Related papers: Brownian Dynamics Studies on DNA Gel Electrophores…
Dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE) is studied by a Brownian dynamics (BD) simulation method which we have developed. The method simulates electrophoresis of DNA in a 3 dimensional (3D) space by a…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
We consider scaled Brownian motion (sBm), a random process described by a diffusion equation with explicitly time-dependent diffusion coefficient $D(t) = D_0 t^{\alpha - 1}$ (Batchelor's equation) which, for $\alpha < 1$, is often used for…
We present a new computational methodology for the investigation of gel electrophoresis of polyelectrolytes. We have developed the method initially to incorporate sliding motion of tight parts of a polymer pulled by an electric field into…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
The scaled Brownian motion (SBM) is regarded as one of the paradigmatic random processes, featuring the anomalous diffusion property characterized by the diffusion exponent. It is a Gaussian, self-similar process with independent…
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…
We present a novel dynamic light scattering setup to probe, with time and space resolution, the microscopic dynamics of soft matter systems confined within millimeter-sized spherical drops. By using an ad-hoc optical layout, we tackle the…
Stochastic Gradient Descent (SGD) is commonly modeled as a Langevin process, assuming that minibatch noise acts as Brownian motion. However, this approximation relies on a continuous-time limit and a sqrt(eta) noise scaling that does not…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
In this thesis, we extend the recently introduced theory of stochastic modified equations (SMEs) for stochastic gradient optimization algorithms. In Ch. 3 we study time-inhomogeneous SDEs driven by Brownian motion. For certain SDEs we prove…
The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the…