arXiv subjects

A. Imparato

Publications and source records attributed to A. Imparato.

At least 19 recordsLinked to original sources

arXiv2026

Quantum fluctuation relations in first-detection processes

We derive two quantum fluctuation relations for systems undergoing repeated projective measurements. These fluctuation relations characterize the work that can be extracted from a quantum device when a first-detection event triggers a mechanical operation leading to positive work production. The correction to the standard quantum Jarzynski equality depends logarithmically on the mean first-detection time for the time-reversed dynamics. Application of Jensen's inequality leads to fundamental limits on both the total work involved in the repeated measurements and final mechanical operation, and the extracted work alone. The general case of a device connected to an external environment is also considered.

quant-ph↗

arXiv2025

On thermalization of a system with discrete phase space

We investigate the thermalization of a stochastic system with discrete phase space, initially at equilibrium at temperature $T_i$ and then termalizing in an environment at temperature $T_f$ , considering both cases $T_i > T_f$ and $T_i < T_f$. For the simple case of a system with constant energy gaps, we show that the relation between the time scales of the cooling and heating processes is not univocal, and depends on the magnitude of the energy gap itself. Specifically the eigenvalues of the corresponding stochastic matrix set the time scales of the relaxation process and for large energy gaps the cooling process is found to exhibit the shortest relaxation times to equilibrium while the heating process is found to be faster at all scales for small gaps. We consider both the Kullback-Leibler divergence and the Fisher information and its related quantities to quantify the degree of thermalization of the system. In the intermediate to long time regime both quantities are found to bear the same type of information concerning the rate of thermalization, and follow the ordering predicted by the dynamic eigenvalues. We then consider a more complex system with a more intricate stochastic matrix, namely a 1D Ising model, and confirm the findings on the existence of two regimes, one in which cooling becomes faster than heating. We make contact with a previous work where an harmonic oscillator was used as working fluid and the heating process was always found to be faster than the cooling one.

cond-mat.stat-mech↗

arXiv2024

Efficient excitation-transfer across fully connected networks via local-energy optimization

We study the excitation transfer across a fully connected quantum network whose sites energies can be artificially designed. Starting from a simplified model of a broadly-studied physical system, we systematically optimize its local energies to achieve high excitation transfer for various environmental conditions, using an adaptive Gradient Descent technique and Automatic Differentiation. We show that almost perfect transfer can be achieved with and without local dephasing, provided that the dephasing rates are not too large. We investigate our solutions in terms of resilience against variations in either the network connection strengths, or size, as well as coherence losses. We highlight the different features of a dephasing-free and dephasing-driven transfer. Our work gives further insight into the interplay between coherence and dephasing effects in excitation-transfer phenomena across fully connected quantum networks. In turn, this will help designing optimal transfer in artificial open networks through the simple manipulation of local energies.

quant-ph↗

arXiv2024

A Reinforcement Learning Approach to the Design of Quantum Chains for Optimal Energy Transfer

We propose a bottom-up approach, based on Reinforcement Learning, to the design of a chain achieving efficient excitation-transfer performances. We assume distance-dependent interactions among particles arranged in a chain under tight-binding conditions. Starting from two particles and a localised excitation, we gradually increase the number of constitutents of the system so as to improve the transfer probability. We formulate the problem of finding the optimal locations and numbers of particles as a Markov Decision Process: we use Proximal Policy Optimization to find the optimal chain-building policies and the optimal chain configurations under different scenarios. We consider both the case in which the target is a sink connected to the end of the chain and the case in which the target is the right-most particle in the chain. We address the problem of disorder in the chain induced by particle positioning errors. We are able to achieve extremely high excitation transfer in all cases, with different chain configurations and properties depending on the specific conditions.

quant-ph↗

arXiv2021

Out-of-equilibrium Frenkel-Kontorova model

A 1D model of interacting particles moving over a periodic substrate and in a position dependent temperature profile is considered. When the substrate and the temperature profile are spatially asymmetric a center-of-mass velocity develops, corresponding to a directed transport of the chain. This autonomous system can thus transform heath currents into motion. The model parameters can be tuned such that the particles exhibit a crossover from an ordered configuration on the substrate to a disordered one, the maximal motor effect being reached in such a disordered phase. In this case the manybody motor outperforms the single motor system, showing the great importance of collective effects in microscopic thermal devices. Such collective effects represent thus a free resource that can be exploited to enhance the dynamic and thermodynamic performances in microscopic machines.

cond-mat.stat-mech↗

arXiv2015

Thermal transport in out of equilibrium quantum harmonic chains

We address the problem of heat transport in a chain of coupled quantum harmonic oscillators, exposed to the influences of local environments of various nature, stressing the effects that the specific nature of the environment has on the phenomenology of the transport process. We study in detail the behavior of thermodynamically relevant quantities such as heat currents and mean energies of the oscillators, establishing rigorous analytical conditions for the existence of a steady state, whose features we analyse carefully. In particular we assess the conditions that should be faced to recover trends reminiscent of the classical Fourier law of heat conduction and highlight how such a possibility depends on the environment linked to our system.

quant-ph↗

arXiv2014

Energy Transfer in molecular devices

Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in protein devices. By studying two different model protein machines, with different biological functions, we show that genuinely non--linear phenomena are responsible for energy transport between the different machine sites involved in the biological functions. The energy transfer turns out to be extremely efficient from an energetic point of view: by changing the energy initially provided to the model device, we identify a well defined range of energies where the time for the energy transport to occur is minimal and the amount of transferred energy is maximum. Furthermore, by introducing an implicit solvent, we show that the energy is localized on the internal residues of the protein structure, thus minimizing the dissipation.

physics.bio-ph↗

arXiv2012

Efficiency at maximum power of interacting molecular machines

We investigate the efficiency of systems of molecular motors operating at maximum power. We consider two models of kinesin motors on a microtubule: for both the simplified and the detailed model, we find that the many-body exclusion effect enhances the efficiency at maximum power of the many-motor system, with respect to the single motor case. Remarkably, we find that this effect occurs in a limited region of the system parameters, compatible with the biologically relevant range.

cond-mat.stat-mech↗

arXiv2012

Efficiency of molecular machines with continuous phase space

We consider a molecular machine described as a Brownian particle diffusing in a tilted periodic potential. We evaluate the absorbed and released power of the machine as a function of the applied molecular and chemical forces, by using the fact that the times for completing a cycle in the forward and the backward direction have the same distribution, and that the ratio of the corresponding splitting probabilities can be simply expressed as a function of the applied force. We explicitly evaluate the efficiency at maximum power for a simple sawtooth potential. We also obtain the efficiency at maximum power for a broad class of 2-D models of a Brownian machine and find that loosely coupled machines operate with a smaller efficiency at maximum power than their strongly coupled counterparts.

cond-mat.stat-mech↗

arXiv2011

Direction dependent mechanical unfolding and Green Fluorescent Protein as a force sensor

An Ising--like model of proteins is used to investigate the mechanical unfolding of the Green Fluorescent Protein along different directions. When the protein is pulled from its ends, we recover the major and minor unfolding pathways observed in experiments. Upon varying the pulling direction, we find the correct order of magnitude and ranking of the unfolding forces. Exploiting the direction dependence of the unfolding force at equilibrium, we propose a force sensor whose luminescence depends on the applied force.

cond-mat.soft↗

arXiv2011

Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $β$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.

cond-mat.dis-nn↗

arXiv2010

Pathways of mechanical unfolding of FnIII_{10}: low force intermediates

We study the mechanical unfolding pathways of the $FnIII_{10}$ domain of fibronectin by means of an Ising--like model, using both constant force and constant velocity protocols. At high forces and high velocities our results are consistent with experiments and previous computational studies. Moreover, the simplicity of the model allows us to probe the biologically relevant low force regime, where we predict the existence of two intermediates with very close elongations. The unfolding pathway is characterized by stochastic transitions between these two intermediates.

cond-mat.soft↗

arXiv2010

On the surface tension of fluctuating quasi-spherical vesicles

We calculate the stress tensor for a quasi-spherical vesicle and we thermally average it in order to obtain the actual, mechanical, surface tension $τ$ of the vesicle. Both closed and poked vesicles are considered. We recover our results for $τ$ by differentiating the free-energy with respect to the proper projected area. We show that $τ$ may become negative well before the transition to oblate shapes and that it may reach quite large negative values in the case of small vesicles. This implies that spherical vesicles may have an inner pressure lower than the outer one.

cond-mat.soft↗

arXiv2009

Out-of-equilibrium versus dynamical and thermodynamical transitions for a model protein

Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctuation relation, the system free energy landscape is evaluated. Three different structural transitions are identified along the unfolding pathways. Furthermore, the reconstruction of the the free and potential energy profiles in terms of inherent structure formalism allows us to put in direct correspondence these transitions with the equilibrium thermal transitions relevant for protein folding/unfolding. Through the study of the fluctuations of the protein structure at different temperatures, we identify the dynamical transitions, related to configurational rearrangements of the protein, which are precursors of the thermal transitions.

cond-mat.soft↗

arXiv2009

Equilibrium properties and force-driven unfolding pathways of RNA molecules

The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two--state behaviour for the hairpin and the presence of intermediate states for the ribozyme. Nonequilibrium simulations give the possible unfolding pathways for the ribozyme, and the dominant pathway corresponds to the experimentally observed one.

cond-mat.soft↗

arXiv2009

Work distribution in manipulated single biomolecules

We consider the relation between the microscopic and effective descriptions of the unfolding experiment on a model polypeptide. We evaluate the probability distribution function of the performed work by Monte Carlo simulations and compare it with that obtained by evaluating the work distribution generating function on an effective Brownian motion model tailored to reproduce exactly the equilibrium properties. The agreement is satisfactory for fast protocols, but deteriorates for slower ones, hinting at the existence of processes on several time scales even in such a simple system.

cond-mat.stat-mech↗

arXiv2008

Reconstructing the free energy landscape of a polyprotein by single-molecule experiments

The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is estimated from pulling experiments. Such a free energy exhibits a regular shape that sets a typical unfolding length at zero force of the order of 20 nm. This length scale turns out to be much larger than the kinetic unfolding length that is also estimated by analyzing the typical rupture force of the molecule under dynamic loading.

cond-mat.soft↗

arXiv2008

Mechanical unfolding and refolding pathways of ubiquitin

Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Go model with binary variables. The exponential dependence of the time constants on the force is verified, and folding and unfolding lengths are computed, with good agreement with experimental results. Furthermore, the model exhibits intermediate kinetic states, as observed in experiments. Unfolding and refolding pathways and intermediate states, obtained by tracing single secondary structure elements, are consistent with simulations of previous all-atom models and with the experimentally observed step sizes.

cond-mat.soft↗