1,008 research outputs found
Explicit factorization of external coordinates in constrained Statistical Mechanics models
If a macromolecule is described by curvilinear coordinates or rigid
constraints are imposed, the equilibrium probability density that must be
sampled in Monte Carlo simulations includes the determinants of different
mass-metric tensors. In this work, we explicitly write the determinant of the
mass-metric tensor G and of the reduced mass-metric tensor g, for any molecule,
general internal coordinates and arbitrary constraints, as a product of two
functions; one depending only on the external coordinates that describe the
overall translation and rotation of the system, and the other only on the
internal coordinates. This work extends previous results in the literature,
proving with full generality that one may integrate out the external
coordinates and perform Monte Carlo simulations in the internal conformational
space of macromolecules. In addition, we give a general mathematical argument
showing that the factorization is a consequence of the symmetries of the metric
tensors involved. Finally, the determinant of the mass-metric tensor G is
computed explicitly in a set of curvilinear coordinates specially well-suited
for general branched molecules.Comment: 22 pages, 2 figures, LaTeX, AMSTeX. v2: Introduccion slightly
extended. Version in arXiv is slightly larger than the published on
Computing Fresnel integrals via modified trapezium rules
In this paper we propose methods for computing Fresnel integrals based on truncated trapezium rule approximations to integrals on the real line, these trapezium rules modified to take into account poles of the integrand near the real axis. Our starting point is a method for computation of the error function of complex argument due to Matta and Reichel (J Math Phys 34:298â307, 1956) and Hunter and Regan (Math Comp 26:539â541, 1972). We construct approximations which we prove are exponentially convergent as a function of N , the number of quadrature points, obtaining explicit error bounds which show that accuracies of 10â15 uniformly on the real line are achieved with N=12 , this confirmed by computations. The approximations we obtain are attractive, additionally, in that they maintain small relative errors for small and large argument, are analytic on the real axis (echoing the analyticity of the Fresnel integrals), and are straightforward to implement
Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide
If constraints are imposed on a macromolecule, two inequivalent classical
models may be used: the stiff and the rigid one. This work studies the effects
of such constraints on the Conformational Equilibrium Distribution (CED) of the
model dipeptide HCO-L-Ala-NH2 without any simplifying assumption. We use ab
initio Quantum Mechanics calculations including electron correlation at the MP2
level to describe the system, and we measure the conformational dependence of
all the correcting terms to the naive CED based in the Potential Energy Surface
(PES) that appear when the constraints are considered. These terms are related
to mass-metric tensors determinants and also occur in the Fixman's compensating
potential. We show that some of the corrections are non-negligible if one is
interested in the whole Ramachandran space. On the other hand, if only the
energetically lower region, containing the principal secondary structure
elements, is assumed to be relevant, then, all correcting terms may be
neglected up to peptides of considerable length. This is the first time, as far
as we know, that the analysis of the conformational dependence of these
correcting terms is performed in a relevant biomolecule with a realistic
potential energy function.Comment: 37 pages, 4 figures, LaTeX, BibTeX, AMSTe
Pattern Formation in Interface Depinning and Other Models: Erratically Moving Spatial Structures
We study erratically moving spatial structures that are found in a driven
interface in a random medium at the depinning threshold. We introduce a
bond-disordered variant of the Sneppen model and study the effect of extremal
dynamics on the morphology of the interface. We find evidence for the formation
of a structure which moves along with the growth site. The time average of the
structure, which is defined with respect to the active spot of growth, defines
an activity-centered pattern. Extensive Monte Carlo simulations show that the
pattern has a tail which decays slowly, as a power law. To understand this sort
of pattern formation, we write down an approximate integral equation involving
the local interface dynamics and long-ranged jumps of the growth spot. We
clarify the nature of the approximation by considering a model for which the
integral equation is exactly derivable from an extended master equation.
Improvements to the equation are considered by adding a second coupled equation
which provides a self-consistent description. The pattern, which defines a
one-point correlation function, is shown to have a strong effect on ordinary
space-fixed two-point correlation functions. Finally we present evidence that
this sort of pattern formation is not confined to the interface problem, but is
generic to situations in which the activity at succesive time steps is
correlated, as for instance in several other extremal models. We present
numerical results for activity-centered patterns in the Bak-Sneppen model of
evolution and the Zaitsev model of low-temperature creep.Comment: RevTeX, 18 pages, 19 eps-figures, To appear in Phys. Rev.
Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing
Single-stranded (ss) transposition, a recently identified mechanism adopted by members of the widespread IS200/IS605 family of insertion sequences (IS), is catalysed by the transposase, TnpA. The transposase of IS608, recognizes subterminal imperfect palindromes (IP) at both IS ends and cleaves at sites located at some distance. The cleavage sites, C, are not recognized directly by the protein but by short sequences 5âČ to the foot of each IP, guide (G) sequences, using a network of canonical (âWatsonâCrickâ) base interactions. In addition a set of non-canonical base interactions similar to those found in RNA structures are also involved. We have reconstituted a biologically relevant complex, the transpososome, including both left and right ends and TnpA, which catalyses excision of a ss DNA circle intermediate. We provide a detailed picture of the way in which the IS608 transpososome is assembled and demonstrate that both C and G sequences are essential for forming a robust transpososome detectable by EMSA. We also address several questions central to the organization and function of the ss transpososome and demonstrate the essential role of non-canonical base interactions in the IS608 ends for its stability by using point mutations which destroy individual non-canonical base interactions
Environmental Impact on Vascular Development Predicted by High-Throughput Screening
Background: Understanding health risks to embryonic development from exposure to environmental chemicals is a significant challenge given the diverse chemical landscape and paucity of data for most of these compounds. High-throughput screening (HTS) in the U.S. Environmental Protection Agency (EPA) ToxCastâą project provides vast data on an expanding chemical library currently consisting of > 1,000 unique compounds across > 500 in vitro assays in phase I (complete) and Phase II (under way). This public data set can be used to evaluate concentration-dependent effects on many diverse biological targets and build predictive models of prototypical toxicity pathways that can aid decision making for assessments of human developmental health and disease
Genotoxic stress causes the accumulation of the splicing regulator Sam68 in nuclear foci of transcriptionally active chromatin
DNA-damaging agents cause a multifaceted cellular stress response. Cells set in motion either repair mechanisms or programmed cell death pathways, depending on the extent of the damage and on their ability to withstand it. The RNA-binding protein (RBP) Sam68, which is up-regulated in prostate carcinoma, promotes prostate cancer cell survival to genotoxic stress. Herein, we have investigated the function of Sam68 in this cellular response. Mitoxantrone (MTX), a topoisomerase II inhibitor, induced relocalization of Sam68 from the nucleoplasm to nuclear granules, together with several other RBPs involved in alternative splicing, such as TIA-1, hnRNP A1 and the SR proteins SC35 and ASF/SF2. Sam68 accumulation in nuclear stress granules was independent of signal transduction pathways activated by DNA damage. Using BrU labelling and immunofluorescence, we demonstrate that MTX-induced nuclear stress granules are transcriptionally active foci where Sam68 and the phosphorylated form of RNA polymerase II accumulate. Finally, we show that MTX-induced relocalization of Sam68 correlates with changes in alternative splicing of its mRNA target CD44, and that MTX-induced CD44 splicing depends on Sam68 expression. These results strongly suggest that Sam68 is part of a RNA-mediated stress response of the cell that modulates alternative splicing in response to DNA damage
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A novel 3D imaging system for strawberry phenotyping
Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. A low cost multi-view stereo (MVS) imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique
Evolutionary games on graphs
Game theory is one of the key paradigms behind many scientific disciplines
from biology to behavioral sciences to economics. In its evolutionary form and
especially when the interacting agents are linked in a specific social network
the underlying solution concepts and methods are very similar to those applied
in non-equilibrium statistical physics. This review gives a tutorial-type
overview of the field for physicists. The first three sections introduce the
necessary background in classical and evolutionary game theory from the basic
definitions to the most important results. The fourth section surveys the
topological complications implied by non-mean-field-type social network
structures in general. The last three sections discuss in detail the dynamic
behavior of three prominent classes of models: the Prisoner's Dilemma, the
Rock-Scissors-Paper game, and Competing Associations. The major theme of the
review is in what sense and how the graph structure of interactions can modify
and enrich the picture of long term behavioral patterns emerging in
evolutionary games.Comment: Review, final version, 133 pages, 65 figure
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