: 4 pages, 3 figures. Will be formally published in PR

Phase transition of a single star polymer: a Wang-Landau sampling study

Star polymer is a typical nonlinear macromolecule possessing special thermodynamic behaviors for the existence of a jointing point. The thermodynamic transitions of a single star polymer are systematically studied with bond fluctuation model using Wang-Landau sampling technique. A new analysis method applying the shape factor is proposed to determine coil-globule (CG) and liquid-crystal (LC) transitions, which shows higher efficiency and precision than canonical specific heat function. It is found that the LC transition of star polymer at lower temperature obeys the identical scaling law as linear polymer. With the increase of the arm density of star polymer, however, the CG transition point, corresponding to {\theta} temperature, shifts towards the LC transition and the reason comes from the high density arms of star polymer, which requires the lower temperature for attracting force to overcome the volume excluding effects of chain. This work clearly demonstrates that the distinction of linear and star polymers in structures only affects CG transition and has no influence on LC transition.Comment: 30 pages, 10 figures, submit to JC