Search results for "Quantitative Biology"
showing 10 items of 1025 documents
A Simple Noise Model with Memory for Biological Systems
2005
A noise source model, consisting of a pulse sequence at random times with memory, is presented. By varying the memory we can obtain variable randomness of the stochastic process. The delay time between pulses, i. e. the noise memory, produces different kinds of correlated noise ranging from white noise, without delay, to quasi-periodical process, with delay close to the average period of the pulses. The spectral density is calculated. This type of noise could be useful to describe physical and biological systems where some delay is present. In particular it could be useful in population dynamics. A simple dynamical model for epidemiological infection with this noise source is presented. We …
Predator population depending on lemming cycles
2016
In this paper, a Langevin equation for predator population with multiplicative correlated noise is analyzed. The noise source, which is a nonnegative random pulse noise with regulated periodicity, corresponds to the prey population cycling. The increase of periodicity of noise affects the average predator density at the stationary state.
Stochastic dynamics and mean field approach in a system of three interacting species
2008
The spatio-temporal dynamics of three interacting species, two preys and one predator, in the presence of two different kinds of noise sources is studied. To describe the spatial distributions of the species we use a model based on Lotka-Volterra equations. A correlated dichotomous noise acts on \beta, the interaction parameter between the two preys, and a multiplicative white noise affects directly the dynamics of each one of the three species. We study the time behaviour of the three species in single site for different values of the multiplicative noise intensity, finding noise-induced oscillations of the three species densities with an anticorrelated behaviour of the two preys. Afterwar…
A Ferrite Tubular Linear Motor (FTLM): Analysis and design
2015
The electromagnetic linear machines have wide applications in the electromagnetic aircraft launch systems [1] and in transportation systems [2]. Additional energy saving and efficiency can be achieved using a linear motor in the refrigeration application [3]. Linear electromagnetic machines are also very suitable for high-speed packaging, manufacturing sectors and precision positioning. There are different linear motor topologies. Tubular permanent-magnets are particularly attractive since they have a high thrust force density and high efficiency, no end windings, and zero net attractive force between stator and armature. There are various tubular motor topologies, in which the armature may…
Information – theoretic characterization of concurrent activity of neural spike trains
2021
The analysis of massively parallel spike train recordings facilitates investigation of communications and synchronization in neural networks. In this work we develop and evaluate a measure of concurrent neural activity, which is based on intrinsic firing properties of the recorded neural units. An overall single neuron activity is unfolded in time and decomposed into working and non-firing state, providing a coarse, binary representation of the neurons functional state. We propose a modified measure of mutual information to reflect the degree of simultaneous activation and concurrency in neural firing patterns. The measure is shown to be sensitive to both correlations and anti-correlations,…
A proof of bistability for the dual futile cycle
2014
Abstract The multiple futile cycle is an important building block in networks of chemical reactions arising in molecular biology. A typical process which it describes is the addition of n phosphate groups to a protein. It can be modelled by a system of ordinary differential equations depending on parameters. The special case n = 2 is called the dual futile cycle. The main result of this paper is a proof that there are parameter values for which the system of ODE describing the dual futile cycle has two distinct stable stationary solutions. The proof is based on bifurcation theory and geometric singular perturbation theory. An important entity built of three coupled multiple futile cycles is…
The influence of solvent on conformational properties of peptides with Aib residue—a DFT study
2017
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results,…
Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics
2000
Serine amino acid in aqueous solution is theoretically studied at the B3PW91/6-31+G** level using a dielectric continuum solvent model. Neutral and zwitterionic structures in the gas phase and in solution are described and the proton-transfer mechanism is discussed. A neutral conformation in which the carboxyl hydrogen atom is already oriented toward the amino group seems to be the absolute energy minimum in the gas phase and the most stable neutral form in solution. The absolute energy minimum in solution is a zwitterionic form. The energy barrier for proton transfer is predicted to be very small, in particular when zero-point-energy contributions are added. Our calculations allow the dyna…
Versatile optimization-based speed-up method for autofocusing in digital holographic microscopy
2021
We propose a speed-up method for the in-focus plane detection in digital holographic microscopy that can be applied to a broad class of autofocusing algorithms that involve repetitive propagation of an object wave to various axial locations to decide the in-focus position. The classical autofocusing algorithms apply a uniform search strategy, i.e., they probe multiple, uniformly distributed axial locations, which leads to heavy computational overhead. Our method substantially reduces the computational load, without sacrificing the accuracy, by skillfully selecting the next location to investigate, which results in a decreased total number of probed propagation distances. This is achieved by…
FPGA implementation of Spiking Neural Networks
2012
Abstract Spiking Neural Networks (SNN) have optimal characteristics for hardware implementation. They can communicate among neurons using spikes, which in terms of logic resources, means a single bit, reducing the logic occupation in a device. Additionally, SNN are similar in performance compared to other neural Artificial Neural Network (ANN) architectures such as Multilayer Perceptron, and others. SNN are very similar to those found in the biological neural system, having weights and delays as adjustable parameters. This work describes the chosen models for the implemented SNN: Spike Response Model (SRM) and temporal coding is used. FPGA implementation using VHDL language is also describe…