arXiv subjects

Michel G. Gauthier

Publications and source records attributed to Michel G. Gauthier.

3 recordsLinked to original sources

arXiv2014

Numerical modeling of inhomogeneous DNA replication kinetics

We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets obtained by molecular combing, a widely used experimental technique for probing replication. We can also infer information about the replication program by fitting our model to experimental data sets and also test the efficacy of planned experiments by fitting our model to simulated data sets. We consider asynchronous data sets and illustrate how a lack of synchrony affects replication profiles. In addition to combing data, our technique is well-adapted to microarray-based studies of replication.

q-bio.QM↗

arXiv2008

Non-driven polymer translocation through a nanopore: computational evidence that the escape and relaxation processes are coupled

Most of the theoretical models describing the translocation of a polymer chain through a nanopore use the hypothesis that the polymer is always relaxed during the complete process. In other words, models generally assume that the characteristic relaxation time of the chain is small enough compared to the translocation time that non-equilibrium molecular conformations can be ignored. In this paper, we use Molecular Dynamics simulations to directly test this hypothesis by looking at the escape time of unbiased polymer chains starting with different initial conditions. We find that the translocation process is not quite in equilibrium for the systems studied, even though the translocation time tau is about 10 times larger than the relaxation time tau_r. Our most striking result is the observation that the last half of the chain escapes in less than ~12% of the total escape time, which implies that there is a large acceleration of the chain at the end of its escape from the channel.

q-bio.BM↗

arXiv2004

A new set of Monte Carlo moves for lattice random-walk models of biased diffusion

We recently demonstrated that standard fixed-time lattice random-walk models cannot be modified to properly represent biased diffusion processes in more than two dimensions. The origin of this fundamental limitation appears to be the fact that traditional Monte Carlo moves do not allow for simultaneous jumps along each spatial direction. We thus propose a new algorithm to transform biased diffusion problems into lattice random walks such that we recover the proper dynamics for any number of spatial dimensions and for arbitrary values of the external field. Using a hypercubic lattice, we redefine the basic Monte Carlo moves, including the transition probabilities and the corresponding time durations, in order to allow for simultaneous jumps along all Cartesian axes. We show that our new algorithm can be used both with computer simulations and with exact numerical methods to obtain the mean velocity and the diffusion coefficient of point-like particles in any dimensions and in the presence of obstacles.

physics.data-an↗