Biomedical subjects

Rémi Monasson

Publications and source records attributed to Rémi Monasson.

5 recordsLinked to original sources

PubMed2004

Field-theoretic approach to metastability in the contact process.

A "quantum" field-theoretic formulation of the dynamics of the contact process on a regular graph of degree z is introduced. A perturbative calculation in powers of 1/z of the effective potential for the density of particles phi(t) and an instantonic field psi(t) emerging from the formalism is performed. Corrections to the mean-field distribution of densities of particles in the out-of-equilibrium stationary state are derived in powers of 1/z. Results for typical (e.g., average density) and rare fluctuation (e.g. lifetime of the metastable state) properties are in very good agreement with numerical simulations carried out on D-dimensional hypercubic (z=2D) and Cayley lattices.

Journal Article↗

PubMed2003

Relaxation and metastability in a local search procedure for the random satisfiability problem.

An analysis of the average properties of a local search procedure (RandomWalkSAT) for the satisfaction of random Boolean constraints is presented. Depending on the ratio alpha of constraints per variable, reaching a solution takes a time T(res) growing linearly [T(res) approximately tau(res)(alpha)N, alpha alpha(d)) with the size N of the instance. The relaxation time tau(res)(alpha) in the linear phase is calculated through a systematic expansion scheme based on a quantum formulation of the evolution operator. For alpha>alpha(d), the system is trapped in some metastable state, and resolution occurs from escape from this state through crossing of a large barrier. An annealed calculation of the height zeta(alpha) of this barrier is proposed. The polynomial to exponential cross-over alpha(d) approximately =2.7 is not related to the onset of clustering among solutions occurring at alpha approximately =3.86.

Journal Article↗

PubMed2002

Unzipping dynamics of long DNAs.

The two strands of the DNA double helix can be "unzipped" by the application of approximately 15 pN force. We analyze the dynamics of unzipping and rezipping for the case where the molecule ends are separated and reapproached at constant velocity. For unzipping of 50-kilobase DNAs at less than about 1000 bases per second, thermal-equilibrium-based theory applies. However, for higher unzipping velocities, rotational viscous drag creates a buildup of elastic torque to levels above k(B)T in the double-stranded DNA region, causing the unzipping force to be well above or well below the equilibrium unzipping force during, respectively, unzipping and rezipping, in accord with recent experimental results of Thomen et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect of sequence on unzipping and rezipping, and the transient delay in buildup of the unzipping force due to the approach to the steady state.

Biophysical Phenomena↗

PubMed2002

Exponentially hard problems are sometimes polynomial, a large deviation analysis of search algorithms for the random satisfiability problem, and its application to stop-and-restart resolutions.

A large deviation analysis of the solving complexity of random 3-satisfiability instances slightly below threshold is presented. While finding a solution for such instances demands an exponential effort with high probability, we show that an exponentially small fraction of resolutions require a computation scaling linearly in the size of the instance only. This exponentially small probability of easy resolutions is analytically calculated, and the corresponding exponent is shown to be smaller (in absolute value) than the growth exponent of the typical resolution time. Our study therefore gives some theoretical basis to heuristic stop-and-restart solving procedures, and suggests a natural cutoff (the size of the instance) for the restart.

Journal Article↗

PubMed2002

Force and kinetic barriers to initiation of DNA unzipping.

A semimicroscopic model of the binding of the two nucleotide strands in a double-stranded DNA is used to describe the effects of applied tension on strand unpairing. We show that the model describes strand separation by elevated temperature, applied torque, and applied force. In particular, we show how the interactions responsible for stabilizing the double helix against thermal denaturation determine the approximately 12 pN force threshold for DNA strand separation. The larger rigidity of the strands when formed into double-stranded DNA, relative to that of isolated strands, gives rise to a potential barrier to unzipping. We show that this barrier results in a approximately 250 pN force barrier opposing the beginning of strand separation. The thermal-fluctuation-assisted "tunnelling" through the barrier is then analyzed using instanton calculations. The resulting kinetics of unzipping initiation is shown to be consistent with solution-phase strand dissociation experiments, and can explain results of two recent unzipping experiments done using atomic-force microscopy.

Base Pairing↗