Biomedical subjects

Olga K Dudko

Publications and source records attributed to Olga K Dudko.

9 recordsLinked to original sources

PubMed2006

Mean time-of-flight of photons in transillumination measurements of optically anisotropic tissue with an inclusion.

We study the effect of optical anisotropy on the mean time-of-flight of photons in a slab of turbid medium containing an inclusion whose optical properties differ from those of the bulk. For this analysis the difference in the mean time for a photon introduced into the slab to reach a specified target point with and without the inclusion is calculated. This difference is defined to be a measure of the contrast. The theoretical model is based on a continuous-time random walk on a lattice, which can be solved exactly and furnishes an exact expression for the contrast. Qualitative and quantitative characteristics of the contrast are analysed as functions of the geometric configuration of the system components (locations of the source, the inclusion and the detector), parameters that specify the optical anisotropy of the medium, and either the scattering properties of the inclusion or the lifetime of the small fluorophore in the case of the time-resolved fluorescence experimental configuration.

Algorithms↗

PubMed2006

Intrinsic rates and activation free energies from single-molecule pulling experiments.

We present a unified framework for extracting kinetic information from single-molecule pulling experiments at constant force or constant pulling speed. Our procedure provides estimates of not only (i) the intrinsic rate coefficient and (ii) the location of the transition state but also (iii) the free energy of activation. By analyzing simulated data, we show that the resulting rates of force-induced rupture are significantly more reliable than those obtained by the widely used approach based on Bell's formula. We consider the uniqueness of the extracted kinetic information and suggest guidelines to avoid over-interpretation of experiments.

Biophysics↗

PubMed2006

Global analysis of X-chromosome dosage compensation.

BACKGROUND: Drosophila melanogaster females have two X chromosomes and two autosome sets (XX;AA), while males have a single X chromosome and two autosome sets (X;AA). Drosophila male somatic cells compensate for a single copy of the X chromosome by deploying male-specific-lethal (MSL) complexes that increase transcription from the X chromosome. Male germ cells lack MSL complexes, indicating that either germline X-chromosome dosage compensation is MSL-independent, or that germ cells do not carry out dosage compensation. RESULTS: To investigate whether dosage compensation occurs in germ cells, we directly assayed X-chromosome transcripts using DNA microarrays and show equivalent expression in XX;AA and X;AA germline tissues. In X;AA germ cells, expression from the single X chromosome is about twice that of a single autosome. This mechanism ensures balanced X-chromosome expression between the sexes and, more importantly, it ensures balanced expression between the single X chromosome and the autosome set. Oddly, the inactivation of an X chromosome in mammalian females reduces the effective X-chromosome dose and means that females face the same X-chromosome transcript deficiency as males. Contrary to most current dosage-compensation models, we also show increased X-chromosome expression in X;AA and XX;AA somatic cells of Caenorhabditis elegans and mice. CONCLUSION: Drosophila germ cells compensate for X-chromosome dose. This occurs by equilibrating X-chromosome and autosome expression in X;AA cells. Increased expression of the X chromosome in X;AA individuals appears to be phylogenetically conserved.

Animals↗

PubMed2005

Time-dependent diffusion coefficients in periodic porous materials.

We derive an approximate solution for the Laplace transform of the time-dependent diffusion coefficient, D(t), of a molecule diffusing in a periodic porous material. In our model, the material is represented by a simple cubic lattice of identical cubic cavities filled with a solvent and connected by small circular apertures in otherwise reflecting cavity walls, the thickness of which can be neglected. The solution describes the decrease of D(t) from its initial value, D(0) = D, where D is the diffusion constant in the free solvent, to its asymptotic value, D(infinity) = D(eff), which is much smaller than D. A simple heuristic formula for the mean-squared displacement of the diffusing molecule is suggested. The theoretically predicted results are in good agreement with the data obtained from Brownian dynamics simulations.

Diffusion↗

PubMed2005

Time-dependent rate coefficients for diffusion-influenced reactions with centrosymmetric potentials.

Simple closed-form expressions are presented for the time-dependent rate coefficients of diffusion-influenced reactions in the presence of spherically symmetric potentials. For diffusion-controlled contact reactions, our expression reproduces the first two terms in both the short- and long-time expansions of the rate coefficient. At intermediate times, agreement with numerical results for the Debye-Hückel potential is found to be within a few percent for a wide range of parameters. For diffusion-influenced contact reactions (described by the radiation boundary condition), the agreement is even better. When the reactivity depends on the distance between the reactants (e.g., exponentially), our analytic result is less accurate, because it reproduces the two terms in the long-time expansion only to the linear order of the reciprocal of the diffusion coefficient. Our results should prove useful in the analysis of experimental data for diffusion-influenced reactions with centrosymmetric interaction potentials.

Diffusion↗

PubMed2005

Estimation of anisotropic optical parameters of tissue in a slab geometry.

The scattering and absorption coefficients of many homogeneous biological tissues such as muscle, skin, white matter in the brain, and dentin are often anisotropically oriented with respect to their bounding interface. In consequence the curves of equal intensity of re-emitted light on the surface of the slab will no longer be circular. We here consider the problem of determining the parameters allowing one to estimate the angles defining anisotropy, directional bias of diffusive spreading, and scattering and absorbing coefficients from data obtained from time-gated measurements of light intensity transmitted through a slab of the tissue. Our model can be solved exactly and leads to accurate approximations in which measured values of the surface intensity are shown to be elliptical. The parameters of the ellipses suffice to estimate the anisotropy of the tissue interior. A summary of the parameter estimates with the observables from which they are found is given in a table. Our analysis is based on a diffusion model.

Algorithms↗

PubMed2004

Diffusion in the presence of periodically spaced permeable membranes.

The diffusion of molecules in biological tissues and some other microheterogeneous systems is affected by the presence of permeable barriers. This leads to the slowdown of diffusion at long times as compared to barrier-free diffusion. At short times the effect of barriers is weak. In consequence, the diffusion coefficient D(t) decreases as a function of time. We derive an exact solution for the Laplace transform of D(t) for diffusion in a space separated into layers by equally spaced, parallel identical planes of arbitrary permeability. Additionally, we give an approximation to D(t) which is reasonably accurate over the whole range of the partition permeability from zero (the case of isolated layers) to infinity (the case of no barriers).

Journal Article↗

PubMed2004

Photon migration in turbid media with anisotropic optical properties.

We analyse properties of photon migration in reflectance measurements made on a semi-infinite medium bounded by a plane, in which optical parameters may vary in directions neither parallel to, nor perpendicular to the bounding plane. Our aim in doing this is to develop the formulae necessary to deduce parameters of directionality from both time-gated and continuous wave measurements. The mathematical development is based on a diffusion picture, in which the bounding plane is regarded as being totally absorbing so that all photons reaching the surface contribute to the reflectance.

Algorithms↗

PubMed2004

Rate constant for diffusion-influenced ligand binding to receptors of arbitrary shape on a cell surface.

The theory of ligand binding to receptors on a cell surface suggested by Berg and Purcell and generalized by Zwanzig and Szabo uses the assumption that receptors are circular absorbing disks on an otherwise reflecting sphere. One of the key ingredients of this theory is a solution for the rate constant for ligand binding to a single circular receptor on a reflecting plane. We give an exact solution for the rate constant for binding to a single elliptic receptor and an approximate solution for binding to a single receptor of more general shape. The latter was tested by Brownian dynamics simulations. We found that the approximate formula predicted the rate constant with better than 10% accuracy for all studied receptor shapes. Using our solutions one can find the rate constant for ligand binding to a cell covered by N noncircular receptors by means of the Zwanzig-Szabo formula.

Cell Membrane↗