Frequency-dependent fitness induces multistability in coevolutionary dynamics

Evolution is simultaneously driven by a number of processes such as mutation, competition and random sampling. Understanding which of these processes is dominating the collective evolutionary dynamics in dependence on system properties is a fundamental aim of theoretical research. Recent works quantitatively studied coevolutionary dynamics of competing species with a focus on linearly frequency-dependent interactions, derived from a game-theoretic viewpoint. However, several aspects of evolutionary dynamics, e.g. limited resources, may induce effectively nonlinear frequency dependencies. Here we study the impact of nonlinear frequency dependence on evolutionary dynamics in a model class that covers linear frequency dependence as a special case. We focus on the simplest non-trivial setting of two genotypes and analyze the co-action of nonlinear frequency dependence with asymmetric mutation rates. We find that their co-action may induce novel metastable states as well as stochastic switching dynamics between them. Our results reveal how the different mechanisms of mutation, selection and genetic drift contribute to the dynamics and the emergence of metastable states, suggesting that multistability is a generic feature in systems with frequency-dependent fitness.Comment: 12 pages, 6 figures; J. R. Soc. Interface (2012

Nonequilibrium electron heating in inter-subband terahertz lasers

Inter-subband laser performance can be critically dependent on the nature of the electron distributions in each subband. In these first Monte Carlo device simulations of optically pumped inter-subband THz lasers, we can see that there are two main causes of electron heating: intersubband decay processes, and inter-subband energy transfer from the "hot" nonequilibrium tails of lower subbands. These processes mean that devices relying on low electron temperatures are disrupted by electron heating, to the extent that slightly populated subbands can have average energies far in excess of the that of either the lattice or other subbands. However, although these heating effects invalidate designs relying on low temperature electron distributions, we see that population inversion is still possible in the high-THz range at 77 K in both stepped and triple-well structures, and that our 11.7 THz triple-well structure even promises inversion at 300 K. © 2002 American Institute of Physics

Sample preparation for point of care molecular diagnostics of STIs

This paper was presented at the 4th Micro and Nano Flows Conference (MNF2014), which was held at University College, London, UK. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute, ASME Press, LCN London Centre for Nanotechnology, UCL University College London, UCL Engineering, the International NanoScience Community, www.nanopaprika.eu.Brunel DoCLab is part of the esti2 consortium developing electronic self-testing instruments for sexually transmitted infections using nucleic acid amplification testing (NAAT). A proprietary sample collection device has been designed to integrate directly with a microfluidic cartridge. Cell lysis was conducted using a chemical method and nucleic acid purification was done on an activated cellulose membrane. The microfluidic device incorporates passive mixing of the lysis-binding buffers and sample. Preliminary results have shown extraction efficiencies for this new membrane of 69% and 57% compared to the commercial Qiagen extraction method of 85% and 59.4% for 0.1ng/μL and 100ng/μL salmon sperm DNA spiked in phosphate buffered solution. Preliminary extraction experiments in the passive mixer cartridges with lysis and nucleic acid purification showed extraction efficiency around 80% of the commercial Qiagen kit. Isothermal amplification was conducted using thermophillic helicase dependant amplification. A low cost benchtop real-time isothermal amplification platform has been developed capable of running six amplifications simultaneously. Work to integrate sample collection, nucleic acid extraction and isothermal amplification is currently underway

Fixation and consensus times on a network: a unified approach

We investigate a set of stochastic models of biodiversity, population genetics, language evolution and opinion dynamics on a network within a common framework. Each node has a state, 0 < x_i < 1, with interactions specified by strengths m_{ij}. For any set of m_{ij} we derive an approximate expression for the mean time to reach fixation or consensus (all x_i=0 or 1). Remarkably in a case relevant to language change this time is independent of the network structure.Comment: 4+epsilon pages, two-column, RevTeX4, 3 eps figures; version accepted by Phys. Rev. Let

Orbitally-driven Behavior: Mott Transition, Quantum Oscillations and Colossal Magnetoresistance in Bilayered Ca3Ru2O7

We report recent transport and thermodynamic experiments over a wide range of temperatures for the Mott-like system Ca3Ru2O7 at high magnetic fields, B, up to 30 T. This work reveals a rich and highly anisotropic phase diagram, where applying B along the a-, b-, and c-axis leads to vastly different behavior. A fully spin-polarized state via a first order metamagnetic transition is obtained for B||a, and colossal magnetoresistance is seen for B||b, and quantum oscillations in the resistivity are observed for B||c, respectively. The interplay of the lattice, orbital and spin degrees of freedom are believed to give rise to this strongly anisotropic behavior.Comment: 26 pages and 8 figure

Assessing the impact of future greenhouse gas emissions from natural gas production

Greenhouse gases (GHGs) produced by the extraction of natural gas are an important contributor to lifecycle emissions and account for a significant fraction of anthropogenic methane emissions in the USA. The timing as well as the magnitude of these emissions matters, as the short term climate warming impact of methane is up to 120 times that of CO 2 . This study uses estimates of CO 2 and methane emissions associated with different upstream operations to build a deterministic model of GHG emissions from conventional and unconventional gas fields as a function of time. By combining these emissions with a dynamic, techno-economic model of gas supply we assess their potential impact on the value of different types of project and identify stranded resources in various carbon price scenarios. We focus in particular on the effects of different emission metrics for methane, using the global warming potential (GWP) and the global temperature potential (GTP), with both fixed 20-year and 100-year CO 2 -equivalent values and in a time-dependent way based on a target year for climate stabilisation. We report a strong time dependence of emissions over the lifecycle of a typical field, and find that bringing forward the stabilisation year dramatically increases the importance of the methane contribution to these emissions. Using a commercial database of the remaining reserves of individual projects, we use our model to quantify future emissions resulting from the extraction of current US non-associated reserves. A carbon price of at least 400 USD/tonne CO 2 is effective in reducing cumulative GHGs by 30–60%, indicating that decarbonising the upstream component of the natural gas supply chain is achievable using carbon prices similar to those needed to decarbonise the energy system as a whole. Surprisingly, for large carbon prices, the choice of emission metric does not have a significant impact on cumulative emissions

Optimal Placement and Control of Unified Power Flow Control Devices Using Evolutionary Computing and Sequential Quadratic Programming

A crucial factor effecting modern power systems today is power flow control. An effective means for controlling and improving power flow is by installing fast reacting devices such as a unified power flow controller (UPFC). For maximum positive impact of this device on the power grid, it should be installed at an optimal location and employ an optimal realtime control algorithm. This paper proposes the combination of an evolutionary algorithm (EA) to find the optimal location and sequential quadratic programming (SQP) to optimize the UPFC control settings. Simulations are conducted using the classic IEEE 118 bus test system. For comparison purposes, results for the combination of a greedy placement heuristic (H) and the SQP control algorithm are provided as well. The EA+SQP combination is shown to outperform the H+SQP approach

Structure of a bacterial toxin-activating acyltransferase.

Secreted pore-forming toxins of pathogenic Gram-negative bacteria such as Escherichia coli hemolysin (HlyA) insert into host-cell membranes to subvert signal transduction and induce apoptosis and cell lysis. Unusually, these toxins are synthesized in an inactive form that requires posttranslational activation in the bacterial cytosol. We have previously shown that the activation mechanism is an acylation event directed by a specialized acyl-transferase that uses acyl carrier protein (ACP) to covalently link fatty acids, via an amide bond, to specific internal lysine residues of the protoxin. We now reveal the 2.15-Å resolution X-ray structure of the 172-aa ApxC, a toxin-activating acyl-transferase (TAAT) from pathogenic Actinobacillus pleuropneumoniae. This determination shows that bacterial TAATs are a structurally homologous family that, despite indiscernible sequence similarity, form a distinct branch of the Gcn5-like N-acetyl transferase (GNAT) superfamily of enzymes that typically use acyl-CoA to modify diverse bacterial, archaeal, and eukaryotic substrates. A combination of structural analysis, small angle X-ray scattering, mutagenesis, and cross-linking defined the solution state of TAATs, with intermonomer interactions mediated by an N-terminal α-helix. Superposition of ApxC with substrate-bound GNATs, and assay of toxin activation and binding of acyl-ACP and protoxin peptide substrates by mutated ApxC variants, indicates the enzyme active site to be a deep surface groove.This work was supported by UK Medical Research Council and the Wellcome Trust Grants (to C.H. and V.K.).This is the author accepted manuscript. The final version is available from PNAS via http://dx.doi.org/10.1073/pnas.150383211

Robustness and epistasis in mutation-selection models

We investigate the fitness advantage associated with the robustness of a phenotype against deleterious mutations using deterministic mutation-selection models of quasispecies type equipped with a mesa shaped fitness landscape. We obtain analytic results for the robustness effect which become exact in the limit of infinite sequence length. Thereby, we are able to clarify a seeming contradiction between recent rigorous work and an earlier heuristic treatment based on a mapping to a Schr\"odinger equation. We exploit the quantum mechanical analogy to calculate a correction term for finite sequence lengths and verify our analytic results by numerical studies. In addition, we investigate the occurrence of an error threshold for a general class of epistatic landscape and show that diminishing epistasis is a necessary but not sufficient condition for error threshold behavior.Comment: 20 pages, 14 figure