D. J. Bicout

Long range correlations in DNA : scaling properties and charge transfer efficiency

We address the relation between long-range correlations and charge transfer efficiency in aperiodic artificial or genomic DNA sequences. Coherent charge transfer through the highest occupied molecular orbital states of the guanine nucleotide is studied using the transmission approach, and the focus is on how the sequence-dependent backscattering profile can be inferred from correlations between base pairs.

Bubble Relaxation Dynamics in Double-Stranded DNA

This paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that includes end effects and derive analytic expressions of the correlation function, survival probability, and lifetimes for the bubble relaxation dynamics. It is shown that the continuous and semi-infinite limit of the model becomes a good approximation to an exact result when aN <<1, where N is bubble size and a, the ratio of opening to closing rates of base pairs, is the control parameter of DNA melting.

Long-range electron transfer in periodic nucleotide base stacks

Abstract A simple model for charge transfer in one-dimensional donor ( D ) – bridges ( B n ) – acceptor ( A ) systems is proposed. The model describes the charge transfer as the conjunction of two non-dichotomic (and probabilistically competing) mechanisms: direct D – A tunneling and incoherent hopping. An analytical expression of the charge transfer rate k ET is derived for this model, and seemingly contradictory observations of a strong followed by a weak influence of D – A distance on k ET are readily reproduced.

Rupture of a biomembrane under dynamic surface tension.

How long will a fluid membrane vesicle stressed with a steady ramp of micropipette last before rupture? Or conversely, how high should the surface tension be to rupture such a membrane? To answer these challenging questions we developed a theoretical framework that allows for the description and reproduction of dynamic tension spectroscopy (DTS) observations. The kinetics of the membrane rupture under ramps of surface tension is described as a succession of an initial pore formation followed by the Brownian process of the pore radius crossing the time-dependent energy barrier. We present the formalism and a derive (formal) analytical expression of the survival probability describing the fate of the membrane under DTS conditions. Using numerical simulations for the membrane prepared in an initial state with a given distribution of times for pore nucleation, we study the membrane lifetime (or inverse of rupture rate) and distribution of membrane surface tension at rupture as a function of membrane characteristics like pore nucleation rate, the energy barrier to failure, and tension loading rate. It is found that simulations reproduce the main features of DTS experiments, particularly the pore nucleation and pore-size diffusion-controlled limits of membrane rupture dynamics. This approach can be adapted and applied to processes of permeation and pore opening in membranes (electroporation, membrane disruption by antimicrobial peptides, vesicle fusion).

The Dynamical Transition of Lipid Multilamellar Bilayers as a Matter of Cooperativity

The present study is the application of a two-state model formerly developed by Bicout and Zaccai [ Bicout , D. J. and Zaccai , G. Biophys. J. 2001 , 80 ( 3 ), 1115 - 1123 ] to describe the dynamical transition exhibited in the atomic mean square displacements of biological samples in terms of dynamic and thermodynamic parameters. Data were obtained by elastic incoherent neutron scattering on 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes in various hydration states and on one partially per-deuterated lipid membrane. Fitting the data with the model allowed investigating which parts of lipid molecules were mainly involved in the dynamical transition, heads, tails, or both. Clear differences were found between the fully protonated and partially deuterated membranes. These findings shed light on the question of what is the degree of dynamical cooperativity of the atoms during the transition. Whereas the level of hydration does not significantly affect it, as the dry, the intermediate dry, and fully hydrated membranes all undergo a rather broad transition, the transition of the lipid tails is much sharper and sets in at much lower temperature than that of the heads. Therefore, the dynamical cooperativity appears high among the particles in the tails. Moreover, the transition of the lipid tails has to be completed first before the one of the head groups starts.

Stabilization of membrane pores by packing

We present a model for pore stabilization in membranes without surface tension. Whereas an isolated pore is always unstable (since it either shrinks, tending to reseal, or grows without bound until membrane disintegration), it is shown that excluded volume interactions in a system of many pores can stabilize individual pores of a given size in a certain range of model parameters. For such a multipore membrane system, the distribution of pore size and associated pore lifetime are calculated within the mean-field approximation. We predict that, above the temperature T(m), when the effective line tension becomes negative, the membrane exhibits a dynamic sievelike porous structure.

Vibrational enhancement of the effective donor-acceptor coupling

This letter deals with a simple three-site model for charge transfer phenomena in a one-dimensional donor (D)-bridge (B)-acceptor (A) system coupled with vibrational dynamics of the B site. It is found that, in a certain range of parameters, the vibrational coupling leads to an enhancement of the effective donor-acceptor electronic coupling as a result of the formation of the polaron on the B site. This enhancement of the charge transfer efficiency is maximum at the resonance, where the effective energy of the fluctuating B site coincides with the donor (acceptor) energy.

Size independence of statistics for boundary collisions of random walks and its implications for spin-polarized gases.

A bounded random walk exhibits strong correlations between collisions with a boundary. For a one-dimensional walk, we obtain the full statistical distribution of the number of such collisions in a time t. In the large t limit, the fluctuations in the number of collisions are found to be size independent (independent of the distance between boundaries). This occurs for any interboundary distance, from less to greater than the mean free path, and means that this boundary effect does not decay with increasing system size. As an application, we consider spin-polarized gases, such as 3-helium, in the three-dimensional diffusive regime. The above results mean that the depolarizing effect of rare magnetic impurities in the container walls is orders of magnitude larger than a Smoluchowski assumption (to neglect correlations) would imply. This could explain why depolarization is so sensitive to the containers treatment with magnetic fields prior to its use.