Biomedical subjects

A V Barzykin

Publications and source records attributed to A V Barzykin.

8 recordsLinked to original sources

PubMed2006

Stochastic model of photodynamics in multichromophoric conjugated polymers.

A stochastic model of triplet exciton dynamics in multichromophoric conjugated polymers is presented and analyzed in detail, with a focus on the single molecule spectroscopy observables. The model deals with the evolution of a discrete statistical distribution of triplets in isolated polymer molecules. This approach should provide more accurate quantitative information on the dynamic processes involved, as compared to the previously used two-state model which assumes that a conjugated polymer cannot contain more than one triplet. In particular, it allows for determination of the triplet-triplet annihilation rate.

Journal Article↗

PubMed2004

Effect of anisotropic diffusion and external electric field on the rate of diffusion-controlled reactions.

In this paper we investigate theoretically the effect of an external electric field on the rate constant of steady-state bulk diffusion-controlled reactions. We generalize previously derived results for isotropic diffusion in the absence of interparticle interaction [J. Chem. Phys. 87, 4622 (1987)] to the case where translational diffusion is anisotropic. A frequently occurring situation of transverse isotropy where D(x)=D(y) not equal to D(z) is considered in detail. We derive the first-order expansion for the reaction rate constant in terms of the electric field strength E, k(E)=k(0) (1+1/2epsilongamma), where gamma=k(0)/4piRD( perpendicular ), epsilon=qER/k(B)T, q is the charge, R is the contact distance, and D( perpendicular ) is the transverse diffusion coefficient. Numerical calculations show that this first-order expansion works well in the whole range of applicability of the Nernst-Einstein relation, i.e., for epsilon<1.

Journal Article↗

PubMed2001

Kinetics of diffusion-assisted reactions in microheterogeneous systems.

This review is focused on the basic theory of diffusion-assisted reactions in microheterogeneous systems, from porous solids to self-organized colloids and biomolecules. Rich kinetic behaviors observed experimentally are explained in a unified fashion using simple concepts of competing distance and time scales of the reaction and the embedding structure. We mainly consider pseudo-first-order reactions, such as luminescence quenching, described by the Smoluchowski type of equation for the reactant pair distribution function with a sink term defined by the reaction mechanism. Microheterogeneity can affect the microscopic rate constant. It also enters the evolution equation through various spatial constraints leading to complicated boundary conditions and, possibly, to the reduction of dimensionality of the diffusion space. The reaction coordinate and diffusive motion along this coordinate are understood in a general way, depending on the problem at hand. Thus, the evolution operator can describe translational and rotational diffusion of molecules in a usual sense, it can be a discrete random walk operator when dealing with hopping of adsorbates in solids, or it can correspond to conformational fluctuations in proteins. Mathematical formulation is universal but physical consequences can be different. Understanding the principal features of reaction kinetics in microheterogeneous systems enables one to extract important structural and dynamical information about the host environments by analyzing suitably designed experiments, it helps building effective strategies for computer simulations, and ultimately opens possibilities for designing systems with controllable reactivity properties.

Animals↗

PubMed2001

Effect of local molecular shape and anisotropic reactivity on the rate of diffusion-controlled reactions.

The role of distance-dependent anisotropic reactivity and molecular geometry in the vicinity of localized reaction centers in influencing the rate of bimolecular diffusion-controlled reactions is analyzed in detail, both analytically and numerically. The effect of local molecular shape is considered within the model of reflective hemispheres of small radius l(h) on the surfaces of otherwise spherical molecules of radius R (l(h) << R). The distance-dependent reactivity is modeled by reactive hemispheres of radius l(r) on top of the reflective hemispheres (l(r) << R). It is shown that the presence of the reflective hemispheres leads to a markedly large increase of the reaction rate. The maximum effect is ~R/l(h) >> 1 times, as described by the ratio of local to average molecular curvature. It is observed for l(h) approximately R(l(r)/R)(1/2) >> l(r). The effect of thickness of the reaction regions is described within the model of reactive cylinders of height l(r) and angular radius theta << 1. It is shown that the characteristic parameter in the expansion of the reaction rate as a function of l(r)/R is l(r)/(Rtheta(2)), and therefore, even for small relative thickness d = l(r)/theta, its effect on the rate is very strong, i.e., the conventional model of reactive patches, which assumes zero thickness of the reaction region, may considerably underestimate the reaction rate.

Anisotropy↗

PubMed2001

Effect of anisotropic reactivity on the rate of diffusion-controlled reactions: comparative analysis of the models of patches and hemispheres.

A comparative analysis of two models of anisotropic reactivity in bimolecular diffusion-controlled reaction kinetics is presented. One is the conventional model of reactive patches (MRP), where the surface of a molecule is assumed to be reactive over a certain region (circular patch) with the rest of the surface being inert. Another one is the model of reactive hemispheres (MRH), assuming that a molecule is reactive within a certain distance from a point on its surface. The accuracy of the known and newly derived simple analytical expressions for the reaction rate is tested by comparison with the simulation results obtained by the original Brownian dynamics method. These formulas prove to be quite accurate in the practically important limit of strong anisotropy corresponding to small size of the reactive patches or hemispheres. Numerical calculations confirm earlier predictions that the MRP rates are much smaller than the MRH rates for the same radii of the reactive regions, especially in the case where both reacting molecules are anisotropic.

Algorithms↗

PubMed1999

Theory of spin echo in restricted geometries under a step-wise gradient pulse sequence.

A closed matrix form solution of the Bloch-Torrey equation is presented for the magnetization density of spins diffusing in a bounded region under a steady gradient field and for the Stejskal-Tanner gradient pulse sequence, assuming straightforward generalization to any step-wise gradient profile. The solution is expressed in terms of the eigenmodes of the diffusion propagator in a given geometry with appropriate boundary conditions (perfectly reflecting or relaxing walls). Applications to rectangular, cylindrical, and spherical geometries are discussed. The relationship with the multiple propagator approach is established and an alternative step-wise gradient discretization procedure is suggested to handle arbitrary gradient waveforms.

Magnetic Resonance Spectroscopy↗

PubMed1998

A model for diffusive transport through a spherical interface probed by pulsed-field gradient NMR.

In biological systems, because of higher intracellular viscosity and/or the restriction of the diffusion space inside cells, the (apparent) diffusion coefficient of an intracellular species (e.g., water) is generally smaller than when it is in the extracellular medium. This difference affects the spin-echo signal attenuation in the pulsed field gradient NMR experiment and thus affords a means of separating the intracellular from the extracellular species, thereby providing a basis for studying transmembrane transport. Such experiments have commonly been analyzed using the macroscopic model of Kärger (see Adv. Magn. Reson. 21:1-89 (1988)). In our previous study, we considered a microscopic model of diffusive transport through a spherical interface using the short gradient pulse approximation (J. Magn. Reson. A114:39-46 (1995)). The spins in the external medium were modeled with the "partially absorbing wall" condition or as having a small but finite lifetime. In the present paper, we extend our treatment to the case in which there is no limitation upon the lifetime in either medium. We also consider a simple modification of Kärger's model that more properly accounts for the restricted intracellular diffusion. Importantly, it was found that the exact solution within the short gradient pulse approximation developed here and the modified Kärger model are in close agreement in the (experimentally relevant) long-time limit. The results of this study show that when there is no limitation upon the lifetime of the transported species in either phase, the spin-echo attenuation curve is very sensitive to transport.

Diffusion↗

PubMed1997

Interpretation of passive permeability measurements on lipid-bilayer vesicles. Effect of fluctuations.

A stochastic model for migration dynamics of solute molecules from the bulk aqueous phase to the intravesicular water pool is developed with a goal to interpret recent passive permeability measurements of bilayer membranes. Previously neglected fluctuations of the number of solubilized species in the inner water pool of a vesicle are naturally incorporated into the model. For a homogeneous one-phase bilayer, the model predicts exponential long-time asymptotics of the migration dynamics with a rate constant given by a sum of the frequencies of exit and entry of a solute molecule from/into the intravesicular water pool into/from the bulk aqueous phase. The long-time constant is directly related to the membrane permeability.

Cell Membrane Permeability↗