Search results for "Quantitative Biology"
showing 10 items of 1025 documents
Experimental study of electrical FitzHugh-Nagumo neurons with modified excitability
2006
International audience; We present an electronical circuit modelling a FitzHugh-Nagumo neuron with a modified excitability. To characterize this basic cell, the bifurcation curves between stability with excitation threshold, bistability and oscillations are investigated. An electrical circuit is then proposed to realize a unidirectional coupling between two cells, mimicking an inter-neuron synaptic coupling. In such a master-slave configuration, we show experimentally how the coupling strength controls the dynamics of the slave neuron, leading to frequency locking, chaotic behavior and synchronization. These phenomena are then studied by phase map analysis. The architecture of a possible ne…
Host–virus evolutionary dynamics with specialist and generalist infection strategies: Bifurcations, bistability, and chaos
2019
In this work, we have investigated the evolutionary dynamics of a generalist pathogen, e.g., a virus population, that evolves toward specialization in an environment with multiple host types. We have particularly explored under which conditions generalist viral strains may rise in frequency and coexist with specialist strains or even dominate the population. By means of a nonlinear mathematical model and bifurcation analysis, we have determined the theoretical conditions for stability of nine identified equilibria and provided biological interpretation in terms of the infection rates for the viral specialist and generalist strains. By means of a stability diagram, we identified stable fixed…
The Extinction of Generations in Generation-Dependent Bellman-Harris Branching Processes with Exponential Lifespan
1978
If V is the time when in a Bellman-Harris branching model the k-th generation disappears out of the population, and if all individuals have exponentially distributed lifespans, the asymptotic behavior of the tail of the distribution of the extinction time V , P(V > t), is obtained, even if the distributions of the lifespans and the offspring sizes vary generation-dependent. Furthermore the times of extinction of several successive generations can be specified for the generation- independent case of the Markov branching model in continuous time. If the initial number of individuals and the absolute time grow up appropriately linked, a Poisson limit theorem for generation sizes will be given.
Supplementary material 2 from: Pérez Santa-Rita JV, Baixeras J (2018) Two new species of Brusqeulia Razowski & Becker, 2000 from the Neotropics, with…
2018
Character matrix : Explanation note: Data matrix for phylogenetic analysis.
CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA
2011
Pyrosequencing technologies are frequently used for sequencing the 16S rRNA marker gene for metagenomic studies of microbial communities. Computing a pairwise genetic distance matrix from the produced reads is an important but highly time consuming task. In this paper, we present a parallelized tool (called CRiSPy) for scalable pairwise genetic distance matrix computation and clustering that is based on the processing pipeline of the popular ESPRIT software package. To achieve high computational efficiency, we have designed massively parallel CUDA algorithms for pairwise k-mer distance and pairwise genetic distance computation. We have also implemented a memory-efficient sparse matrix clust…
A Review of Mathematical and Computational Methods in Cancer Dynamics.
2022
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires the integration of information dynamics across multidimensional spatiotemporal scales, including genetic, transcriptional, metabolic, proteomic, epigenetic, and multi-cellular networks. However, the time-series analysis of these complex networks remains vastly absent in cancer research. With longitudinal screening and time-series analysis of cellular dynamics, universally observed causal patterns pertaining to dynamical systems, may self-organize in the si…
Intrinsic Acidity of Surface Sites in Calcium Silicate Hydrates and Its Implication to Their Electrokinetic Properties
2014
Calcium Silicate Hydrates (C–S–H) are the major hydration products of portland cement paste. The accurate description of acid–base reactions at the surface of C–S–H particles is essential for both understanding the ion sorption equilibrium in cement and prediction of mechanical properties of the hardened cement paste. Ab initio molecular dynamics simulations at the density functional level of theory were applied to calculate intrinsic acidity constants (pKa’s) of the relevant ≡SiOH and ≡CaOH2 groups on the C–S–H surfaces using a thermodynamic integration technique. Ion sorption equilibrium in C–S–H was modeled applying ab initio calculated pKa’s in titrating Grand Canonical Monte Carlo simu…
Simulations of the cultured granule neuron excitability
2003
Abstract We have developed a biophysical model of a cultured rat cerebellar granule neuron and simulated its excitability under different experimental conditions. The basic excitability properties of such a small neuron; the specific action potential waveforms, the overall firing patterns induced by current stimulations, and the linear frequency-current relation, are the main model constraints. Simulations show that for a one-compartmental granule neuron model, the constraints are met using six voltage- and time-dependent ion channel types and calcium dynamics linked to BK Ca ion channel function. This kind of model of a single neuron forms a solid basis for building the increasingly more c…
On localization of moving objects in the visual system of cats.
1980
In cortical areas direction-specific receptive fields occur systematically. Direction specifity is based on unsymmetric coupling of neurons. Such a coupling allows an exact localization of moved stimuli. For this task, the asymmetry in the time domain is compensated for by a spatial asymmetry.
Computer simulation of bottle-brush polymers with flexible backbone: good solvent versus theta solvent conditions.
2011
By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\sigma$ side chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range $5 \le N \le 40$, backbone chain lengths are in the range $50 \le N_b \le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, $N_b \le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of …