Monte Carlo Protein Folding: Simulations of Met-Enkephalin with Solvent-Accessible Area Parameterizations

Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of Metropolis simulations of the brain peptide Met-Enkephalin. For the phenomenological energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied that had been proposed by previous authors. The simulations are compared with each other, with simulations with a distance dependent electrostatic permittivity $\epsilon (r)$, and with vacuum simulations ($\epsilon =2$). Parallel tempering and a recently proposed biased Metropolis technique are employed and their performances are evaluated. The measured observables include energy and dihedral probability densities (pds), integrated autocorrelation times, and acceptance rates. Two of the ASP sets turn out to be unsuitable for these simulations. For all other sets, selected configurations are minimized in search of the global energy minima. Unique minima are found for the vacuum and the $\epsilon(r)$ system, but for none of the ASP models. Other observables show a remarkable dependence on the ASPs. In particular, autocorrelation times vary dramatically with the ASP parameters. Three ASP sets have much smaller autocorrelations at 300 K than the vacuum simulations, opening the possibility that simulations can be speeded up vastly by judiciously chosing details of the forceComment: 10 pages; published in "NIC Symposium 2004", eds. D. Wolf at el. (NIC, Juelich, 2004

Aerodynamic properties of turbulent combustion fields

Flow fields involving turbulent flames in premixed gases under a variety of conditions are modeled by the use of a numerical technique based on the random vortex method to solve the Navier-Stokes equations and a flame propagation algorithm to trace the motion of the front and implement the Huygens principle, both due to Chorin. A successive over-relaxation hybrid method is applied to solve the Euler equation for flows in an arbitrarily shaped domain. The method of images, conformal transformation, and the integral-equation technique are also used to treat flows in special cases, according to their particular requirements. Salient features of turbulent flame propagation in premixed gases are interpreted by relating them to the aerodynamic properties of the flow field. Included among them is the well-known cellular structure of flames stabilized by bluff bodies, as well as the formation of the characteristic tulip shape of flames propagating in ducts. In its rudimentary form, the mechanism of propagation of a turbulent flame is shown to consist of: (1) rotary motion of eddies at the flame front, (2) self-advancement of the front at an appropriate normal burning speed, and (3) dynamic effects of expansion due to exothermicity of the combustion reaction. An idealized model is used to illustrate these fundamental mechanisms and to investigate basic aerodynamic features of flames in premixed gases. The case of a confined flame stabilized behind a rearward-facing step is given particular care and attention. Solutions are shown to be in satisfactory agreement with experimental results, especially with respect to global properties such as the average velocity profiles and reattachment length

Harness processes and harmonic crystals

In the Hammersley harness processes the real-valued height at each site i in Z^d is updated at rate 1 to an average of the neighboring heights plus a centered random variable (the noise). We construct the process "a la Harris" simultaneously for all times and boxes contained in Z^d. With this representation we compute covariances and show L^2 and almost sure time and space convergence of the process. In particular, the process started from the flat configuration and viewed from the height at the origin converges to an invariant measure. In dimension three and higher, the process itself converges to an invariant measure in L^2 at speed t^{1-d/2} (this extends the convergence established by Hsiao). When the noise is Gaussian the limiting measures are Gaussian fields (harmonic crystals) and are also reversible for the process.Comment: 21 pages. Revised version with minor changes. Version almost identical to the one to be published in SP

How to Define Variation of Physical Properties Normal to an Undulating One-Dimensional Object

One-dimensional flexible objects are abundant in physics, from polymers to vortex lines to defect lines and many more. These objects structure their environment and it is natural to assume that the influence these objects exert on their environment depends on the distance from the line-object. But how should this be defined? We argue here that there is an intrinsic length scale along the undulating line that is a measure of its "stiffness" (i.e., orientational persistence), which yields a natural way of defining the variation of physical properties normal to the undulating line. We exemplify how this normal variation can be determined from a computer simulation for the case of a so-called bottle-brush polymer, where side chains are grafted onto a flexible backbone.Comment: 4 pages, 4 figure

Progressor: Social navigation support through open social student modeling

The increased volumes of online learning content have produced two problems: how to help students to find the most appropriate resources and how to engage them in using these resources. Personalized and social learning have been suggested as potential ways to address these problems. Our work presented in this paper combines the ideas of personalized and social learning in the context of educational hypermedia. We introduce Progressor, an innovative Web-based tool based on the concepts of social navigation and open student modeling that helps students to find the most relevant resources in a large collection of parameterized self-assessment questions on Java programming. We have evaluated Progressor in a semester-long classroom study, the results of which are presented in this paper. The study confirmed the impact of personalized social navigation support provided by the system in the target context. The interface encouraged students to explore more topics attempting more questions and achieving higher success rates in answering them. A deeper analysis of the social navigation support mechanism revealed that the top students successfully led the way to discovering most relevant resources by creating clear pathways for weaker students. © 2013 Taylor and Francis Group, LLC

Testing for inconsistencies in the estimation of UK capital structure determinants

This article analyses the determinants of the capital structure of 1054 UK companies from 1991 to 1997, and the extent to which the influence of these determinants are affected by time-invariant firm-specific heterogeneity. Comparing the results of pooled OLS and fixed effects panel estimation, significant differences in the results are found. While the OLS results are generally consistent with prior literature, the results of our fixed effects panel estimation contradict many of the traditional theories of the determinants of corporate financial structure. This suggests that results of traditional studies may be biased owing to a failure to control for firm-specific, time-invariant heterogeneity. The results of the fixed effects panel estimation find larger companies to have higher levels of both long-term and short-term debt than do smaller firms, profitability to be negatively correlated with the level of gearing, although profitable firms tend to have more short-term bank borrowing than less profitable firms, and tangibility to positively influence the level of short-term bank borrowing, as well as all long-term debt elements. However, the level of growth opportunities appears to have little influence on the level of gearing, other than short-term bank borrowing, where a significant negative relationship is observed

The extent of chemically enriched gas around star-forming dwarf galaxies

Supernova driven winds are often invoked to remove chemically enriched gas from dwarf galaxies to match their low observed metallicities. In such shallow potential wells, outflows may produce massive amounts of enriched halo gas (circum-galactic medium or CGM) and pollute the intergalactic medium (IGM). Here, we present a survey of the CGM and IGM around 18 star-forming field dwarfs with stellar masses of $\log\,M_*/M_\odot\approx8-9$ at $z\approx0.2$. Eight of these have CGM probed by quasar absorption spectra at projected distances, $d$, less than the host virial radius, $R_{\rm h}$. Ten are probed in the surrounding IGM at $d/R_{\rm h}=1-3$. The absorption measurements include neutral hydrogen, the dominant silicon ions for diffuse cool gas ($T\sim10^4$ K; Si II, Si III, and Si IV), moderately ionized carbon (C IV), and highly ionized oxygen (O VI). Metal absorption from the CGM of the dwarfs is less common and $\approx4\times$ weaker compared to massive star-forming galaxies though O VI absorption is still common. None of the dwarfs probed at $d/R_{\rm h}=1-3$ have definitive metal-line detections. Combining the available silicon ions, we estimate that the cool CGM of the dwarfs accounts for only $2-6\%$ of the expected silicon budget from the yields of supernovae associated with past star-formation. The highly ionized O VI accounts for $\approx8\%$ of the oxygen budget. As O VI traces an ion with expected equilibrium ion fractions of $\lesssim 0.2$, the highly ionized CGM may represent a significant metal reservoir even for dwarfs not expected to maintain gravitationally shock heated hot halos.Comment: Accepted to ApJL, 10 pages, 3 figures, 2 tables. Please contact the corresponding author for additional column density measurements if needed. v3 includes additional references and clarification in the introductio

Explicit Space-Time Codes Achieving The Diversity-Multiplexing Gain Tradeoff

A recent result of Zheng and Tse states that over a quasi-static channel, there exists a fundamental tradeoff, referred to as the diversity-multiplexing gain (D-MG) tradeoff, between the spatial multiplexing gain and the diversity gain that can be simultaneously achieved by a space-time (ST) block code. This tradeoff is precisely known in the case of i.i.d. Rayleigh-fading, for T>= n_t+n_r-1 where T is the number of time slots over which coding takes place and n_t,n_r are the number of transmit and receive antennas respectively. For T < n_t+n_r-1, only upper and lower bounds on the D-MG tradeoff are available. In this paper, we present a complete solution to the problem of explicitly constructing D-MG optimal ST codes, i.e., codes that achieve the D-MG tradeoff for any number of receive antennas. We do this by showing that for the square minimum-delay case when T=n_t=n, cyclic-division-algebra (CDA) based ST codes having the non-vanishing determinant property are D-MG optimal. While constructions of such codes were previously known for restricted values of n, we provide here a construction for such codes that is valid for all n. For the rectangular, T > n_t case, we present two general techniques for building D-MG-optimal rectangular ST codes from their square counterparts. A byproduct of our results establishes that the D-MG tradeoff for all T>= n_t is the same as that previously known to hold for T >= n_t + n_r -1.Comment: Revised submission to IEEE Transactions on Information Theor