Structure preserving schemes for mean-field equations of collective behavior

In this paper we consider the development of numerical schemes for mean-field equations describing the collective behavior of a large group of interacting agents. The schemes are based on a generalization of the classical Chang-Cooper approach and are capable to preserve the main structural properties of the systems, namely nonnegativity of the solution, physical conservation laws, entropy dissipation and stationary solutions. In particular, the methods here derived are second order accurate in transient regimes whereas they can reach arbitrary accuracy asymptotically for large times. Several examples are reported to show the generality of the approach.Comment: Proceedings of the XVI International Conference on Hyperbolic Problem

Synthetically tuneable biomimetic artificial photosynthetic reaction centres that closely resemble the natural system in purple bacteria

© 2016 The Royal Society of Chemistry. Porphyrin-based photosynthetic reaction centre (PRC) mimics, ZnPQ-Q2HP-C60 and MP2Q-Q2HP-C60 (M = Zn or 2H), designed to have a similar special-pair electron donor and similar charge-separation distances, redox processes and photochemical reaction rates to those in the natural PRC from purple bacteria, have been synthesised and extensive photochemical studies performed. Mechanisms of electron-transfer reactions are fully investigated using femtosecond and nanosecond transient absorption spectroscopy. In benzonitrile, all models show picosecond-timescale charge-separations and the final singlet charge-separations with the microsecond-timescale. The established lifetimes are long compared to other processes in organic solar cells or other organic light harvesting systems. These rigid, synthetically flexible molecules provide the closest mimics to the natural PRC so far synthesised and present a future direction for the design of light harvesters with controllable absorption, redox, and kinetics properties

The signalling channel of Central Bank interventions:modelling the Yen/US dollar exchange rate

This paper presents a theoretical framework analysing the signalling channel of exchange rate interventions as an informational trigger. We develop an implicit target zone framework with learning in order to model the signalling channel. The theoretical premise of the model is that interventions convey signals that communicate information about the exchange rate objectives of the central bank. The model is used to analyse the impact of Japanese FX interventions during the period 1999--2011 on the yen/US dollar dynamics

Satellite remote sensing data can be used to model marine microbial metabolite turnover

Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

© 2014. Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes

Uncertainty quantification for kinetic models in socio-economic and life sciences

Kinetic equations play a major rule in modeling large systems of interacting particles. Recently the legacy of classical kinetic theory found novel applications in socio-economic and life sciences, where processes characterized by large groups of agents exhibit spontaneous emergence of social structures. Well-known examples are the formation of clusters in opinion dynamics, the appearance of inequalities in wealth distributions, flocking and milling behaviors in swarming models, synchronization phenomena in biological systems and lane formation in pedestrian traffic. The construction of kinetic models describing the above processes, however, has to face the difficulty of the lack of fundamental principles since physical forces are replaced by empirical social forces. These empirical forces are typically constructed with the aim to reproduce qualitatively the observed system behaviors, like the emergence of social structures, and are at best known in terms of statistical information of the modeling parameters. For this reason the presence of random inputs characterizing the parameters uncertainty should be considered as an essential feature in the modeling process. In this survey we introduce several examples of such kinetic models, that are mathematically described by nonlinear Vlasov and Fokker--Planck equations, and present different numerical approaches for uncertainty quantification which preserve the main features of the kinetic solution.Comment: To appear in "Uncertainty Quantification for Hyperbolic and Kinetic Equations

Tracking Dehydration Mechanisms in Crystalline Hydrates with Molecular Dynamics Simulations

Dehydration of crystalline solids is a widespread phenomenon, yet the fundamental mechanisms by which dehydration occurs is not properly understood. This arises due to technical limitations in studying such fast processes with sufficient sensitivity, nevertheless understanding dehydration pathways is critical for designing optimal properties for materials, particularly in the case of pharmaceutical solids. The computational methods presented here allow for accurate determination of the dehydrated species' crystal structure and to develop an understanding of the mechanism of dehydration at the molecular level. This work also highlights the critical role of explicitly taking into account the dynamical aspect of molecules using computational techniques, rather then relying on static energy minimization approaches. Specifically, the crystalline active pharmaceutical agent naproxen sodium, and its hydrates, is studied in silico using density functional theory and molecular dynamics, ultimately elucidating the face-specific dehydration mechanisms and revealing highly complex diffusion and nucleation behaviour. Additionally, the results indicate that the method is a viable way to explore dehydration pathways and predict new dehydrated crystal structures.A.S.L, K.E.J and J.R. gratefully acknowledges the Villum Foundation (Denmark) for financial support (project No. VKR023111). M.T.R. and J.A.Z. would like to acknowledge funding from the U.K. Engineering and Physical Sciences Research Council (EP/N022769/1)

Universal contributions to scalar masses from five dimensional supergravity

We compute the effective Kahler potential for matter fields in warped compactifications, starting from five dimensional gauged supergravity, as a function of the matter fields localization. We show that truncation to zero modes is inconsistent and the tree-level exchange of the massive gravitational multiplet is needed for consistency of the four-dimensional theory. In addition to the standard Kahler coming from dimensional reduction, we find the quartic correction coming from integrating out the gravity multiplet. We apply our result to the computation of scalar masses, by assuming that the SUSY breaking field is a bulk hypermultiplet. In the limit of extreme opposite localization of the matter and the spurion fields, we find zero scalar masses, consistent with sequestering arguments. Surprisingly enough, for all the other cases the scalar masses are tachyonic. This suggests the holographic interpretation that a CFT sector always generates operators contributing in a tachyonic way to scalar masses. Viability of warped su- persymmetric compactifications necessarily asks then for additional contributions. We discuss the case of additional bulk vector multiplets with mixed boundary conditions, which is a partic- ularly simple and attractive way to generate large positive scalar masses. We show that in this case successful fermion mass matrices implies highly degenerate scalar masses for the first two generations of squarks and sleptons.Comment: 23 pages. v2: References added, new section on effect of additional bulk vector multiplets and phenomenolog

A Spin Chain for the Symmetric Product CFT_2

We consider "gauge invariant" operators in Sym^N T^4, the symmetric product orbifold of N copies of the 2d supersymmetric sigma model with T^4 target. We discuss a spin chain representation for single-cycle operators and study their two point functions at large N. We perform systematic calculations at the orbifold point ("tree level"), where non-trivial mixing is already present, and some sample calculations to first order in the blow-up mode of the orbifold ("one loop").Comment: 52 pages, 10 figure