arXiv subjects

David Lacoste

Publications and source records attributed to David Lacoste.

At least 37 records · Page 2Linked to original sources

arXiv2018

Mechanical factors affecting the mobility of membrane proteins

The mobility of membrane proteins controls many biological functions. The application of the model of Saffman and Delbrück to the diffusion of membrane proteins does not account for all the experimental measurements. These discrepancies have triggered a lot of studies on the role of the mechanical factors in the mobility. After a short review of the Saffman and Delbrück model and of some key experiments, we explore the various ways to incorporate the effects of the different mechanical factors. Our approach focuses on the coupling of the protein to the membrane, which is the central element in the modelling. We present a general, polaron-like model, its recent application to the mobility of a curvature sensitive protein, and its various extensions to other couplings that may be relevant in future experiments.

physics.bio-ph↗

arXiv2018

Reaction kinetics in open reactors and serial transfers between closed reactors

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.

cond-mat.stat-mech↗

arXiv2018

Degree of coupling and efficiency of energy converters far-from-equilibrium

In this paper, we introduce a real symmetric and positive semi-definite matrix, which we call the non-equilibrium conductance matrix, and which generalizes the Onsager response matrix for a system in a non-equilibrium stationary state. We then express the thermodynamic efficiency in terms of the coefficients of this matrix using a parametrization similar to the one used near equilibrium. This framework, then valid arbitrarily far from equilibrium allows to set bounds on the thermodynamic efficiency by a universal function depending only on the degree of coupling between input and output currents. It also leads to new general power-efficiency trade-offs valid for macroscopic machines that are compared to trade-offs previously obtained from uncertainty relations. We illustrate our results on an unicycle heat to heat converter and on a discrete model of molecular motor.

cond-mat.stat-mech↗

arXiv2018

Selection dynamics in transient compartmentalization

Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Motivated by this experiment, we show that a broad class of selection dynamics is able to achieve this goal. We identify two key parameters, the relative amplification of non-active replicators (parasites) and the size of compartments. Since the basic ingredients of our model are the competition between a host and its parasite, and the diversity generated by small size compartments, our results are relevant to various phage-bacteria or virus-host ecology problems.

q-bio.PE↗

arXiv2017

Information-theoretic analysis of the directional influence between cellular processes

Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback. We re-analyze the experimental data from Kiviet et al. (2014) where fluctuations in gene expression of metabolic enzymes and growth rate have been measured in single cells of E. coli. We confirm the formerly detected modes between growth and gene expression, while prescribing more stringent conditions on the structure of noise sources. We furthermore point out practical requirements in terms of length of time series and sampling time which must be satisfied in order to infer optimally transfer entropy from times series of fluctuations.

q-bio.QM↗

arXiv2017

Length and sequence relaxation of copolymers under recombination reactions

We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law describes the infinite size limit, while the second one, based on the chemical master equation, describes systems of finite size. We compare the predictions of both approaches for the relaxation of thermodynamic quantities towards equilibrium. We find that for some choice of initial conditions, the entropy of the sequence distribution can be lowered at the expense of increasing the entropy of the length distribution. We consider mainly energetically neutral reactions, except for one simple case of non-neutral reactions.

cond-mat.soft↗

arXiv2016

Glucans monomer-exchange dynamics as an open chemical network

We describe the oligosaccharides-exchange dynamics performed by 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.

physics.chem-ph↗

arXiv2015

Thermodynamic inference based on coarse-grained data or noisy measurements

Fluctuation theorems have become an important tool in single molecule biophysics to measure free energy differences from non-equilibrium 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 non-trivial correlations between the error and the work, we also consider measurements with delay, as described by linear Langevin equations.

cond-mat.stat-mech↗

arXiv2015

Fluctuation relations for equilibrium states with broken discrete or continuous symmetries

Isometric fluctuation relations are deduced for the fluctuations of the order parameter in equilibrium systems of condensed-matter physics with broken discrete or continuous symmetries. These relations are similar to their analogues obtained for non-equilibrium systems where the broken symmetry is time reversal. At equilibrium, these relations show that the ratio of the probabilities of opposite fluctuations goes exponentially with the symmetry-breaking external field and the magnitude of the fluctuations. These relations are applied to the Curie-Weiss, Heisenberg, and $XY$~models of magnetism where the continuous rotational symmetry is broken, as well as to the $q$-state Potts model and the $p$-state clock model where discrete symmetries are broken. Broken symmetries are also considered in the anisotropic Curie-Weiss model. For infinite systems, the results are calculated using large-deviation theory. The relations are also applied to mean-field models of nematic liquid crystals where the order parameter is tensorial. Moreover, their extension to quantum systems is also deduced.

cond-mat.stat-mech↗

arXiv2015

Kinetics and thermodynamics of reversible polymerization in closed systems

Motivated by a recent work on the metabolism of carbohydrates in bacteria, we study the kinetics and thermodynamics of two classic models for reversible polymerization, one preserving the total polymer concentration and the other one not. The chemical kinetics is described by rate equations following the mass-action law. We consider a closed system and nonequilibrium initial conditions and show that the system dynamically evolves towards equilibrium where detailed balance is satisfied. The entropy production during this process can be expressed as the time derivative of a Lyapunov function. When the solvent is not included in the description and the dynamics conserves the total concentration of polymer, the Lyapunov function can be expressed as a Kullback-Leibler divergence between the nonequilibrium and the equilibrium polymer length distribution. The same result holds true when the solvent is explicitly included in the description and the solution is assumed dilute, whether or not the total polymer concentration is conserved. Furthermore, in this case a consistent nonequilibrium thermodynamic formulation can be established and the out-of-equilibrium thermodynamic enthalpy, entropy and free energy can be identified. Such a framework is useful in complementing standard kinetics studies with the dynamical evolution of thermodynamic quantities during polymerization.

cond-mat.stat-mech↗

arXiv2015

Stochastic thermodynamics of a tagged particle within a harmonic chain

We study the stochastic thermodynamics of an overdamped harmonic chain, which can be viewed equivalently as a 1D 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.

cond-mat.stat-mech↗

arXiv2012

Fluctuation theorems and inequalities generalizing the second law of thermodynamics off equilibrium

We present a general framework for systems which are prepared in a non-stationary non-equilibrium state in the absence of any perturbation, and which are then further driven through the application of a time-dependent perturbation. We distinguish two different situations depending on the way the non-equilibrium state is prepared, either it is created by some driving; or it results from a relaxation following some initial non-stationary conditions. Our approach is based on a recent generalization of the Hatano-Sasa relation for non-stationary probability distributions. We also investigate whether a form of second law holds for separate parts of the entropy production, in a way similar to the work of M. Esposito et al., Phys. Rev. Lett., 104:090601 (2010), but for a non-stationary reference process instead of a stationary one. We find that although the special structure of the theorems derived in this reference is not recovered in the general case, detailed fluctuation theorems still hold separately for parts of the entropy production in this case. These detailed fluctuation theorems lead to interesting generalizations of the second-law of thermodynamics off equilibrium.

cond-mat.stat-mech↗

arXiv2012

Inequalities generalizing the second law of thermodynamics for transitions between non-stationary states

We discuss the consequences of a variant of the Hatano-Sasa relation in which a non-stationary distribution is used in place of the usual stationary one. We first show that this non-stationary distribution is related to a difference of traffic between the direct and dual dynamics. With this formalism, we extend the definition of the adiabatic and non-adiabatic entropies introduced by M. Esposito and C. Van den Broeck in Phys. Rev. Lett. 104, 090601 (2010) for the stationary case. We also obtain interesting second-law like inequalities for transitions between non-stationary states.

cond-mat.stat-mech↗

arXiv2011

Modified fluctuation-dissipation theorem near non-equilibrium states and applications to the Glauber-Ising chain

In this paper, we present a general derivation of a modified fluctuation-dissipation theorem (MFDT) valid near an arbitrary non-stationary state for a system obeying markovian dynamics. We show that the method to derive modified fluctuation-dissipation theorems near non-equilibrium stationary states used by J. Prost et al., PRL 103, 090601 (2009), is generalizable to non-stationary states. This result follows from both standard linear response theory and from a transient fluctuation theorem, analogous to the Hatano-Sasa relation. We show that this modified fluctuation-dissipation theorem can be interpreted at the trajectory level using the notion of stochastic trajectory entropy, in a way which is similar to what has been done recently in the case of MFDT near non-equilibrium steady states (NESS). We illustrate this framework with two solvable examples: the first example corresponds to a brownian particle in an harmonic trap submitted to a quench of temperature and to a time-dependent stiffness. The second example is a classic model of coarsening systems, namely the 1D Ising model with Glauber dynamics.

cond-mat.stat-mech↗

arXiv2011

The random release of phosphate controls the dynamic instability of microtubules

A simple stochastic model which describes microtubule dynamics and explicitly takes into account the relevant biochemical processes is presented. The model incorporates binding and unbinding of monomers and random phosphate release inside the polymer. It is shown that this theoretical approach provides a microscopic picture of the dynamic instability phenomena of microtubules. The cap size, the concentration dependence of the catastrophe times and the delay before observing catastrophes following a dilution can be quantitatively predicted by this approach in a direct and simple way. Furthermore, the model can be solved analytically to a large extend, thus offering a valuable starting point for more refined studies of microtubules dynamics.

cond-mat.stat-mech↗

arXiv2011

A planar lipid bilayer in an electric field: membrane instability, flow field and electrical impedance

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 e.g. ion channels embedded in planar bilayers.

cond-mat.soft↗

arXiv2010

A Poisson-Boltzmann approach for a lipid membrane in an electric field

The behavior of a non-conductive quasi-planar lipid membrane in an electrolyte and in a static (DC) electric field is investigated theoretically in the nonlinear (Poisson-Boltzmann) regime. Electrostatic effects due to charges in the membrane lipids and in the double layers lead to corrections to the membrane elastic moduli which are analyzed here. We show that, especially in the low salt limit, i) the electrostatic contribution to the membrane's surface tension due to the Debye layers crosses over from a quadratic behavior in the externally applied voltage to a linear voltage regime. ii) the contribution to the membrane's bending modulus due to the Debye layers saturates for high voltages. Nevertheless, the membrane undulation instability due to an effectively negative surface tension as predicted by linear Debye-Hückel theory is shown to persist in the nonlinear, high voltage regime.

cond-mat.soft↗

arXiv2010

Role of ATP-hydrolysis in the dynamics of a single actin filament

We study the stochastic dynamics of growth and shrinkage of single actin filaments taking into account insertion, removal, and ATP hydrolysis of subunits either according to the vectorial mechanism or to the random mechanism. In a previous work, we developed a model for a single actin or microtubule filament where hydrolysis occurred according to the vectorial mechanism: the filament could grow only from one end, and was in contact with a reservoir of monomers. Here we extend this approach in several ways, by including the dynamics of both ends and by comparing two possible mechanisms of ATP hydrolysis. Our emphasis is mainly on two possible limiting models for the mechanism of hydrolysis within a single filament, namely the vectorial or the random model. We propose a set of experiments to test the nature of the precise mechanism of hydrolysis within actin filaments.

q-bio.BM↗