A finite population model of mlecular evolution: theory and computation

This article is concerned with the evolution of haploid organisms that reproduce asexually. In a seminal piece of work, Eigen and coauthors proposed the quasispecies model in an attempt to understand such an evolutionary process. Their work has impacted antiviral treatment and vaccine design strategies. Yet, predictions of the quasispecies model are at best viewed as a guideline, primarily because it assumes an infinite population size, whereas realistic population sizes can be quite small. In this paper we consider a population genetics-based model aimed at understanding the evolution of such organisms with finite population sizes and present a rigorous study of the convergence and computational issues that arise therein. Our first result is structural and shows that, at any time during the evolution, as the population size tends to infinity, the distribution of genomes predicted by our model converges to that predicted by the quasispecies model. This justifies the continued use of the quasispecies model to derive guidelines for intervention. While the stationary state in the quasispecies model is readily obtained, due to the explosion of the state space in our model, exact computations are prohibitive. Our second set of results are computational in nature and address this issue. We derive conditions on the parameters of evolution under which our stochastic model mixes rapidly. Further, for a class of widely used fitness landscapes we give a fast deterministic algorithm which computes the stationary distribution of our model. These computational tools are expected to serve as a framework for the modeling of strategies for the deployment of mutagenic drugs.

Consistency tests of Ampcalculator and chiral amplitudes in SU(3) Chiral Perturbation Theory: A tutorial-based approach

Ampcalculator (AMPC) is a Mathematica (c) based program that was made publicly available some time ago by Unterdorfer and Ecker. It enables the user to compute several processes at one loop (upto O(p(4))) in SU(3) chiral perturbation theory. They include computing matrix elements and form factors for strong and non-leptonic weak processes with at most six external states. It was used to compute some novel processes and was tested against well-known results by the original authors. Here we present the results of several thorough checks of the package. Exhaustive checks performed by the original authors are not publicly available, and hence the present effort. Some new results are obtained from the software especially in the kaon odd-intrinsic parity non-leptonic decay sector involving the coupling G(27). Another illustrative set of amplitudes at tree level we provide is in the context of tau-decays with several mesons including quark mass effects, of use to the BELLE experiment. All eight meson-meson scattering amplitudes have been checked. The Kaon-Compton amplitude has been checked and a minor error in the published results has been pointed out. This exercise is a tutorial-based one, wherein several input and output notebooks are also being made available as ancillary files on the arXiv. Some of the additional notebooks we provide contain explicit expressions that we have used for comparison with established results. The purpose is to encourage users to apply the software to suit their specific needs. An automatic amplitude generator of this type can provide error-free outputs that could be used as inputs for further simplification, and in varied scenarios such as applications of chiral perturbation theory at finite temperature, density and volume. This can also be used by students as a learning aid in low-energy hadron dynamics.

Postcards from oases in the desert: phenomenology of SUSY with intermediate scales

The presence of new matter fields charged under the Standard Model gauge group at intermediate scales below the Grand Unification scale modifies the renormalization group evolution of the gauge couplings. This can in turn significantly change the running of the Minimal Supersymmetric Standard Model parameters, in particular the gaugino and the scalar masses. In the absence of new large Yukawa couplings we can parameterise all the intermediate scale models in terms of only two parameters controlling the size of the unified gauge coupling. As a consequence of the modified running, the low energy spectrum can be strongly affected with interesting phenomenological consequences. In particular, we show that scalar over gaugino mass ratios tend to increase and the regions of the parameter space with neutralino Dark Matter compatible with cosmological observations get drastically modified. Moreover, we discuss some observables that can be used to test the intermediate scale physics at the LHC in a wide class of models.

Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.

A UNIFIED APPROACH FOR OPTIMIZATION OF SNAKUSCULES AND OVUSCULES

Automated image segmentation techniques are useful tools in biological image analysis and are an essential step in tracking applications. Typically, snakes or active contours are used for segmentation and they evolve under the influence of certain internal and external forces. Recently, a new class of shape-specific active contours have been introduced, which are known as Snakuscules and Ovuscules. These contours are based on a pair of concentric circles and ellipses as the shape templates, and the optimization is carried out by maximizing a contrast function between the outer and inner templates. In this paper, we present a unified approach to the formulation and optimization of Snakuscules and Ovuscules by considering a specific form of affine transformations acting on a pair of concentric circles. We show how the parameters of the affine transformation may be optimized for, to generate either Snakuscules or Ovuscules. Our approach allows for a unified formulation and relies only on generic regularization terms and not shape-specific regularization functions. We show how the calculations of the partial derivatives may be made efficient thanks to the Green's theorem. Results on synthesized as well as real data are presented.

Pattern clustering using cooperative game theory

In this paper, we approach the classical problem of clustering using solution concepts from cooperative game theory such as Nucleolus and Shapley value. We formulate the problem of clustering as a characteristic form game and develop a novel algorithm DRAC (Density-Restricted Agglomerative Clustering) for clustering. With extensive experimentation on standard data sets, we compare the performance of DRAC with that of well known algorithms. We show an interesting result that four prominent solution concepts, Nucleolus, Shapley value, Gately point and \tau-value coincide for the defined characteristic form game. This vindicates the choice of the characteristic function of the clustering game and also provides strong intuitive foundation for our approach.

USHA: unified software and hardware architecture for video decoding

Video decoders used in emerging applications need to be flexible to handle a large variety of video formats and deliver scalable performance to handle wide variations in workloads. In this paper we propose a unified software and hardware architecture for video decoding to achieve scalable performance with flexibility. The light weight processor tiles and the reconfigurable hardware tiles in our architecture enable software and hardware implementations to co-exist, while a programmable interconnect enables dynamic interconnection of the tiles. Our process network oriented compilation flow achieves realization agnostic application partitioning and enables seamless migration across uniprocessor, multi-processor, semi hardware and full hardware implementations of a video decoder. An application quality of service aware scheduler monitors and controls the operation of the entire system. We prove the concept through a prototype of the architecture on an off-the-shelf FPGA. The FPGA prototype shows a scaling in performance from QCIF to 1080p resolutions in four discrete steps. We also demonstrate that the reconfiguration time is short enough to allow migration from one configuration to the other without any frame loss.

Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4, 5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule. (C) 2012 Elsevier B.V. All rights reserved.

A unified model for the dynamics of driven ribbon with strain and magnetic order parameters

We develop a unified model to explain the dynamics of driven one dimensional ribbon for materials with strain and magnetic order parameters. We show that the model equations in their most general form explain several results on driven magnetostrictive metallic glass ribbons such as the period doubling route to chaos as a function of a dc magnetic field in the presence of a sinusoidal field, the quasiperiodic route to chaos as a function of the sinusoidal field for a fixed dc field, and induced and suppressed chaos in the presence of an additional low amplitude near resonant sinusoidal field. We also investigate the influence of a low amplitude near resonant field on the period doubling route. The model equations also exhibit symmetry restoring crisis with an exponent close to unity. The model can be adopted to explain certain results on magnetoelastic beam and martensitic ribbon under sinusoidal driving conditions. In the latter case, we find interesting dynamics of a periodic one orbit switching between two equivalent wells as a function of an ac magnetic field that eventually makes a direct transition to chaos under resonant driving condition. The model is also applicable to magnetomartensites and materials with two order parameters. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4790845]

Can the viscosity in astrophysical black hole accretion disks be close to its string theory bound?

String theory and gauge/gravity duality suggest the lower bound of shear viscosity (eta) to entropy density (s) for any matter to be mu h/4 pi k(B), when h and k(B) are reduced Planck and Boltzmann constants respectively and mu <= 1. Motivated by this, we explore eta/s in black hole accretion flows, in order to understand if such exotic flows could be a natural site for the lowest eta/s. Accretion flow plays an important role in black hole physics in identifying the existence of the underlying black hole. This is a rotating shear flow with insignificant molecular viscosity, which could however have a significant turbulent viscosity, generating transport, heat and hence entropy in the flow. However, in presence of strong magnetic field, magnetic stresses can help in transporting matter independent of viscosity, via celebrated Blandford-Payne mechanism. In such cases, energy and then entropy produces via Ohmic dissipation. In,addition, certain optically thin, hot, accretion flows, of temperature greater than or similar to 10(9) K, may be favourable for nuclear burning which could generate/absorb huge energy, much higher than that in a star. We find that eta/s in accretion flows appears to be close to the lower bound suggested by theory, if they are embedded by strong magnetic field or producing nuclear energy, when the source of energy is not viscous effects. A lower bound on eta/s also leads to an upper bound on the Reynolds number of the flow.

Analytical theory and stability analysis of an elongated nanoscale object under external torque

We consider the rotational motion of an elongated nanoscale object in a fluid under an external torque. The experimentally observed dynamics could be understood from analytical solutions of the Stokes equation, with explicit formulae derived for the dynamical states as a function of the object dimensions and the parameters defining the external torque. Under certain conditions, multiple analytical solutions to the Stokes equations exist, which have been investigated through numerical analysis of their stability against small perturbations and their sensitivity towards initial conditions. These experimental results and analytical formulae are general enough to be applicable to the rotational motion of any isolated elongated object at low Reynolds numbers, and could be useful in the design of non-spherical nanostructures for diverse applications pertaining to microfluidics and nanoscale propulsion technologies.

Hydrodynamics of soft active matter

This review summarizes theoretical progress in the field of active matter, placing it in the context of recent experiments. This approach offers a unified framework for the mechanical and statistical properties of living matter: biofilaments and molecular motors in vitro or in vivo, collections of motile microorganisms, animal flocks, and chemical or mechanical imitations. A major goal of this review is to integrate several approaches proposed in the literature, from semimicroscopic to phenomenological. In particular, first considered are ``dry'' systems, defined as those where momentum is not conserved due to friction with a substrate or an embedding porous medium. The differences and similarities between two types of orientationally ordered states, the nematic and the polar, are clarified. Next, the active hydrodynamics of suspensions or ``wet'' systems is discussed and the relation with and difference from the dry case, as well as various large-scale instabilities of these nonequilibrium states of matter, are highlighted. Further highlighted are various large-scale instabilities of these nonequilibrium states of matter. Various semimicroscopic derivations of the continuum theory are discussed and connected, highlighting the unifying and generic nature of the continuum model. Throughout the review, the experimental relevance of these theories for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular material is discussed. Promising extensions toward greater realism in specific contexts from cell biology to animal behavior are suggested, and remarks are given on some exotic active-matter analogs. Last, the outlook for a quantitative understanding of active matter, through the interplay of detailed theory with controlled experiments on simplified systems, with living or artificial constituents, is summarized.

DETERMINATION OF THE STRONG COUPLING FROM HADRONIC TAU DECAYS USING RENORMALIZATION GROUP SUMMED PERTURBATION THEORY

Be the strong coupling constant alpha(s) from the tau hadronn width using a renormalization group summed (RGS) expansion of the QCD Adler lunction. The main theoretical uncertainty in the extraction of as is due to the manner in which renormalization group invariance is implemented, and the as yet uncalculated higher order terms in the QCD perturbative series. We show that new expansion exhibits good renormalization group improvement and the behavior of the series is similar to that of the standard RGS expansion. The value of the strong coupling in (MS) over bar scheme obtained with the RCS expansion is alpha(s) (M-tau(2)) = 0.338 +/- 0.010. The convergence properties of the new expansion can be improved by Bond transformation and analytic continuation in t he Bond plane. This is discussed elsewhere in these issues.

Expansions of tau hadronic spectral function moments in a nonpower QCD perturbation theory with tamed large order behavior

The moments of the hadronic spectral functions are of interest for the extraction of the strong coupling alpha(s) and other QCD parameters from the hadronic decays of the tau lepton. Motivated by the recent analyses of a large class of moments in the standard fixed-order and contour-improved perturbation theories, we consider the perturbative behavior of these moments in the framework of a QCD nonpower perturbation theory, defined by the technique of series acceleration by conformal mappings, which simultaneously implements renormalization-group summation and has a tame large-order behavior. Two recently proposed models of the Adler function are employed to generate the higher-order coefficients of the perturbation series and to predict the exact values of the moments, required for testing the properties of the perturbative expansions. We show that the contour-improved nonpower perturbation theories and the renormalization-group-summed nonpower perturbation theories have very good convergence properties for a large class of moments of the so-called ``reference model,'' including moments that are poorly described by the standard expansions. The results provide additional support for the plausibility of the description of the Adler function in terms of a small number of dominant renormalons.