Search results for " Genetics"
showing 10 items of 4169 documents
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…
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…
Ancestral processes in population genetics-the coalescent.
2000
A special stochastic process, called the coalescent, is of fundamental interest in population genetics. For a large class of population models this process is the appropriate tool to analyse the ancestral structure of a sample of n individuals or genes, if the total number of individuals in the population is sufficiently large. A corresponding convergence theorem was first proved by Kingman in 1982 for the Wright-Fisher model and the Moran model. Generalizations to a large class of exchangeable population models and to models with overlying mutation processes followed shortly later. One speaks of the "robustness of the coalescent, as this process appears in many models as the total populati…
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
Antibacterial Activity of Flavonoids Against Methicillin-resistant Staphylococcus aureus strains
2000
An experimental and theoretical study was performed on the anti-staphylococcal activity of 18 natural and synthetic flavonoids against methicillin-resistant Staphylococcus aureus strains. The analysed flavonoids belong to three well-differentiated structural patterns: chalcones, flavanones and flavones. The quantitative analysis of the anti-staphylococcal activity of the compounds was carried out by determining their percent inhibition degree. The hierarchical cluster analysis method was used to analyse the anti-MRSA activity of the compounds. With this methodology, the flavonoids were classified into four groups according to their anti-staphylococcal activity (high, sufficient, intermediat…
A hypothetical model of the influence of inorganic phosphate on the kinetics of pyruvate kinase
2000
This paper presents a simple solution to the problem of approximating the calculated curve of reaction progress to the measured curve which is usually disturbed by initial oscillation of auxiliary lactate dehydrogenase (LDH) reaction. The experiments leading to the determination of the apparent Km for phosphoenolpyruvate (PEP) and Vm were performed. For precise estimation of kinetic parameters (Km and Vm) of the M1 isozyme of pyruvate kinase (PK), measured by coupling it to LDH reaction, the sequence of Michaelis‐Menten for pyruvate kinase and second-order kinetics for lactate dehydrogenase reaction as well as a non-zero initial concentration of lactate was assumed. The functions of apparen…
Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs
2016
Abstract One of use cases for metabolic network optimisation of biotechnologically applied microorganisms is the in silico design of new strains with an improved distribution of metabolic fluxes. Global stochastic optimisation methods (genetic algorithms, evolutionary programing, particle swarm and others) can optimise complicated nonlinear kinetic models and are friendly for unexperienced user: they can return optimisation results with default method settings (population size, number of generations and others) and without adaptation of the model. Drawbacks of these methods (stochastic behaviour, undefined duration of optimisation, possible stagnation and no guaranty of reaching optima) cau…
Basic networks: Definition and applications
2009
7 pages, 4 figures, 1 table.-- PMID: 19490867 [PubMed]
Comment on "Ecological importance of the thermal emissivity of avian eggshells".
2012
Eggshell emissivity must be known to determine accurately the cooling rate of avian eggs when the parent, after heating by conduction during the incubation, is temporarily absent. We estimate possible values of eggshell emissivities from in-situ measurements and spectral libraries. Emissivity is near to 1 (probably higher than 0.95) and therefore its effect on cooling rate may be negligible, with differences between the temperature of the egg assuming a value of e=0.95 and that of a blackbody (e=1) below 0.2 °C.