Search results for "genetics [Transcriptome]"
showing 10 items of 3033 documents
Influence of inorganic pyrophosphate on the kinetics of muscle pyruvate kinase: a simple nonallosteric feedback model.
2002
Potassium pyrophosphate was used instead of ATP as a model ligand for magnesium cation for the study of effector influence on the kinetics of pyruvate kinase muscle isozyme M1. The pyruvate kinase activation by low concentration of pyrophosphate and inhibition by high concentration of pyrophosphate was considered to be the result of reversible reactions of magnesium cation with pyrophosphate, ADP, ATP, and PEP. The apparent Km and Vm or in some cases the pseudo-first order reaction rate constant (instead of Km and Vm) of pyruvate kinase at any given pyrophosphate concentration were analysed as a function of concentration of free magnesium cation and its complexes with all ligands present in…
Multitype spatial point patterns with hierarchical interactions.
2001
Multitype spatial point patterns with hierarchical interactions are considered. Here hierarchical interaction means directionality: points on a higher level of hierarchy affect the locations of points on the lower levels, but not vice versa. Such relations are common, for example, in ecological communities. Interacting point patterns are often modeled by Gibbs processes with pairwise interactions. However, these models are inherently symmetric, and the hierarchy can be acknowledged only when interpreting the results. We suggest the following in allowing the inclusion of the hierarchical structure in the model. Instead of regarding the pattern as a realization of a stationary multivariate po…
Splitting the dynamics of large biochemical interaction networks
2003
This article is inscribed in the general motivation of understanding the dynamics on biochemical networks including metabolic and genetic interactions. Our approach is continuous modeling by differential equations. We address the problem of the huge size of those systems. We present a mathematical tool for reducing the size of the model, master-slave synchronization, and fit it to the biochemical context.
Distribution of oxygen partial pressure in a two-dimensional tissue supplied by capillary meshes and concurrent and countercurrent systems
1969
Abstract For the calculations of oxygen partial pressure in a two-dimensional tissue model supplied by a capillary network (inhomogeneously perfused tissue), two differential equations are given that describe the process in the tissue and capillaries. The differential equations are coupled by the boundary conditions. Results obtained by using the method of successive displacements are given for the two-dimensional problem. This method exhibits a satisfactory convergence. The accuracy of the results is about ±5% based on the initial concentration. The results for the network model are compared with those for equivalent concurrent and countercurrent systems. Equivalence means in this connecti…
Sample Size Requirements of a Mixture Analysis Method with Applications in Systematic Biology
1999
The available information on sample size requirements of mixture analysis methods is insufficient to permit a precise evaluation of the potential problems facing practical applications of mixture analysis. We use results from Monte Carlo simulation to assess the sample size requirements of a simple mixture analysis method under conditions relevant to biological applications of mixture analysis. The mixture model used includes two univariate normal components with equal variances but assumes that the researcher is ignorant as to the equality of the variances. The method used relies on the EM algorithm to compute the maximum likelihood estimates of the mixture parameters, and the likelihood r…
On a set of data for the membrane potential in a neuron
2006
We consider a set of data where the membrane potential in a pyramidal neuron is measured almost continuously in time, under varying experimental conditions. We use nonparametric estimates for the diffusion coefficient and the drift in view to contribute to the discussion which type of diffusion process is suitable to model the membrane potential in a neuron (more exactly: in a particular type of neuron under particular experimental conditions).
RNA viruses as complex adaptive systems
2004
RNA viruses have high mutation rates and so their populations exist as dynamic and complex mutant distributions. It has been consistently observed that when challenged with a new environment, viral populations adapt following hyperbolic-like kinetics: adaptation is initially very rapid, but then slows down as fitness reaches an asymptotic value. These adaptive dynamics have been explained in terms of populations moving towards the top of peaks on rugged fitness landscapes. Fitness fluctuations of varying magnitude are observed during adaptation. Often the presence of fluctuations in the evolution of physical systems indicates some form of self-organization, or where many components of the s…
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 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…