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In the first paper of this series, we developed a new one-dimensional Monte Carlo approach for the study of flexible chains that are translocating through a small channel. We also presented a numerical scheme that can be used to obtain exact values for both the escape times and the escape probabilities given an initial pore-polymer configuration. We now present and discuss the fundamental scaling behaviors predicted by this Monte Carlo method. Our most important result is the fact that, in the presence of an external bias E, we observe a change in the scaling law for the translocation time τ as function of the polymer length N: In the general expression τ∼Nβ/E, the exponent changes from β=1 for moderately long chains to β=1+ν or β=2ν for very large values of N (for Rouse and Zimm dynamics, respectively). We also observe an increase in the effective diffusion coefficient due to the presence of entropic pulling on unbiased polymer chains. [ABSTRACT FROM AUTHOR]

By using a recently developed Monte Carlo algorithm and an exact numerical method, we calculate the translocation probability and the average translocation time for charged heterogeneous polymers driven through a nanopore by an external electric field. The heteropolymer chains are composed of two types of monomers (A and B) which differ only in terms of their electric charge. We present an exhaustive study of chains composed of eight monomers by calculating the average translocation time associated with the 256 possible arrangements for various ratios of the monomer charges (λA/λB) and electric field intensities E. We find that each sequence leads to a unique value of the translocation probability and time. We also show that the distribution of translocation times is strongly dependent on the two forces felt by the monomers (∼λAE and ∼λBE). Finally, we present results that highlight the effect of having repetitive patterns by studying the translocation times of various block copolymer structures for a very long chain composed of N=218 monomers (all with the same number of A and B monomers). [ABSTRACT FROM AUTHOR]

The process during which a polymer translocates through a nanopore depends on many physical parameters and fundamental mechanisms. We propose a new one-dimensional lattice Monte Carlo algorithm that integrates various effects such as the entropic forces acting on the subchains that are outside the channel, the external forces that are pulling the polymer through the pore, and the frictional effects that involve the chain and its environment. Our novel approach allows us to study the polymer as a single Brownian particle diffusing while subjected to a position-dependent force that includes both the external driving forces and the internal entropic bias. Frictional effects outside and inside the pore are also considered. This Monte Carlo method is much more efficient than other simulation methods, and it can be used to obtain scaling laws for various polymer translocation regimes. In this first part, we derive the model and describe a subtle numerical approach that gives exact results for both the escape probability and the mean translocation time (and higher moments of its distribution). The scaling laws obtained from this model will be presented and discussed in the second part of this series. [ABSTRACT FROM AUTHOR]

We derive a mean-field expression for the effective diffusion coefficient of a probe molecule in a two-phase medium consisting of a hydrogel with large gel-free solvent inclusions, in terms of the homogeneous diffusion coefficients in the gel and in the solvent. Upon comparing with exact numerical lattice calculations, we find that our expression provides a remarkably accurate prediction for the effective diffusion coefficient, over a wide range of gel concentration and relative volume fraction of the two phases. Moreover, we extend our model to handle spatial variations of viscosity, thereby allowing us to treat cases where the solvent viscosity itself is inhomogeneous. This work provides robust grounds for the modeling and design of multiphase systems for specific applications, e.g., hydrogels as novel food agents or efficient drug-delivery platforms. [ABSTRACT FROM AUTHOR]

Traditionally, the Ogston regime is studied solely in the limit of low field intensities. This explains why the theoretical discussion has focused until now on the relative roles of the fractional volume available to the analyte and the subtleties of the gel architecture. Over the past several years, we have developed a lattice model of gel electrophoresis that has allowed us to revisit the fundamental assumptions of the standard Ogston model. In particular, we demonstrated that the fractional free volume is not the relevant parameter for gel sieving. In this article, we continue the development of this model and we generalize our mathematical approach to treat nonvanishing electric field intensities. To do so, we must revisit the way biased random walks are normally modeled by stochastic processes. Straightforward generalizations based on standard Metropolis-like schemes fail at high field intensities. Moreover, our generalization requires the complete decoupling of the spatial directions parallel and perpendicular to the field direction. We show that our novel theoretical approach makes it possible to calculate exact mobilities in the presence of lattice obstacles. Several two-dimensional examples are then studied, including one that includes topological dead ends that act like traps. In the latter case, we recover results very similar to those reported by Serwer et al. [Biopolymers 29, 1863 (1990)] on the trapping electrophoresis of charged spheres in agarose gels. In the absence of such traps, the mobility is shown to be a very weak function of the electric field, thus validating the historical neglect of the field intensity in the development of obstruction models for the Ogston sieving regime of small analytes. Finally, we describe how the present model could be improved to treat more realistic cases and we discuss the problem of the field dependence of the diffusion coefficient during electrophoresis. [ABSTRACT FROM AUTHOR]

During their career, members of the Canadian Armed Forces (CAF) are frequently assigned to a new position and can even change profession. This high, but normal, level of mobility within the CAF can potentially hide indicators of mobility pattern differences among women and men. This article presents a method to study the mobility of the CAF members over the last decade. We propose a series of statistical tests to detect trends and identify a list of conditions for which the mobility indicators differ from one subpopulation to another. Our analysis uses Fisher's exact test to compare various populations for which sizes can vary from very small (less than 50) to large (tens of thousands). Since our approach allows us to do tests of statistical signifi cance on small samples, we were able to perform a detailed breakdown of the CAF population (down to the occupational level). [ABSTRACT FROM AUTHOR]

New technologies such as DNA combing have led to the availability of large quantities of data that describe the state of DNA while undergoing replication in S phase. In this chapter, we describe methods used to extract various parameters of replication--fork velocity, origin initiation rate, fork density, numbers of potential and utilized origins--from such data. We first present a version of the technique that applies to "ideal" data. We then show how to deal with, a number of real-world complications, such as the asynchrony of starting times of a population of cells, the finite length of fragments used in the analysis, and the finite amount of DNA in a chromosome.

Over the last two decades, the introduction of new methods such as pulsed-field gel electrophoresis and capillary array electrophoresis has made it possible to map and sequence entire genomes, including our own. The development of these experimental methods has been helped by the progress of theoretical and computational sciences, and the interactions between these three modi operandi of modern science are still pushing the limits of our technologies. We now see a clear trend towards proteomics and microfluidic (even nanofluidic!) devices. In this review, we take a look at the progress of the field over the last 3 years using the glasses of the theoretical scientist and focusing mostly on new ideas and concepts. About a dozen different subfields are discussed and reviewed. We conclude by giving a commented list of some of the best review articles published over the last 2-3 years.