Search results for "computer simulation"
showing 10 items of 1054 documents
Simulation of the dynamics of hard ellipsoids
2008
We study a system of uniaxial hard ellipsoids by molecular dynamics simulations, changing both the aspect-ratio X-0 (X-0 = a/b, where a is the length of the revolution axis and b is the length of the two other axes) and the packing fraction phi. We calculate the translational and rotational mean squared displacements, the translational D-trans and the rotational D-rot diffusion coefficients and the associated isodiffusivity lines in the phi - X-0 plane. For the first time, we characterize the cage effect through the logarithmic time derivative of log and log . These quantities exhibit a minimum if the system is supercooled and we show that, consistently with our previous findings, for large…
Estimating the extent of horizontal gene transfer in metagenomic sequences
2008
Abstract Background Although the extent of horizontal gene transfer (HGT) in complete genomes has been widely studied, its influence in the evolution of natural communities of prokaryotes remains unknown. The availability of metagenomic sequences allows us to address the study of global patterns of prokaryotic evolution in samples from natural communities. However, the methods that have been commonly used for the study of HGT are not suitable for metagenomic samples. Therefore it is important to develop new methods or to adapt existing ones to be used with metagenomic sequences. Results We have created two different methods that are suitable for the study of HGT in metagenomic samples. The …
The intentional stance as structure learning: a computational perspective on mindreading
2015
Recent theories of mindreading explain the recognition of action, intention, and belief of other agents in terms of generative architectures that model the causal relations between observables (e.g., observed movements) and their hidden causes (e.g., action goals and beliefs). Two kinds of probabilistic generative schemes have been proposed in cognitive science and robotics that link to a "theory theory" and "simulation theory" of mindreading, respectively. The former compares perceived actions to optimal plans derived from rationality principles and conceptual theories of others' minds. The latter reuses one's own internal (inverse and forward) models for action execution to perform a look…
A framework for assessing frequency domain causality in physiological time series with instantaneous effects.
2013
We present an approach for the quantification of directional relations in multiple time series exhibiting significant zero-lag interactions. To overcome the limitations of the traditional multivariate autoregressive (MVAR) modelling of multiple series, we introduce an extended MVAR (eMVAR) framework allowing either exclusive consideration of time-lagged effects according to the classic notion of Granger causality, or consideration of combined instantaneous and lagged effects according to an extended causality definition. The spectral representation of the eMVAR model is exploited to derive novel frequency domain causality measures that generalize to the case of instantaneous effects the kno…
Extending the spectral decomposition of Granger causality to include instantaneous influences: application to the control mechanisms of heart rate va…
2021
Assessing Granger causality (GC) intended as the influence, in terms of reduction of variance of surprise, that a driver variable exerts on a given target, requires a suitable treatment of ‘instantaneous’ effects, i.e. influences due to interactions whose time scale is much faster than the time resolution of the measurements, due to unobserved confounders or insufficient sampling rate that cannot be increased because the mechanism of generation of the variable is inherently slow (e.g. the heartbeat). We exploit a recently proposed framework for the estimation of causal influences in the spectral domain and include instantaneous interactions in the modelling, thus obtaining (i) a novel index…
On a Retarded Nonlocal Ordinary Differential System with Discrete Diffusion Modeling Life Tables
2021
In this paper, we consider a system of ordinary differential equations with non-local discrete diffusion and finite delay and with either a finite or an infinite number of equations. We prove several properties of solutions such as comparison, stability and symmetry. We create a numerical simulation showing that this model can be appropriate to model dynamical life tables in actuarial or demographic sciences. In this way, some indicators of goodness and smoothness are improved when comparing with classical techniques.
Two-Color Radiation Generated in a Seeded Free-Electron Laser with Two Electron Beams.
2015
We present the experimental evidence of the generation of coherent and statistically stable two-color free-electron laser radiation obtained by seeding an electron beam double peaked in energy with a laser pulse single spiked in frequency. The radiation presents two neat spectral lines, with time delay, frequency separation, and relative intensity that can be accurately controlled. The analysis of the emitted radiation shows a temporal coherence and a shot-to-shot regularity in frequency significantly enhanced with respect to the self-amplified spontaneous emission. © 2015 American Physical Society. © 2015 American Physical Society.
Calcium binding and ionic conduction in single conical nanopores with polyacid chains: model and experiments.
2012
Calcium binding to fixed charge groups confined over nanoscale regions is relevant to ion equilibrium and transport in the ionic channels of the cell membranes and artificial nanopores. We present an experimental and theoretical description of the dissociation equilibrium and transport in a single conical nanopore functionalized with pH-sensitive carboxylic acid groups and phosphonic acid chains. Different phenomena are simultaneously present in this basic problem of physical and biophysical chemistry: (i) the divalent nature of the phosphonic acid groups fixed to the pore walls and the influence of the pH and calcium on the reversible dissociation equilibrium of these groups; (ii) the asym…
Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection
2003
Abstract Genetic variability in a subdivided population under stabilizing and diversifying selection was investigated at three levels: neutral markers, QTL coding for a trait, and the trait itself. A quantitative model with additive effects was used to link genotypes to phenotypes. No physical linkage was introduced. Using an analytical approach, we compared the diversity within deme (HS) and the differentiation (FST) at the QTL with the genetic variance within deme (VW) and the differentiation (QST) for the trait. The difference between FST and QST was shown to depend on the relative amounts of covariance between QTL within and between demes. Simulations were used to study the effect of se…
The Origins of Lactase Persistence in Europe
2009
Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (−13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the −13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model w…