David Lacoste

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Oleg Yu Vorobyev

Siberian Federal University

Kathryn LaFevers Evans, Three Eagles

Pacifica Graduate Institute

Aephraim Steinberg

University of Toronto

Jack Sarfatti

Cornell University

Richard Gauthier

Santa Rosa Junior College

María Cecilia Tomasini

Universidad de Buenos Aires

Anatoly Kolomeisky

Rice University

Edward Bormashenko

Ariel University

C. Malagù

Università degli Studi di Ferrara

Cristina Mogosan

University of Medicine and Pharmacy "Iuliu Hatieganu" Cluj-Napoca

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Papers by David Lacoste

Thermodynamic inference based on coarse-grained data or noisy measurements

Physical Review E, 2016

Fluctuation theorems have become an important tool in single-molecule biophysics to measure free-... more Fluctuation theorems have become an important tool in single-molecule biophysics to measure free-energy differences from nonequilibrium experiments. When significant coarse-graining or noise affect the measurements, the determination of the free energies becomes challenging. In order to address this thermodynamic inference problem, we propose improved estimators of free-energy differences based on fluctuation theorems, which we test on a number of examples. The effect of the noise can be described by an effective temperature, which only depends on the signal-to-noise ratio, when the work is Gaussian distributed and uncorrelated with the error made on the work. The notion of effective temperature appears less useful for non-Gaussian work distributions or when the error is correlated with the work, but nevertheless, as we show, improved estimators can still be constructed for such cases. As an example of nontrivial correlations between the error and the work, we also consider measurements with delay, as described by linear Langevin equations.

Glucans monomer-exchange dynamics as an open chemical network

The Journal of chemical physics, Jan 28, 2015

We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysa... more We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.

A Planar Lipid Bilayer in an Electric Field

For many biotechnological applications it would be useful to better understand the effects produc... more For many biotechnological applications it would be useful to better understand the effects produced by electric fields on lipid membranes. This review discusses several aspects of the electrostatic properties of a planar lipid membrane with its surrounding electrolyte in a normal DC or AC electric field.In the planar geometry, the analysis of electrokinetic equations can be carried out quite far, allowing to characterize analytically the steady state and the dynamics of the charge accumulation in the Debye layers, which results from the application of the electric field. For a conductive membrane in an applied DC electric field, we characterize the corrections to the elastic moduli, the appearance of a membrane undulation instability and the associated flows which are built up near the membrane. For a membrane in an applied AC electric field, we analytically derive the impedance from the underlying electrokinetic equations. We discuss different relevant effects due to the membrane conductivity or due to the bulk diffusion coefficients of the ions. Of particular interest is the case where the membrane has selective conductivity for only one type of ion. These results, and future extensions thereof, should be useful for the interpretation of impedance spectroscopy data used to characterize, for example, ion channels embedded in planar bilayers.

Stochastic thermodynamics of a tagged particle within a harmonic chain

Physical review. E, Statistical, nonlinear, and soft matter physics, 2015

We study the stochastic thermodynamics of an overdamped harmonic chain, which can be viewed equiv... more We study the stochastic thermodynamics of an overdamped harmonic chain, which can be viewed equivalently as a one-dimensional Rouse chain or as an approximate model of single file diffusion. We discuss mainly two levels of description of this system: the Markovian level for which the trajectories of all the particles of the chain are known and the non-Markovian level in which only the motion of a tagged particle is available. For each case, we analyze the energy dissipation and its dependence on initial conditions. Surprisingly, we find that the average coarse-grained entropy production rate can become transiently negative when an oscillating force is applied to the tagged particle. This occurs due to memory effects as shown in a framework based on path integrals or on a generalized Langevin equation.

David Lacoste

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