Searching low-energy conformations of two elastin sequences

The three-dimensional structures of two common repeat motifs Val$^1$-Pro$^2$-Gly$^3$-Val$^4$-Gly$^5$ and Val$^1$-Gly$^2$-Val$^3$-Pro$^4$-Gly$^5$-Val$^6$-Gly$^7$-Val$^8$-Pro$^9$ of tropoelastin are investigated by using the multicanonical simulation procedure. By minimizing the energy structures along the trajectory the thermodynamically most stable low-energy microstates of the molecule are determined. The structural predictions are in good agreement with X-ray diffraction experiments.Comment: 16 pages, 5 figure

Simple flexible polymers in a spherical cage

We report the results of Monte Carlo simulations investigating the effect of a spherical confinement within a simple model for a flexible homopolymer. We use the parallel tempering method combined with multi-histogram reweighting analysis and multicanonical simulations to investigate thermodynamical observables over a broad range of temperatures, which enables us to describe the behavior of the polymer and to locate the freezing and collapse transitions. We find a strong effect of the spherical confinement on the location of the collapse transition, whereas the freezing transition is hardly effected.Comment: 7 pages, 4 figure

A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters and is particularly well-suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation and demonstrate the utility of the method via illustrative examples.Comment: v4: 12 pages, 5 figures, final accepted version. Error found and fixed in Appendi

Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm

There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in biology and nanoscale materials science, where the common assumptions of deterministic dynamics and well-mixed reaction volumes often break down. In this article, we present a spatial version of the partitioned-leaping algorithm (PLA), a multiscale accelerated-stochastic simulation approach built upon the tau-leaping framework of Gillespie. We pay special attention to the details of the implementation, particularly as it pertains to the time step calculation procedure. We point out conceptual errors that have been made in this regard in prior implementations of spatial tau-leaping and illustrate the manifestation of these errors through practical examples. Finally, we discuss the fundamental difficulties associated with incorporating efficient exact-stochastic techniques, such as the next-subvolume method, into a spatial-leaping framework and suggest possible solutions.Comment: 15 pages, 9 figures, 2 table

Structure of the Energy Landscape of Short Peptides

We have simulated, as a showcase, the pentapeptide Met-enkephalin (Tyr-Gly-Gly-Phe-Met) to visualize the energy landscape and investigate the conformational coverage by the multicanonical method. We have obtained a three-dimensional topographic picture of the whole energy landscape by plotting the histogram with respect to energy(temperature) and the order parameter, which gives the degree of resemblance of any created conformation with the global energy minimum (GEM).Comment: 17 pages, 4 figure

Maximizing Maximal Angles for Plane Straight-Line Graphs

Let $G=(S, E)$ be a plane straight-line graph on a finite point set $S\subset\R^2$ in general position. The incident angles of a vertex $p \in S$ of $G$ are the angles between any two edges of $G$ that appear consecutively in the circular order of the edges incident to $p$. A plane straight-line graph is called $\phi$-open if each vertex has an incident angle of size at least $\phi$. In this paper we study the following type of question: What is the maximum angle $\phi$ such that for any finite set $S\subset\R^2$ of points in general position we can find a graph from a certain class of graphs on $S$ that is $\phi$-open? In particular, we consider the classes of triangulations, spanning trees, and paths on $S$ and give tight bounds in most cases.Comment: 15 pages, 14 figures. Apart of minor corrections, some proofs that were omitted in the previous version are now include

A novel method for accurate operon predictions in all sequenced prokaryotes

We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacter pylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from six phylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC 6803 has many operons even though it has unusually wide spacings between conserved adjacent genes