Cumulants of the three state Potts model and of nonequilibrium models with C3v symmetry

The critical behavior of two-dimensional stochastic lattice gas models with C3v symmetry is analyzed. We study the cumulants of the order parameter for the three state (equilibrium) Potts model and for two irreversible models whose dynamic rules are invariant under the symmetry operations of the point group C3v. By means of extensive numerical analysis of the phase transition we show that irreversibility does not affect the critical behavior of the systems. In particular we find that the Binder reduced fourth order cumulant takes a universal value U* which is the same for the three state Potts model and for the irreversible models. The same universal behavior is observed for the reduced third-order cumulant.Comment: gzipped tar file containing: 1 latex file + 6 eps figure

Mean Field Behavior of Cluster Dynamics

The dynamic behavior of cluster algorithms is analyzed in the classical mean field limit. Rigorous analytical results below $T_c$ establish that the dynamic exponent has the value $z_{sw}=1$ for the Swendsen-Wang algorithm and $z_{uw}=0$ for the Wolff algorithm. An efficient Monte Carlo implementation is introduced, adapted for using these algorithms for fully connected graphs. Extensive simulations both above and below $T_c$ demonstrate scaling and evaluate the finite-size scaling function by means of a rather impressive collapse of the data.Comment: Revtex, 9 pages with 7 figure

Driven diffusive system with non-local perturbations

We investigate the impact of non-local perturbations on driven diffusive systems. Two different problems are considered here. In one case, we introduce a non-local particle conservation along the direction of the drive and in another case, we incorporate a long-range temporal correlation in the noise present in the equation of motion. The effect of these perturbations on the anisotropy exponent or on the scaling of the two-point correlation function is studied using renormalization group analysis.Comment: 11 pages, 2 figure

The Iterative Signature Algorithm for the analysis of large scale gene expression data

We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster, we assign both genes and conditions to context-dependent and potentially overlapping transcription modules. We provide a rigorous definition of a transcription module as the object to be retrieved from the expression data. An efficient algorithm, that searches for the modules encoded in the data by iteratively refining sets of genes and conditions until they match this definition, is established. Each iteration involves a linear map, induced by the normalized expression matrix, followed by the application of a threshold function. We argue that our method is in fact a generalization of Singular Value Decomposition, which corresponds to the special case where no threshold is applied. We show analytically that for noisy expression data our approach leads to better classification due to the implementation of the threshold. This result is confirmed by numerical analyses based on in-silico expression data. We discuss briefly results obtained by applying our algorithm to expression data from the yeast S. cerevisiae.Comment: Latex, 36 pages, 8 figure

A Study of Two-Temperature Non-Equilibrium Ising Models: Critical Behavior and Universality

We study a class of 2D non-equilibrium Ising models based on competing dynamics induced by contact with heat-baths at two different temperatures. We make a comparative study of the non-equilibrium versions of Metropolis, heat bath/Glauber and Swendsen-Wang dynamics and focus on their critical behavior in order to understand their universality classes. We present strong evidence that some of these dynamics have the same critical exponents and belong to the same universality class as the equilibrium 2D Ising model. We show that the bond version of the Swendsen-Wang update algorithm can be mapped into an equilibrium model at an effective temperature.Comment: 12 pages of LaTeX plus 18 pages of postscript figures in a uuencoded file (608k

Critical Exponents of the Classical 3D Heisenberg Model: A Single-Cluster Monte Carlo Study

We have simulated the three-dimensional Heisenberg model on simple cubic lattices, using the single-cluster Monte Carlo update algorithm. The expected pronounced reduction of critical slowing down at the phase transition is verified. This allows simulations on significantly larger lattices than in previous studies and consequently a better control over systematic errors. In one set of simulations we employ the usual finite-size scaling methods to compute the critical exponents $\nu,\alpha,\beta,\gamma, \eta$ from a few measurements in the vicinity of the critical point, making extensive use of histogram reweighting and optimization techniques. In another set of simulations we report measurements of improved estimators for the spatial correlation length and the susceptibility in the high-temperature phase, obtained on lattices with up to $100^3$ spins. This enables us to compute independent estimates of $\nu$ and $\gamma$ from power-law fits of their critical divergencies.Comment: 33 pages, 12 figures (not included, available on request). Preprint FUB-HEP 19/92, HLRZ 77/92, September 199

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

sPLA2-V inhibits EPCR anticoagulant and antiapoptotic properties by accommodating lysophosphatidylcholine or PAF in the hydrophobic groove

The endothelial protein C receptor (EPCR) plays an important role in cardiovascular disease by binding protein C/activated protein C (APC). EPCR structure contains a hydrophobic groove filled with an unknown phospholipid needed to perform its function. It has not been established whether lipid exchange takes place in EPCR as a regulatory mechanism of its activity. Our objective was to identify this phospholipid and to explore the possibility of lipid exchange as a regulatory mechanism of EPCR activity driven by the endothelially expressed secretory group V phospholipase A2 (sPLA2-V). We identified phosphatidylcholine (PCh) as the major phospholipid bound to human soluble EPCR (sEPCR). PCh in EPCR could be exchanged for lysophosphatidylcholine (lysoPCh) and platelet activating factor (PAF). Remarkably, lysoPCh and PAF impaired the protein C binding ability of sEPCR. Inhibition of sPLA2-V, responsible for lysoPCh and PAF generation, improved APC binding to endothelial cells. EPCR-dependent protein C activation and APC antiapoptotic effect were thus significantly enhanced. In contrast, endothelial cell supplementation with sPLA2-V inhibited both APC generation and its antiapoptotic effects. We conclude that APC generation and function can be modulated by changes in phospholipid occupancy of its endothelial cell receptor

A new view of electrochemistry at highly oriented pyrolytic graphite

Major new insights on electrochemical processes at graphite electrodes are reported, following extensive investigations of two of the most studied redox couples, Fe(CN)64–/3– and Ru(NH3)63+/2+. Experiments have been carried out on five different grades of highly oriented pyrolytic graphite (HOPG) that vary in step-edge height and surface coverage. Significantly, the same electrochemical characteristic is observed on all surfaces, independent of surface quality: initial cyclic voltammetry (CV) is close to reversible on freshly cleaved surfaces (>400 measurements for Fe(CN)64–/3– and >100 for Ru(NH3)63+/2+), in marked contrast to previous studies that have found very slow electron transfer (ET) kinetics, with an interpretation that ET only occurs at step edges. Significantly, high spatial resolution electrochemical imaging with scanning electrochemical cell microscopy, on the highest quality mechanically cleaved HOPG, demonstrates definitively that the pristine basal surface supports fast ET, and that ET is not confined to step edges. However, the history of the HOPG surface strongly influences the electrochemical behavior. Thus, Fe(CN)64–/3– shows markedly diminished ET kinetics with either extended exposure of the HOPG surface to the ambient environment or repeated CV measurements. In situ atomic force microscopy (AFM) reveals that the deterioration in apparent ET kinetics is coupled with the deposition of material on the HOPG electrode, while conducting-AFM highlights that, after cleaving, the local surface conductivity of HOPG deteriorates significantly with time. These observations and new insights are not only important for graphite, but have significant implications for electrochemistry at related carbon materials such as graphene and carbon nanotubes

Economic Losses From COVID-19 Cases in the Philippines: A Dynamic Model of Health and Economic Policy Trade-Offs

The COVID-19 pandemic forced governments globally to impose lockdown measures and mobility restrictions to curb the transmission of the virus. As economies slowly reopen, governments face a trade-off between implementing economic recovery and health policy measures to control the spread of the virus and to ensure it will not overwhelm the health system. We developed a mathematical model that measures the economic losses due to the spread of the disease and due to different lockdown policies. This is done by extending the subnational SEIR model to include two differential equations that capture economic losses due to COVID-19 infection and due to the lockdown measures imposed by the Philippine government. We then proceed to assess the trade-off policy space between health and economic measures faced by the Philippine government. The study simulates the cumulative economic losses for 3 months in 8 scenarios across 5 regions in the country, including the National Capital Region (NCR), to capture the trade-off mechanism. These scenarios present the various combinations of either retaining or easing lockdown policies in these regions. Per region, the trade-off policy space was assessed through minimising the 3-month cumulative economic losses subject to the constraint that the average health-care utilisation rate (HCUR) consistently falls below 70%, which is the threshold set by the government before declaring that the health system capacity is at high risk. The study finds that in NCR, a policy trade-off exists where the minimum cumulative economic losses comprise 10.66% of its Gross Regional Domestic Product. Meanwhile, for regions that are non-adjacent to NCR, a policy that hinges on trade-off analysis does not apply. Nevertheless, for all simulated regions, it is recommended to improve and expand the capacity of the health system to broaden the policy space for the government in easing lockdown measures