638 research outputs found
Solution of the Fokker-Planck transport equation by matrix factorization
A matrix factorization method is used to solve the Fokker-Planck (Landau) charged particle transport equation. By treating all phase space variables as discrete in analogy to Sn neutronics, the collision term takes on a five-point difference form which is readily treatable by this method. In order to illustrate this technique, the energy deposited by fast ions in a geometrically spherical, Maxwellian background plasma is calculated. Although this technique can be generalized to other geometries, its essential elements are best illustrated in this simple context.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24295/1/0000561.pd
In-depth analysis of the Naming Game dynamics: the homogeneous mixing case
Language emergence and evolution has recently gained growing attention
through multi-agent models and mathematical frameworks to study their behavior.
Here we investigate further the Naming Game, a model able to account for the
emergence of a shared vocabulary of form-meaning associations through
social/cultural learning. Due to the simplicity of both the structure of the
agents and their interaction rules, the dynamics of this model can be analyzed
in great detail using numerical simulations and analytical arguments. This
paper first reviews some existing results and then presents a new overall
understanding.Comment: 30 pages, 19 figures (few in reduced definition). In press in IJMP
Calibration of optimal execution of financial transactions in the presence of transient market impact
Trading large volumes of a financial asset in order driven markets requires
the use of algorithmic execution dividing the volume in many transactions in
order to minimize costs due to market impact. A proper design of an optimal
execution strategy strongly depends on a careful modeling of market impact,
i.e. how the price reacts to trades. In this paper we consider a recently
introduced market impact model (Bouchaud et al., 2004), which has the property
of describing both the volume and the temporal dependence of price change due
to trading. We show how this model can be used to describe price impact also in
aggregated trade time or in real time. We then solve analytically and calibrate
with real data the optimal execution problem both for risk neutral and for risk
averse investors and we derive an efficient frontier of optimal execution. When
we include spread costs the problem must be solved numerically and we show that
the introduction of such costs regularizes the solution.Comment: 31 pages, 8 figure
A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase
Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets
Hofstadter butterflies of carbon nanotubes: Pseudofractality of the magnetoelectronic spectrum
The electronic spectrum of a two-dimensional square lattice in a
perpendicular magnetic field has become known as the Hofstadter butterfly
[Hofstadter, Phys. Rev. B 14, 2239 (1976).]. We have calculated
quasi-one-dimensional analogs of the Hofstadter butterfly for carbon nanotubes
(CNTs). For the case of single-wall CNTs, it is straightforward to implement
magnetic fields parallel to the tube axis by means of zone folding in the
graphene reciprocal lattice. We have also studied perpendicular magnetic fields
which, in contrast to the parallel case, lead to a much richer, pseudofractal
spectrum. Moreover, we have investigated magnetic fields piercing double-wall
CNTs and found strong signatures of interwall interaction in the resulting
Hofstadter butterfly spectrum, which can be understood with the help of a
minimal model. Ubiquitous to all perpendicular magnetic field spectra is the
presence of cusp catastrophes at specific values of energy and magnetic field.
Resolving the density of states along the tube circumference allows recognition
of the snake states already predicted for nonuniform magnetic fields in the
two-dimensional electron gas. An analytic model of the magnetic spectrum of
electrons on a cylindrical surface is used to explain some of the results.Comment: 14 pages, 12 figures update to published versio
A Comprehensive Workflow for General-Purpose Neural Modeling with Highly Configurable Neuromorphic Hardware Systems
In this paper we present a methodological framework that meets novel
requirements emerging from upcoming types of accelerated and highly
configurable neuromorphic hardware systems. We describe in detail a device with
45 million programmable and dynamic synapses that is currently under
development, and we sketch the conceptual challenges that arise from taking
this platform into operation. More specifically, we aim at the establishment of
this neuromorphic system as a flexible and neuroscientifically valuable
modeling tool that can be used by non-hardware-experts. We consider various
functional aspects to be crucial for this purpose, and we introduce a
consistent workflow with detailed descriptions of all involved modules that
implement the suggested steps: The integration of the hardware interface into
the simulator-independent model description language PyNN; a fully automated
translation between the PyNN domain and appropriate hardware configurations; an
executable specification of the future neuromorphic system that can be
seamlessly integrated into this biology-to-hardware mapping process as a test
bench for all software layers and possible hardware design modifications; an
evaluation scheme that deploys models from a dedicated benchmark library,
compares the results generated by virtual or prototype hardware devices with
reference software simulations and analyzes the differences. The integration of
these components into one hardware-software workflow provides an ecosystem for
ongoing preparative studies that support the hardware design process and
represents the basis for the maturity of the model-to-hardware mapping
software. The functionality and flexibility of the latter is proven with a
variety of experimental results
Recombination rate and selection strength in HIV intra-patient evolution
The evolutionary dynamics of HIV during the chronic phase of infection is
driven by the host immune response and by selective pressures exerted through
drug treatment. To understand and model the evolution of HIV quantitatively,
the parameters governing genetic diversification and the strength of selection
need to be known. While mutation rates can be measured in single replication
cycles, the relevant effective recombination rate depends on the probability of
coinfection of a cell with more than one virus and can only be inferred from
population data. However, most population genetic estimators for recombination
rates assume absence of selection and are hence of limited applicability to
HIV, since positive and purifying selection are important in HIV evolution.
Here, we estimate the rate of recombination and the distribution of selection
coefficients from time-resolved sequence data tracking the evolution of HIV
within single patients. By examining temporal changes in the genetic
composition of the population, we estimate the effective recombination to be
r=1.4e-5 recombinations per site and generation. Furthermore, we provide
evidence that selection coefficients of at least 15% of the observed
non-synonymous polymorphisms exceed 0.8% per generation. These results provide
a basis for a more detailed understanding of the evolution of HIV. A
particularly interesting case is evolution in response to drug treatment, where
recombination can facilitate the rapid acquisition of multiple resistance
mutations. With the methods developed here, more precise and more detailed
studies will be possible, as soon as data with higher time resolution and
greater sample sizes is available.Comment: to appear in PLoS Computational Biolog
Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a phase 3 HIV vaccine efficacy trial
This study documents a case of coinfection (simultaneous infection of an individual with two or more strains) of two HIV-1 subtype B strains in an individual from a Phase 3 HIV-1 vaccine efficacy trial, conducted in North American and the Netherlands. We examined 86 full-length gp120 (env) gene sequences from this individual collected from nine different time points over a 20-month period. We estimated evolutionary relationships using maximum likelihood and Bayesian methods and inferred recombination breakpoints and recombinant sequences using phylogenetic and substitutional methods. These analyses identified two strongly supported monophyletic clades (clades A and B) of 14 and 69 sequences each and a small paraphyletic recombinant clade of three sequences. We then studied the genetic characteristics of these lineages by comparing estimates of genetic diversity generated by mutation and recombination and adaptive selection within a coalescent and maximum likelihood framework. Our results suggest significant differences on the evolutionary dynamics of these strains. We then discuss the implications of these results for vaccine development
Information transmission in oscillatory neural activity
Periodic neural activity not locked to the stimulus or to motor responses is
usually ignored. Here, we present new tools for modeling and quantifying the
information transmission based on periodic neural activity that occurs with
quasi-random phase relative to the stimulus. We propose a model to reproduce
characteristic features of oscillatory spike trains, such as histograms of
inter-spike intervals and phase locking of spikes to an oscillatory influence.
The proposed model is based on an inhomogeneous Gamma process governed by a
density function that is a product of the usual stimulus-dependent rate and a
quasi-periodic function. Further, we present an analysis method generalizing
the direct method (Rieke et al, 1999; Brenner et al, 2000) to assess the
information content in such data. We demonstrate these tools on recordings from
relay cells in the lateral geniculate nucleus of the cat.Comment: 18 pages, 8 figures, to appear in Biological Cybernetic
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