Steric repulsion and van der Waals attraction between flux lines in disordered high Tc superconductors

We show that in anisotropic or layered superconductors impurities induce a van der Waals attraction between flux lines. This attraction together with the disorder induced repulsion may change the low B - low T phase diagram significantly from that of the pure thermal case considered recently by Blatter and Geshkenbein [Phys. Rev. Lett. 77, 4958 (1996)].Comment: Latex, 4 pages, 1 figure (Phys. Rev. Lett. 79, 139 (1997)

DNA sequence from the unzipping force? : one mutation problem

The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the zipped from the unzipped regions. We propose a comparison method (``differential force microscope'') to detect mutations. Two lattice models are treated as specific examples.Comment: 11 pages, 4 figures. Revised version with minor changes. Paragraph with discussion on experiments added. Accepted for publication in J. Phys. A as a Letter to the Edito

Corrections to the Cardy-Verlinde formula from the generalized uncertainty principle

In this letter, we compute the corrections to the Cardy-Verlinde formula of $d-$dimensional Schwarzschild black hole. These corrections stem from the generalized uncertainty principle. Then we show, one can taking into account the generalized uncertainty principle corrections of the Cardy-Verlinde entropy formula by just redefining the Virasoro operator $L_0$ and the central charge $c$.Comment: 8 pages, no figure

Critical properties of an aperiodic model for interacting polymers

We investigate the effects of aperiodic interactions on the critical behavior of an interacting two-polymer model on hierarchical lattices (equivalent to the Migadal-Kadanoff approximation for the model on Bravais lattices), via renormalization-group and tranfer-matrix calculations. The exact renormalization-group recursion relations always present a symmetric fixed point, associated with the critical behavior of the underlying uniform model. If the aperiodic interactions, defined by s ubstitution rules, lead to relevant geometric fluctuations, this fixed point becomes fully unstable, giving rise to novel attractors of different nature. We present an explicit example in which this new attractor is a two-cycle, with critical indices different from the uniform model. In case of the four-letter Rudin-Shapiro substitution rule, we find a surprising closed curve whose points are attractors of period two, associated with a marginal operator. Nevertheless, a scaling analysis indicates that this attractor may lead to a new critical universality class. In order to provide an independent confirmation of the scaling results, we turn to a direct thermodynamic calculation of the specific-heat exponent. The thermodynamic free energy is obtained from a transfer matrix formalism, which had been previously introduced for spin systems, and is now extended to the two-polymer model with aperiodic interactions.Comment: 19 pages, 6 eps figures, to appear in J. Phys A: Math. Ge

Thermal Re-emission Model

Starting from a continuum description, we study the non-equilibrium roughening of a thermal re-emission model for etching in one and two spatial dimensions. Using standard analytical techniques, we map our problem to a generalized version of an earlier non-local KPZ (Kardar-Parisi-Zhang) model. In 2+1 dimensions, the values of the roughness and the dynamic exponents calculated from our theory go like $\alpha \approx z \approx 1$ and in 1+1 dimensions, the exponents resemble the KPZ values for low vapor pressure, supporting experimental results. Interestingly, Galilean invariance is maintained althrough.Comment: 4 pages, minor textual corrections and typos, accepted in Physical Review B (rapid

3D visualization processes for recreating and studying organismal form

The study of biological form is a vital goal of evolutionary biology and functional morphology. We review an emerging set of methods that allow scientists to create and study accurate 3D models of living organisms and animate those models for biomechanical and fluid dynamic analyses. The methods for creating such models include 3D photogrammetry, laser and CT-scanning, and 3D software. New multi-camera devices can be used to create accurate 3D models of living animals in the wild and captivity. New websites and virtual reality/augmented reality devices now enable the visualization and sharing of these data. We provide examples of these approaches for animals ranging from large whales to lizards and show applications for several areas: Natural history collections; body condition/scaling, bioinspired robotics, computational fluids dynamics (CFD), machine learning, and education. We provide two data sets to demonstrate the efficacy of CFD and machine learning approaches and conclude with a prospectus

Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs

Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA-RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting e.g. the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell's proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.Comment: review article, 29 pages, 7 figure

Back reaction, covariant anomaly and effective action

In the presence of back reaction, we first produce the one-loop corrections for the event horizon and Hawking temperature of the Reissner-Nordstr\"om black hole. Then, based on the covariant anomaly cancelation method and the effective action technique, the modified expressions for the fluxes of gauge current and energy momentum tensor, due to the effect of back reaction, are obtained. The results are consistent with the Hawking fluxes of a (1+1)-dimensional blackbody at the temperature with quantum corrections, thus confirming the robustness of the covariant anomaly cancelation method and the effective action technique for black holes with back reaction.Comment: 17 page

In silico evolution of signaling networks using rule-based models: bistable response dynamics

One of the ultimate goals in biology is to understand the design principles of biological systems. Such principles, if they exist, can help us better understand complex, natural biological systems and guide the engineering of de novo ones. Towards deciphering design principles, in silico evolution of biological systems with proper abstraction is a promising approach. Here, we demonstrate the application of in silico evolution combined with rule-based modelling for exploring design principles of cellular signaling networks. This application is based on a computational platform, called BioJazz, which allows in silico evolution of signaling networks with unbounded complexity. We provide a detailed introduction to BioJazz architecture and implementation and describe how it can be used to evolve and/or design signaling networks with defined dynamics. For the latter, we evolve signaling networks with switch-like response dynamics and demonstrate how BioJazz can result in new biological insights on network structures that can endow bistable response dynamics. This example also demonstrated both the power of BioJazz in evolving and designing signaling networks and its limitations at the current stage of development.Comment: 24 pages, 7 figure

Modeling Stem Cell Induction Processes

Technology for converting human cells to pluripotent stem cell using induction processes has the potential to revolutionize regenerative medicine. However, the production of these so called iPS cells is still quite inefficient and may be dominated by stochastic effects. In this work we build mass-action models of the core regulatory elements controlling stem cell induction and maintenance. The models include not only the network of transcription factors NANOG, OCT4, SOX2, but also important epigenetic regulatory features of DNA methylation and histone modification. We show that the network topology reported in the literature is consistent with the observed experimental behavior of bistability and inducibility. Based on simulations of stem cell generation protocols, and in particular focusing on changes in epigenetic cellular states, we show that cooperative and independent reaction mechanisms have experimentally identifiable differences in the dynamics of reprogramming, and we analyze such differences and their biological basis. It had been argued that stochastic and elite models of stem cell generation represent distinct fundamental mechanisms. Work presented here suggests an alternative possibility that they represent differences in the amount of information we have about the distribution of cellular states before and during reprogramming protocols. We show further that unpredictability and variation in reprogramming decreases as the cell progresses along the induction process, and that identifiable groups of cells with elite-seeming behavior can come about by a stochastic process. Finally we show how different mechanisms and kinetic properties impact the prospects of improving the efficiency of iPS cell generation protocols.Fundação para a Ciência e a Tecnologia (BD 42942)MIT-Portugal ProgramNational Institutes of Health (U.S.) (CA112967)Singapore–MIT Alliance for Research and TechnologyIntel Corporatio