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Luca Peliti

Publications and source records attributed to Luca Peliti.

At least 37 records · Page 2Linked to original sources

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↗

Einstein's Approach to Statistical Mechanics: The 1902-04 Papers

We summarize the papers published by Einstein in the Annalen der Physik in the years 1902-04 on the derivation of the properties of thermal equilibrium on the basis of the mechanical equations of motion and of the calculus of probabilities. We point out the line of thought that led Einstein to an especially economical foundation of the discipline, and to focus on fluctuations of the energy as a possible tool for establishing the validity of this foundation. We also sketch a comparison of Einstein's approach with that of Gibbs, suggesting that although they obtained similar results, they had different motivations and interpreted them in very different ways.

physics.hist-ph↗

Elementary derivation of the expressions of momentum and energy in special relativity

The expressions of momentum and energy of a particle in special relativity are often derived in a quite unconvincing manner in elementary text, by resorting either to electrodynamic or quantum considerations, or via the introduction of the less-than-elementary concept of a four-vector. It is instead possible, by exploiting considerations introduced by P. Epstein and A. Einstein and exploited later by Feynman, to obtain a fully elementary derivation of these expressions and of the $E=mc^2$ formula exploiting only Lorentz transformations and the postulate of the conservation of quantities defined for point-like particles which reduce to the Newtonian expressions of momentum and energy in the classical limit.

physics.class-ph↗

Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs

The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide a consistent thermodynamic description of enzyme-assisted assembly processes involving competing substrates, in a Master Equation framework. We introduce and evaluate a measure of the efficiency based on rigorous non-equilibrium inequalities. The performance of several proofreading models are thus analyzed and the related time, dissipation and efficiency vs. error trade-offs exhibited for different discrimination regimes. We finally introduce and analyze in the same framework a simple model which takes into account correlations between consecutive enzyme-assisted assembly steps. This work highlights the relevance of the distinction between energetic and kinetic discrimination regimes in enzyme-substrate interactions.

cond-mat.stat-mech↗

Entropy Production in Quantum Brownian Motion

We investigate how to coherently define entropy production for a process of transient relaxation in the Quantum Brownian Motion model for harmonic potential. We compare a form, called "Poised" (P), which after non-Markovian transients corresponds to a definition of heat as the change in the system Hamiltonian of mean force, with a recent proposal by Esposito (ELB) based on a definition of heat as the energy change in the bath. Both expressions yield a positive-defined entropy production and coincide for vanishing coupling strength, but their difference is proved to be always positive (after non-Markovian transients disappear) and to grow as the coupling strength increases. In the classical over-damped limit the "Poised" entropy production converges to the entropy production used in stochastic thermodynamics. We also investigate the effects of the system size, and of the ensuing Poincaré recurrences, and how the classical limit is approached. We close by discussing the strong-coupling limit, in which the ideal canonical equilibrium of the bath is violated.

cond-mat.stat-mech↗

Heat release by controlled continuous-time Markov jump processes

We derive the equations governing the protocols minimizing the heat released by a continuous-time Markov jump process on a one-dimensional countable state space during a transition between assigned initial and final probability distributions in a finite time horizon. In particular, we identify the hypotheses on the transition rates under which the optimal control strategy and the probability distribution of the Markov jump problem obey a system of differential equations of Hamilton-Bellman-Jacobi-type. As the state-space mesh tends to zero, these equations converge to those satisfied by the diffusion process minimizing the heat released in the Langevin formulation of the same problem. We also show that in full analogy with the continuum case, heat minimization is equivalent to entropy production minimization. Thus, our results may be interpreted as a refined version of the second law of thermodynamics.

cond-mat.stat-mech↗

The rate of beneficial mutations surfing on the wave of a range expansion

Many theoretical and experimental studies suggest that range expansions can have severe consequences for the gene pool of the expanding population. Due to strongly enhanced genetic drift at the advancing frontier, neutral and weakly deleterious mutations can reach large frequencies in the newly colonized regions, as if they were surfing the front of the range expansion. These findings raise the question of how frequently beneficial mutations successfully surf at shifting range margins, thereby promoting adaptation towards a range-expansion phenotype. Here, we use individual-based simulations to study the surfing statistics of recurrent beneficial mutations on wave-like range expansions in linear habitats. We show that the rate of surfing depends on two strongly antagonistic factors, the probability of surfing given the spatial location of a novel mutation and the rate of occurrence of mutations at that location. The surfing probability strongly increases towards the tip of the wave. Novel mutations are unlikely to surf unless they enjoy a spatial head start compared to the bulk of the population. The needed head start is shown to be proportional to the inverse fitness of the mutant type, and only weakly dependent on the carrying capacity. The second factor is the mutation occurrence which strongly decreases towards the tip of the wave. Thus, most successful mutations arise at an intermediate position in the front of the wave. We present an analytic theory for the tradeoff between these factors that allows to predict how frequently substitutions by beneficial mutations occur at invasion fronts. We find that small amounts of genetic drift increase the fixation rate of beneficial mutations at the advancing front, and thus could be important for adaptation during species invasions.

q-bio.PE↗

Modeling microevolution in a changing environment: The evolving quasispecies and the Diluted Champion Process

Several pathogens use evolvability as a survival strategy against acquired immunity of the host. Despite their high variability in time, some of them exhibit quite low variability within the population at any given time, a somehow paradoxical behavior often called the evolving quasispecies. In this paper we introduce a simplified model of an evolving viral population in which the effects of the acquired immunity of the host are represented by the decrease of the fitness of the corresponding viral strains, depending on the frequency of the strain in the viral population. The model exhibits evolving quasispecies behavior in a certain range of its parameters, ans suggests how punctuated evolution can be induced by a simple feedback mechanism.

q-bio.PE↗

Membrane stress tensor in the presence of lipid density and composition inhomogeneities

We derive the expression of the stress tensor for one and two-component lipid membranes with density and composition inhomogeneities. We first express the membrane stress tensor as a function of the free-energy density by means of the principle of virtual work. We then apply this general result to a monolayer model which is shown to be a local version of the area-difference elasticity (ADE) model. The resulting stress tensor expression generalizes the one associated with the Helfrich model, and can be specialized to obtain the one associated with the ADE model. Our stress tensor directly gives the force exchanged through a boundary in a monolayer with density and composition inhomogeneities. Besides, it yields the force density, which is also directly obtained in covariant formalism. We apply our results to study the forces induced in a membrane by a local perturbation.

cond-mat.soft↗

Population size effects in evolutionary dynamics on neutral networks and toy landscapes

We study the dynamics of a population subject to selective pressures, evolving either on RNA neutral networks or in toy fitness landscapes. We discuss the spread and the neutrality of the population in the steady state. Different limits arise depending on whether selection or random drift are dominant. In the presence of strong drift we show that observables depend mainly on $M μ$, $M$ being the population size and $μ$ the mutation rate, while corrections to this scaling go as 1/M: such corrections can be quite large in the presence of selection if there are barriers in the fitness landscape. Also we find that the convergence to the large $M μ$ limit is linear in $1/M μ$. Finally we introduce a protocol that minimizes drift; then observables scale like 1/M rather than $1/(Mμ)$, allowing one to determine the large $M$ limit faster when $μ$ is small; furthermore the genotypic diversity increases from $O(\ln M)$ to $O(M)$.

q-bio.PE↗

Direct evaluation of large-deviation functions

We introduce a numerical procedure to evaluate directly the probabilities of large deviations of physical quantities, such as current or density, that are local in time. The large-deviation functions are given in terms of the typical properties of a modified dynamics, and since they no longer involve rare events, can be evaluated efficiently and over a wider ranges of values. We illustrate the method with the current fluctuations of the Totally Asymmetric Exclusion Process and with the work distribution of a driven Lorentz gas.

cond-mat.stat-mech↗

Amphiphilic Membranes

Contents: 1. Introduction 2. Amphiphilic molecules and the phases they form 3. Isolated membranes: the Helfrich hamiltonian 4. Vesicle shapes 5. Shape fluctuations in vesicles 6. Interacting fluid membranes 7. Conclusions A. Differential equations for vesicle shapes B. The Faddeev-Popov determinant C. One-loop calculation of the renormalization group D. The Liouville model

cond-mat↗

A minimal stochastic model for influenza evolution

We introduce and discuss a minimal individual-based model for influenza dynamics. The model takes into account the effects of specific immunization against viral strains, but also infectivity randomness and the presence of a short-lived strain transcending immunity recently suggested in the literature. We show by simulations that the resulting model exhibits substitution of viral strains along the years, but that their divergence remains bounded. We also show that dropping any of these features results in a drastically different behavior, leading either to the extinction of the disease, to the proliferation of the viral strains, or to their divergence.

q-bio.PE↗

Work probability distribution in single molecule experiments

We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an energy landscape. The Jarzynski equality is recovered as an identity, independent of the pulling protocol. This approach allows one to evaluate easily, by numerical integration, the work distribution, once a few parameters of the energy landscape are known.

cond-mat.soft↗

Kinetic barriers in RNA unzipping

We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting two-barrier energy landscape accounts for the dependence of the unfolding kinetics on the pulling rate. Furthermore at intermediate force, the two barriers cannot be distinguished by the analysis of the opening kinetic, which turns out to be dominated by a single macro-barrier, whose properties depend non-trivially on the two single barriers. Our results suggest that in pulling experiments on RNA molecule containing tertiary structures, the details of the single kinetic barriers can only be obtained using a low pulling rate value, or in the high force regime.

q-bio.BM↗

Quasispecies evolution in general mean-field landscapes

I consider a class of fitness landscapes, in which the fitness is a function of a finite number of phenotypic "traits", which are themselves linear functions of the genotype. I show that the stationary trait distribution in such a landscape can be explicitly evaluated in a suitably defined "thermodynamic limit", which is a combination of infinite-genome and strong selection limits. These considerations can be applied in particular to identify relevant features of the evolution of promoter binding sites, in spite of the shortness of the corresponding sequences.

cond-mat.dis-nn↗