Search results for " Simulation"
showing 10 items of 4034 documents
An Extended Filament Based Lamellipodium Model Produces Various Moving Cell Shapes in the Presence of Chemotactic Signals
2015
The Filament Based Lamellipodium Model (FBLM) is a two-phase two-dimensional continuum model, describing the dynamcis of two interacting families of locally parallel actin filaments (C.Schmeiser and D.Oelz, How do cells move? Mathematical modeling of cytoskeleton dynamics and cell migration. Cell mechanics: from single scale-based models to multiscale modeling. Chapman and Hall, 2010). It contains accounts of the filaments' bending stiffness, of adhesion to the substrate, and of cross-links connecting the two families. An extension of the model is presented with contributions from nucleation of filaments by branching, from capping, from contraction by actin-myosin interaction, and from a pr…
A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model.
2006
Abstract Motivation: The general-time-reversible (GTR) model is one of the most popular models of nucleotide substitution because it constitutes a good trade-off between mathematical tractability and biological reality. However, when it is applied for inferring evolutionary distances and/or instantaneous rate matrices, the GTR model seems more prone to inapplicability than more restrictive time-reversible models. Although it has been previously noted that the causes for intractability are caused by the impossibility of computing the logarithm of a matrix characterised by negative eigenvalues, the issue has not been investigated further. Results: Here, we formally characterize the mathematic…
A Hooke's law-based approach to protein folding rate
2014
Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke[U+05F3]s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons am…
Dynamics of the Selkov oscillator.
2018
A classical example of a mathematical model for oscillations in a biological system is the Selkov oscillator, which is a simple description of glycolysis. It is a system of two ordinary differential equations which, when expressed in dimensionless variables, depends on two parameters. Surprisingly it appears that no complete rigorous analysis of the dynamics of this model has ever been given. In this paper several properties of the dynamics of solutions of the model are established. With a view to studying unbounded solutions a thorough analysis of the Poincar\'e compactification of the system is given. It is proved that for any values of the parameters there are solutions which tend to inf…
A dynamic extraversion model. The brain's response to a single dose of a stimulant drug.
2008
The aim of this paper is to present a mathematical dynamic modelling of the effect a stimulant drug has on different people which, at the same time, can be a useful tool for future brain studies. To this end, a dynamic model of the evolution of extraversion (considering its tonic and phasic aspects) has been constructed taking into account the unique personality trait theory and the general modelling methodology. This model consists of a delayed differential equation which, on one hand, considers that the active stimulus, a consequence of a single intake, is not constant; on the other hand, it contemplates that the state variable representing the phasic extraversion also represents the brai…
Generalized Heisenberg algebra and (non linear) pseudo-bosons
2018
We propose a deformed version of the generalized Heisenberg algebra by using techniques borrowed from the theory of pseudo-bosons. In particular, this analysis is relevant when non self-adjoint Hamiltonians are needed to describe a given physical system. We also discuss relations with nonlinear pseudo-bosons. Several examples are discussed.
Energy efficient modulation of dendritic processing functions
1998
The voltage dependent ionic conductances and the passive properties of the neural membrane determine how external inputs are processed by the dendritic tree, and define the computational characteristics of neurons. However, what controls these characteristics and how they are implemented at the single neuron level, in such a way that an external input results in the coding of the appropriate output, is essentially unknown. We show here that a slow inactivation of the Na+ channel, involved in the attenuation and/or failure of APs in the dendrites, acts as an active and energy efficient filter of synaptic input, and results in an activity-dependent control of the properties of individual neur…
Coulomb-interacting billiards in circular cavities
2013
We apply a molecular dynamics scheme to analyze classically chaotic properties of a two-dimensional circular billiard system containing two Coulomb-interacting electrons. As such, the system resembles a prototype model for a semiconductor quantum dot. The interaction strength is varied from the noninteracting limit with zero potential energy up to the strongly interacting regime where the relative kinetic energy approaches zero. At weak interactions the bouncing maps show jumps between quasi-regular orbits. In the strong-interaction limit we find an analytic expression for the bouncing map. Its validity in the general case is assessed by comparison with our numerical data. To obtain a more …
Microscopic approach to a class of 1D quantum critical models
2015
Starting from the finite volume form factors of local operators, we show how and under which hypothesis the $c=1$ free boson conformal field theory in two-dimensions emerges as an effective theory governing the large-distance regime of multi-point correlation functions in a large class of one dimensional massless quantum Hamiltonians. In our approach, in the large-distance critical regime, the local operators of the initial model are represented by well suited vertex operators associated to the free boson model. This provides an effective field theoretic description of the large distance behaviour of correlation functions in 1D quantum critical models. We develop this description starting f…
Zeno dynamics and high-temperature master equations beyond secular approximation
2013
Complete positivity of a class of maps generated by master equations derived beyond the secular approximation is discussed. The connection between such class of evolutions and physical properties of the system is analyzed in depth. It is also shown that under suitable hypotheses a Zeno dynamics can be induced because of the high temperature of the bath.