Translocation of a Single Stranded DNA Through a Conformationally Changing Nanopore

We investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation process is calculated, displaying a triple, double or mono peaked behavior, depending on the interconversion rates between the conformations, the applied electric field, and the initial conditions. The cumulative probability function of the FPT, in a field-free environment, is shown to have two regimes, characterized by fast and slow timescales. An analytical expression for the mean first passage time of the translocation process is derived, and provides, in addition to the interconversion rates, an extensive characterization of the translocation process. Relationships to experimental observations are discussed.Comment: 8 pages, 5 figures, Biophys. J., in pres

Disorder and Funneling Effects on Exciton Migration in Tree-Like Dendrimers

The center-bound excitonic diffusion on dendrimers subjected to several types of non-homogeneous funneling potentials, is considered. We first study the mean-first passage time (MFPT) for diffusion in a linear potential with different types of correlated and uncorrelated random perturbations. Increasing the funneling force, there is a transition from a phase in which the MFPT grows exponentially with the number of generations $g$, to one in which it does so linearly. Overall the disorder slows down the diffusion, but the effect is much more pronounced in the exponential compared to the linear phase. When the disorder gives rise to uncorrelated random forces there is, in addition, a transition as the temperature $T$ is lowered. This is a transition from a high-$T$ regime in which all paths contribute to the MFPT to a low-$T$ regime in which only a few of them do. We further explore the funneling within a realistic non-linear potential for extended dendrimers in which the dependence of the lowest excitonic energy level on the segment length was derived using the Time-Dependent Hatree-Fock approximation. Under this potential the MFPT grows initially linearly with $g$ but crosses-over, beyond a molecular-specific and $T$-dependent optimal size, to an exponential increase. Finally we consider geometrical disorder in the form of a small concentration of long connections as in the {\it small world} model. Beyond a critical concentration of connections the MFPT decreases significantly and it changes to a power-law or to a logarithmic scaling with $g$, depending on the strength of the funneling force.Comment: 13 pages, 9 figure

Excitonic Funneling in Extended Dendrimers with Non-Linear and Random Potentials

The mean first passage time (MFPT) for photoexcitations diffusion in a funneling potential of artificial tree-like light-harvesting antennae (phenylacetylene dendrimers with generation-dependent segment lengths) is computed. Effects of the non-linearity of the realistic funneling potential and slow random solvent fluctuations considerably slow down the center-bound diffusion beyond a temperature-dependent optimal size. Diffusion on a disordered Cayley tree with a linear potential is investigated analytically. At low temperatures we predict a phase in which the MFPT is dominated by a few paths.Comment: 4 pages, 4 figures, To be published in Phys. Rev. Let

Spermatic Vein Tumor Thrombus In Renal Cell Carcinoma

Renal cell carcinoma has the tendency to form venous thrombi. This may involve the renal veins or the inferior vena cava and may extend cephalad/antegrade into the right atrium. We report a patient with renal cell carcinoma who had an intracaval tumor thrombus that had extended into the right spermatic vein. We believe this to be the first description in English literature of a histologically proven renal cell carcinoma thrombus in the spermatic vein

Single Stranded DNA Translocation Through A Nanopore: A Master Equation Approach

We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows that it can be either double or mono-peaked, depending on the system parameters. We show that the most probable translocation time is proportional to the polymer length, and inversely proportional to the first or second power of the voltage, depending on the initial conditions. The model recovers experimental observations on hetro-polymers when using their properties inside the pore, such as stiffness and polymer-pore interaction.Comment: 7 pages submitted to PR

The cognitive and emotional effects of cognitive bias modification in interpretations in behaviorally inhibited youth

Cognitive bias modification (CBM) procedures follow from the view that interpretive biases play an important role in the development and maintenance of anxiety. As such, understanding the link between interpretive biases and anxiety in youth at risk for anxiety (e.g., behaviorally inhibited children) could elucidate the mechanisms involved in the development of pediatric anxiety. However, to date, the majority of CBM-I work only studies adult populations. The present article presents the results of a CBM study examining effects of positive interpretive bias modification on mood, stress vulnerability, and threat-related attention bias in a group of behaviorally inhibited children (n = 45). Despite successful modification of interpretive bias in the at-risk youth, minimal effects on stress vulnerability or threat-related attention bias were found. The current findings highlight the need for continued research on cognitive biases in anxiety

Controlling Viral Capsid Assembly with Templating

We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can dramatically enhance rates and robustness of assembly, as compared to the spontaneous assembly of subunits into empty capsids. For large core-subunit interactions, subunits adsorb onto core surfaces en masse in a disordered manner, and then undergo a cooperative rearrangement into an ordered capsid structure. These assembly pathways are unlike any identified for empty capsid formation. Our models can be directly applied to recent experiments in which viral capsid proteins assemble around the functionalized inorganic nanoparticles [Sun et al., Proc. Natl. Acad. Sci (2007) 104, 1354]. In addition, we discuss broader implications for understanding the dynamic encapsidation of single-stranded genomic molecules during viral replication and for developing multicomponent nanostructured materials.Comment: submitted to Phys. Rev.

On the joint residence time of N independent two-dimensional Brownian motions

We study the behavior of several joint residence times of N independent Brownian particles in a disc of radius $R$ in two dimensions. We consider: (i) the time T_N(t) spent by all N particles simultaneously in the disc within the time interval [0,t]; (ii) the time T_N^{(m)}(t) which at least m out of N particles spend together in the disc within the time interval [0,t]; and (iii) the time {\tilde T}_N^{(m)}(t) which exactly m out of N particles spend together in the disc within the time interval [0,t]. We obtain very simple exact expressions for the expectations of these three residence times in the limit t\to\infty.Comment: 8 page