Search results for "PERTURBATION"
showing 10 items of 811 documents
Dynamical Features of the MAP Kinase Cascade
2017
The MAP kinase cascade is an important signal transduction system in molecular biology for which a lot of mathematical modelling has been done. This paper surveys what has been proved mathematically about the qualitative properties of solutions of the ordinary differential equations arising as models for this biological system. It focuses, in particular, on the issues of multistability and the existence of sustained oscillations. It also gives a concise introduction to the mathematical techniques used in this context, bifurcation theory and geometric singular perturbation theory, as they relate to these specific examples. In addition further directions are presented in which the application…
Molecular Mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a Twister Ribozyme
2017
Published as part of the special collection of articles derived from the 10th Congress on Electronic Structure: Principles and Applications (ESPA-2016). The catalytic activity of some classes of natural RNA, named as ribozymes, has been discovered just in the past decades. In this paper, the cleavage of the RNA phosphodiester backbone has been studied in aqueous solution and in a twister ribozyme from Oryza sativa. The free energy profiles associated with a baseline substrate-assisted mechanism for the reaction in the enzyme and in solution were computed by means of free energy perturbation methods within hybrid QM/MM potentials, describing the chemical system by the M06-2× functional and t…
Amyloid β-peptide insertion in liposomes containing GM1-cholesterol domains.
2015
Neuronal membrane damage is related to the early impairments appearing in Alzheimer's disease due to the interaction of the amyloid β-peptide (Aβ) with the phospholipid bilayer. In particular, the ganglioside GM1, present with cholesterol in lipid rafts, seems to be able to initiate Aβ aggregation on membrane. We studied the thermodynamic and structural effects of the presence of GM1 on the interaction between Aβ and liposomes, a good membrane model system. Isothermal Titration Calorimetry highlighted the importance of the presence of GM1 in recruiting monomeric Aβ toward the lipid bilayer. Light and Small Angle X-ray Scattering revealed a different pattern for GM1 containing liposomes, bot…
Sustained oscillations in the MAP kinase cascade.
2016
Abstract The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This paper focuses on the existence of parameters for which Hopf bifurcations occur and generate periodic orbits. Furthermore it is explained how geometric singular perturbation theory allows to generalize results from simple models to more complex ones.
Adaptive synchronization of master-slave systems with mixed neutral and discrete time-delays and nonlinear perturbations
2011
This paper investigates the delay-dependent adaptive synchronization problem of the master and slave structure of linear systems with both constant neutral and time-varying discrete time-delays and nonlinear perturbations based on the Barbalat lemma and matching conditions. An adaption law which includes the master-slave parameters is obtained by using the Lyapunov functional method and inequality techniques to synchronize the master-slave systems without the knowledge of upper bounds of perturbation terms. Particularly, it is shown that the synchronization speed can be controlled by adjusting the update gain of the synchronization signal. A numerical example has been given to show the effe…
A theoretical study of the 1B2u and 1B1u vibronic bands in benzene
2000
The two lowest bands, 1B2u and 1B1u, of the electronic spectrum of the benzene molecule have been studied theoretically using a new method to compute vibronic excitation energies and intensities. The complete active space (CAS) self-contained field (SCF) method (with six active π-orbitals) was used to compute harmonic force field for the ground state and the 1B2u and 1B1u electronic states. A linear approximation has been used for the transition dipole as a function of the nuclear displacement coordinates. Derivatives of the transition dipole were computed using a variant of the CASSCF state interaction method. Multiconfigurational second-order perturbation theory (CASPT2) was used to obtai…
Asymptotic potentials and rate constants in the adiabatic capture centrifugal sudden approximation for X + OH(X-2 Pi) -> OX + H(S-2) reactions where …
2012
International audience; New long-range multipolar coefficients for the X + OH(X-2 Pi) interactions, where X = O(P-3), S(P-3) and N(S-4), are given here. They have been evaluated on the basis or monomer properties of the atoms and OH such as the dipole and quadrupole moments, and the static and dynamic polarizabilities. Each matrix element of the 18 x 18 (8 x 8 for N + OH) quasi-degenerate asymptotic potentials has been built up by means of the perturbation theory up to second order including or not the fine-structure of O, S and OH. The adiabatic potentials, obtained after diagonalization of the full matrix, show many crossings and complex behaviors near the asymptotes. Using the entrance c…
Abelian integrals and limit cycles
2006
Abstract The paper deals with generic perturbations from a Hamiltonian planar vector field and more precisely with the number and bifurcation pattern of the limit cycles. In this paper we show that near a 2-saddle cycle, the number of limit cycles produced in unfoldings with one unbroken connection, can exceed the number of zeros of the related Abelian integral, even if the latter represents a stable elementary catastrophe. We however also show that in general, finite codimension of the Abelian integral leads to a finite upper bound on the local cyclicity. In the treatment, we introduce the notion of simple asymptotic scale deformation.
Effects of gait speed on stability of walking revealed by simulated response to tripping perturbation
2013
The objective of this work was to study stability of walking over a range of gait speeds by means of muscle-driven simulations. Fast walking has previously been related to high likelihood of falling due to tripping. Various measures of stability have shown different relationships between walking speed and stability. These measures may not be associated with tripping, so it is unclear whether the increase in likelihood of falling is explicable by an increase in instability. Here, stability with respect to a constant tripping perturbation was quantified as the immediate passive response of torso to the perturbation. Subject-specific muscle-driven simulations of eight young healthy subjects wa…
Are postural responses to backward and forward perturbations processed by different neural circuits?
2013
Item does not contain fulltext Startle pathways may contribute to rapid accomplishment of postural stability. Here we investigate the possible influence of a startling auditory stimulus (SAS) on postural responses. We formulated four specific questions: (1) can a concurrent SAS shorten the onset of automatic postural responses?; and if so (2) is this effect different for forward versus backward perturbations?; (3) does this effect depend on prior knowledge of the perturbation direction?; and (4) is this effect different for low- and high-magnitude perturbations? Balance was perturbed in 11 healthy participants by a movable platform that suddenly translated forward or backward. Each particip…