Fractional diffusion modeling of ion channel gating

An anomalous diffusion model for ion channel gating is put forward. This scheme is able to describe non-exponential, power-law like distributions of residence time intervals in several types of ion channels. Our method presents a generalization of the discrete diffusion model by Millhauser, Salpeter and Oswald [Proc. Natl. Acad. Sci. USA 85, 1503 (1988)] to the case of a continuous, anomalous slow conformational diffusion. The corresponding generalization is derived from a continuous time random walk composed of nearest neighbor jumps which in the scaling limit results in a fractional diffusion equation. The studied model contains three parameters only: the mean residence time, a characteristic time of conformational diffusion, and the index of subdiffusion. A tractable analytical expression for the characteristic function of the residence time distribution is obtained. In the limiting case of normal diffusion, our prior findings [Proc. Natl. Acad. Sci. USA 99, 3552 (2002)] are reproduced. Depending on the chosen parameters, the fractional diffusion model exhibits a very rich behavior of the residence time distribution with different characteristic time-regimes. Moreover, the corresponding autocorrelation function of conductance fluctuations displays nontrivial features. Our theoretical model is in good agreement with experimental data for large conductance potassium ion channels

Levy stable distributions via associated integral transform

We present a method of generation of exact and explicit forms of one-sided, heavy-tailed Levy stable probability distributions g_{\alpha}(x), 0 \leq x < \infty, 0 < \alpha < 1. We demonstrate that the knowledge of one such a distribution g_{\alpha}(x) suffices to obtain exactly g_{\alpha^{p}}(x), p=2, 3,... Similarly, from known g_{\alpha}(x) and g_{\beta}(x), 0 < \alpha, \beta < 1, we obtain g_{\alpha \beta}(x). The method is based on the construction of the integral operator, called Levy transform, which implements the above operations. For \alpha rational, \alpha = l/k with l < k, we reproduce in this manner many of the recently obtained exact results for g_{l/k}(x). This approach can be also recast as an application of the Efros theorem for generalized Laplace convolutions. It relies solely on efficient definite integration.Comment: 12 pages, typos removed, references adde

Static Solitons of the Sine-Gordon Equation and Equilibrium Vortex Structure in Josephson Junctions

The problem of vortex structure in a single Josephson junction in an external magnetic field, in the absence of transport currents, is reconsidered from a new mathematical point of view. In particular, we derive a complete set of exact analytical solutions representing all the stationary points (minima and saddle-points) of the relevant Gibbs free-energy functional. The type of these solutions is determined by explicit evaluation of the second variation of the Gibbs free-energy functional. The stable (physical) solutions minimizing the Gibbs free-energy functional form an infinite set and are labelled by a topological number Nv=0,1,2,... Mathematically, they can be interpreted as nontrivial ''vacuum'' (Nv=0) and static topological solitons (Nv=1,2,...) of the sine-Gordon equation for the phase difference in a finite spatial interval: solutions of this kind were not considered in previous literature. Physically, they represent the Meissner state (Nv=0) and Josephson vortices (Nv=1,2,...). Major properties of the new physical solutions are thoroughly discussed. An exact, closed-form analytical expression for the Gibbs free energy is derived and analyzed numerically. Unstable (saddle-point) solutions are also classified and discussed.Comment: 17 pages, 4 Postscript figure

First Passage Time Distribution and Number of Returns for Ultrametric Random Walk

In this paper, we consider a homogeneous Markov process \xi(t;\omega) on an ultrametric space Q_p, with distribution density f(x,t), x in Q_p, t in R_+, satisfying the ultrametric diffusion equation df(x,t)/dt =-Df(x,t). We construct and examine a random variable \tau (\omega) that has the meaning the first passage times. Also, we obtain a formula for the mean number of returns on the interval (0,t] and give its asymptotic estimates for large t.Comment: 20 page

Prediction of infrared light emission from pi-conjugated polymers: a diagrammatic exciton basis valence bond theory

There is currently a great need for solid state lasers that emit in the infrared, as this is the operating wavelength regime for applications in telecommunications. Existing $\pi$--conjugated polymers all emit in the visible or ultraviolet, and whether or not $\pi$--conjugated polymers that emit in the infrared can be designed is an interesting challenge. On the one hand, the excited state ordering in trans-polyacetylene, the $\pi$--conjugated polymer with relatively small optical gap, is not conducive to light emission because of electron-electron interaction effects. On the other hand, excited state ordering opposite to that in trans-polyacetylene is usually obtained by chemical modification that increases the effective bond-alternation, which in turn increases the optical gap. We develop a theory of electron correlation effects in a model $\pi$-conjugated polymer that is obtained by replacing the hydrogen atoms of trans-polyacetylene with transverse conjugated groups, and show that the effective on-site correlation in this system is smaller than the bare correlation in the unsubstituted system. An optical gap in the infrared as well as excited state ordering conducive to light emission is thereby predicted upon similar structural modifications.Comment: 15 pages, 15 figures, 1 tabl

МикроРНК и малые интерферирующие РНК как инструменты направленной регуляции клеточных процессов для терапии онкологических заболеваний

MicroRNAs and small interfering RNAs (siRNAs) belong to an extensive class of small non-coding RNAs and play an important role in gene expression regulation in cells. It is shown that changes in the amount or activity of these molecules may lead to the development of various diseases, including cancer. This made it possible to consider them as promising diagnostic and prognostic markers, as well as tools for the directed regulation of protein synthesis in the cell and targets for therapy. This review summarizes the basic knowledge about the biogenesis, distribution and the mechanisms of action of microRNA and siRNA, as well as currently used ways of target genes expression management with their help. Possible methods of these molecules delivery into the cell in vitro and in vivo are considered.МикроРНК и малые интерферирующие РНК (миРНК) относятся к обширному классу малых некодирующих РНК и играют важную роль в регуляции экспрессии генов в клетках. Показано, что изменения в количестве или эффективности воздействия этих молекул могут сопровождать развитие различных заболеваний, включая онкологические. Это позволило рассматривать их как перспективные диагностические и прогностические маркеры, а также инструменты для направленной регуляции синтеза белков в клетке и мишени для терапии. В данном обзоре суммированы основные знания о биогенезе, распространении и механизмах воздействия микроРНК и миРНК, а также способы направленного влияния на экспрессию генов с их помощью, используемые в настоящее время. Рассмотрены возможные варианты доставки молекул в клетку in vitro и in vivo

A theoretical investigation of the low lying electronic structure of poly(p-phenylene vinylene)

The two-state molecular orbital model of the one-dimensional phenyl-based semiconductors is applied to poly(p-phenylene vinylene). The energies of the low-lying excited states are calculated using the density matrix renormalization group method. Calculations of both the exciton size and the charge gap show that there are both Bu and Ag excitonic levels below the band threshold. The energy of the 1Bu exciton extrapolates to 2.60 eV in the limit of infinite polymers, while the energy of the 2Ag exciton extrapolates to 2.94 eV. The calculated binding energy of the 1Bu exciton is 0.9 eV for a 13 phenylene unit chain and 0.6 eV for an infinite polymer. This is expected to decrease due to solvation effects. The lowest triplet state is calculated to be at ca. 1.6 eV, with the triplet-triplet gap being ca. 1.6 eV. A comparison between theory, and two-photon absorption and electroabsorption is made, leading to a consistent picture of the essential states responsible for most of the third-order nonlinear optical properties. An interpretation of the experimental nonlinear optical spectroscopies suggests an energy difference of ca. 0.4 eV between the vertical energy and ca. 0.8 eV between the relaxed energy, of the 1Bu exciton and the band gap, respectively.Comment: LaTeX, 19 pages, 7 eps figures included using epsf. To appear in Physical Review B, 199

Bulk and surface properties in the critical phase of the two-dimensional XY model

Monte Carlo simulations of the two-dimensional XY model are performed in a square geometry with various boundary conditions (BC). Using conformal mappings we deduce the exponent $\eta_\sigma(T)$ of the order parameter correlation function and its surface analogue $\eta_\|(T)$ as a function of the temperature in the critical (low-temperature) phase of the model.Comment: 26 pages, iop macro, one reference added, typos correcte

Magnetic critical behavior of two-dimensional random-bond Potts ferromagnets in confined geometries

We present a numerical study of 2D random-bond Potts ferromagnets. The model is studied both below and above the critical value $Q_c=4$ which discriminates between second and first-order transitions in the pure system. Two geometries are considered, namely cylinders and square-shaped systems, and the critical behavior is investigated through conformal invariance techniques which were recently shown to be valid, even in the randomness-induced second-order phase transition regime Q>4. In the cylinder geometry, connectivity transfer matrix calculations provide a simple test to find the range of disorder amplitudes which is characteristic of the disordered fixed point. The scaling dimensions then follow from the exponential decay of correlations along the strip. Monte Carlo simulations of spin systems on the other hand are generally performed on systems of rectangular shape on the square lattice, but the data are then perturbed by strong surface effects. The conformal mapping of a semi-infinite system inside a square enables us to take into account boundary effects explicitly and leads to an accurate determination of the scaling dimensions. The techniques are applied to different values of Q in the range 3-64.Comment: LaTeX2e file with Revtex, revised versio