arXiv subjects

Fabrizio Cleri

Publications and source records attributed to Fabrizio Cleri.

18 recordsLinked to original sources

arXiv2026

Quantum Thermodynamics of Electron Transport along Chains of Redox Centers

Intramolecular electron transport in biological systems is typically described as a diffusive hopping process, according to the semi-classical rate theories of Marcus and Hopfield combined with classical Pauli-type master equations. However, the possibility that non-trivial quantum mechanical effects could play a functional role in the transport dynamics in certain biomolecular processes has attracted increasing attention. Here, we extend the quantum mechanical model of open system dynamics by the Lindblad equation to a key biological component, the long chains of redox centers based on iron-sulfur clusters or heme groups that are widespread in many biological organisms, where they realize the cellular respiration. This approach allows to explore a wide range of physical parameters, showing key features of electron transport in these multi-domain protein structures. We pay particular attention to heat and entropy transfer between the electrons and the protein bath, which constitutes a benchmark of physical realism for the models. Electron currents, average transfer times and relative efficiency of the transport process are also explicitly characterized.

physics.chem-ph↗

arXiv2026

A trick of the tail: how electrostatics helps a DNA repair enzyme to localize on nucleosomes

Electrostatic interactions are key to the recognition processes of proteins and DNA and have been previously documented for the action of repair enzymes. Uracil-DNA glycosylase (UDG) is the first in a sequence of enzymes that act in the base-excision repair process (BER) and whose task is the extraction of uracil bases from nuclear DNA. The question of how the molecule targets uracil bases in chromatin, in particular in the condensed protein-DNA complexes of nucleosomes, has only recently become a subject of detailed studies. Here we show that the presence of an arginine anchor motif on the N-terminal tail of UDG can favor its localization on nucleosomes by binding to their acidic patches on their top and bottom surfaces via electrostatic interactions. We argue that this mechanism can play a key role in the detection of uracil defects in nucleosomal DNA.

cond-mat.soft↗

arXiv2025

Boltzmann to Lindblad: Classical and Quantum Approaches to Out-of-Equilibrium Statistical Mechanics

Open quantum systems play a central role in contemporary nanoscale technologies, including molecular electronics, quantum heat engines, quantum computation and information processing. A major theoretical challenge is to construct dynamical models that are simultaneously consistent with classical thermodynamics and complete positivity. In this work, we develop a framework that addresses this issue by extending classical stochastic dynamics to the quantum domain. We begin by formulating a generalized Langevin equation in which both friction and noise act symmetrically on the two Hamiltonian equations. From this, we derive a generalized Klein-Kramers equation expressed in terms of Poisson brackets, and we show that it admits the Boltzmann distribution as its stationary solution while satisfying the first and second laws of thermodynamics along individual trajectories. Applying canonical quantization to this classical framework yields two distinct quantum master equations, depending on whether the friction operators are taken to be Hermitian or non-Hermitian. By analyzing the dynamics of a harmonic oscillator, we determine the conditions under which these equations reduce to a Lindblad-type generator. Our results demonstrate that complete positivity is ensured only when friction and noise are included in both Hamiltonian equations, thus fully justifying the classical construction. Moreover, we find that the friction coefficients must satisfy the same positivity condition in both the Hermitian and non-Hermitian formulations, revealing a form of universality that transcends the specific operator representation. The formalism offers a versatile tool for deriving quantum versions of the thermodynamic laws and is directly applicable to a wide class of nonequilibrium nanoscale systems.

quant-ph↗

arXiv2025

Explicit noise and dissipation operators for quantum stochastic thermodynamics

The theory of open quantum systems plays a fundamental role in several scientific and technological disciplines, from quantum computing and information science to molecular electronics and quantum thermodynamics. Despite its widespread relevance, a rigorous formulation of quantum dissipation in conjunction with thermal noise remains a topic of active research. In this work, we establish a formal correspondence between classical stochastic thermodynamics, in particular the Fokker-Planck and Klein-Kramers equations, and the quantum master equation. Building on prior studies of multiplicative noise in classical stochastic differential equations, we demonstrate that thermal noise at the quantum level manifests as a multidimensional geometric stochastic process. By applying canonical quantization, we introduce a novel Hermitian dissipation operator that serves as a quantum analogue of classical viscous friction. This operator allows for a well-defined expression of heat exchange between a system and its environment, enabling the formulation of an alternative quantum equipartition theorem. Our framework ensures a precise energy balance that aligns with the first law of thermodynamics and an entropy balance consistent with the second law. The theoretical formalism is applied to two prototypical quantum systems, the harmonic oscillator and a particle in an infinite potential well, for which it provides new insights into nonequilibrium thermodynamics at the quantum scale. Our results advance the understanding of dissipation in quantum systems and establish a foundation for future studies on stochastic thermodynamics in the quantum domain.

quant-ph↗

arXiv2024

Quantum Computers, Quantum Computing and Quantum Thermodynamics

Quantum thermodynamics aims at extending standard thermodynamics and non-equilibrium statistical physics to systems with sizes well below the thermodynamic limit. A rapidly evolving research field, which promises to change our understanding of the foundations of physics, while enabling the discovery of novel thermodynamic techniques and applications at the nanoscale. Thermal management has turned into a major obstacle in pushing the limits of conventional digital computers, and could likely represent a crucial issue also for quantum computers. The practical realization of quantum computers with superconducting loops requires working at cryogenic temperatures to eliminate thermal noise; ion-trap qubits need as well low temperatures to minimize collisional noise; in both cases, the sub-nanometric sizes also bring about thermal broadening of the quantum states; and even room-temperature photonic computers require cryogenic detectors. A number of thermal and thermodynamic questions therefore take center stage, such as quantum redefinitions of work and heat, thermalization and randomization of quantum states, the overlap of quantum and thermal fluctuations, and many other, even including a proper definition of temperature for the small open systems constantly out of equilibrium that are the qubits. This overview provides an introductory perspective on a selection of current trends in quantum thermodynamics and their impact on quantum computers and quantum computing, with a language accessible also to postgraduate students and researchers from different fields.

quant-ph↗

arXiv2024

Short-time expansion of one-dimensional Fokker-Planck equations with heterogeneous diffusion

We formulate a short-time expansion for one-dimensional Fokker-Planck equations with spatially dependent diffusion coefficients, derived from stochastic processes with Gaussian white noise, for general values of the discretization parameter $0 \leq \alpha \leq 1$ of the stochastic integral. The kernel of the Fokker-Planck equation (the propagator) can be expressed as a product of a singular and a regular term. While the singular term can be given in closed form, the regular term can be computed from a Taylor expansion whose coefficients obey simple ordinary differential equations. We illustrate the application of our approach with examples taken from statistical physics and biophysics. Further, we show how our formalism allows to define a class of stochastic equations which can be treated exactly. The convergence of the expansion cannot be guaranteed independently from the discretization parameter $\alpha$.

physics.bio-ph↗

arXiv2023

On the effect of electronic stopping in molecular dynamics simulations of collision cascades in Gallium Arsenide

Understanding the generation and evolution of defects induced in matter by ion irradiation is of fundamental importance to estimate the degradation of functional properties of materials. Computational approaches used in dierent communities, from space radiation eects to nuclear energy experiments, are based on a number of approximations that, among others, traditionally neglect the coupling between electronic and ionic degrees of freedom in the description of displacements. In this work, we study collision cascades in GaAs, including the electronic stopping power for selfprojectiles in dierent directions obtained via real time Time Dependent Density Functional Theory in Molecular Dynamics simulations of collision cascades, using the recent electron-phonon model and the previously developed two-temperature model. We show that the former can be well applied to describe the eects of electronic stopping in molecular dynamics simulations of collision cascades in a multielement semiconductor and that the number of defects is considerably aected by electronic stopping eects. The results are also discussed in the wider context of the commonly used non-ionizing energy loss model to estimate degradation of materials by cumulative displacements.

physics.comp-ph↗

arXiv2022

Infinite ergodicity for geometric Brownian motion

Geometric Brownian motion is an exemplary stochastic processes obeying multiplicative noise, with widespread applications in several fields, e.g. in finance, in physics and biology. The definition of the process depends crucially on the interpretation of the stochastic integrals which involves the discretization parameter $\alpha$ with $0 \leq \alpha \leq 1$ , giving rise to the well-known special cases $\alpha=0$ (It\^{o}), $\alpha=1/2$ (Fisk-Stratonovich) and $\alpha=1$ (H\"{a}nggi-Klimontovich or anti-It\^{o}). In this paper we study the asymptotic limits of the probability distribution functions (PDFs) of geometric Brownian motion and some related generalizations. We establish the conditions for the existence of normalizable asymptotic distributions depending on the discretization parameter $\alpha$. Using the infinite ergodicity approach, recently applied to stochastic processes with multiplicative noise by E. Barkai and collaborators, we show how meaningful asymptotic results can be formulated in a transparent way.

cond-mat.stat-mech↗

arXiv2022

Bragg's Additivity Rule and Core and Bond model studied by real-time TDDFT electronic stopping simulations: the case of water vapor

The electronic stopping power ($S_e$) of water vapor (H$_2$O), hydrogen (H$_2$) and oxygen (O$_2$) gases for protons in a broad range of energies, centered in the Bragg peak, was calculated using real-time time-dependent density functional theory (rt-TDDFT) simulations with Gaussian basis sets. This was done for a kinetic energy of incident protons ($E_k$) ranging from 1.56 keV/amu to 1.6 MeV/amu. $S_e$ was calculated as the average over geometrically pre-sampled short ion trajectories. The average $S_e(E_k)$ values were found to rapidly converge with 25-30 pre-sampled, 2 nm-long ion trajectories. The rt-TDDFT $S_e(E_k)$ curves were compared to experimental and SRIM data, and used to validate the Bragg's Additivity Rule (BAR). Discrepancies were analyzed in terms of basis set effects and omitted nuclear stopping at low energies. At variance with SRIM, we found that BAR is applicable to our rt-TDDFT simulations of $\mathrm{2H_2+O_2}$ $\mathrm{\rightarrow 2H_2O}$ without scaling for $E_k>40$ keV/amu. The hydrogen and oxygen Core and Bond (CAB) contributions to electronic stopping were calculated and found to be slightly smaller than SRIM values as a result of a red-shift in our rt-TDDFT $S_e(E_k)$ curves and a re-distribution of weights due to some bond contributions being neglected in SRIM.

physics.chem-ph↗

arXiv2018

Interface thermal behavior in nanomaterials by thermal grating relaxation

We study the relaxation of a thermal grating in multilayer materials with interface thermal resistances. The analytical development allows for the nu- merical determination of this thermal property in Approach to Equilibrium Molecular Dynamics and suggests an experimental setup for its measurement. Possible non-diffusive effects at the nanoscale are take into consideration by a non-local formulation of the heat equation. As a case study, we numerically apply the present approach to silicon grain boundary thermal resistance

cond-mat.mtrl-sci↗

arXiv2016

Length dependence of thermal conductivity by approach-to-equilibrium molecular dynamics

The length dependence of the thermal conductivity over more than two decades is systematically studied for a range of materials, interatomic potentials and temperatures, by the atomistic approach-to-equilibrium molecular dynamics method (AEMD). By comparing the values of conductivity obtained for a given supercell length and maximum phonon mean-free-path (MFP), we find that such values are strongly correlated, demonstrating that the AEMD calculation with a supercell of finite length, actually probes the thermal conductivity corresponding to a maximum phonon MFP. As a consequence, the less pronounced length dependence usually observed for poorer thermal conductors, such as amorphous silica, is physically justified by their shorter average phonon MFP. Finally, we compare different analytical extrapolations of the conductivity to infinite length, and demonstrate that the frequently used Matthiessen rule is not applicable in AEMD. An alternative extrapolation more suitable for transient-time, finite-supercell simulations is derived. This approximation scheme can also be used to classify the quality of different interatomic potential models with respect to their capability of predicting the experimental thermal conductivity.

physics.comp-ph↗

arXiv2015

Random walks over a super-percolating two dimensional lattice

Two-dimensional networks of ordered quantum dots beyond the percolation threshold are studied, as typical example of conducting nanostructures with quenched random disorder. Theory predicts anomalous diffusion with stretched-exponential relaxation at short distances, and computer simulations on lattices of crossing, straight paths of random length confirm such a behavior. Anomalous diffusion is interpreted as resulting from the higher probability of taking straight, or ballistic paths, when the traveled distance is comparable or shorter than the lattice characteristic length. Diffusion turns over to normal for longer traveled distances, whence all paths tend to become equiprobable. Such random lattice structures represent a model for realistic quantum dot networks, with potential applications in optoelectronics, photovoltaics or spintronics.

cond-mat.stat-mech↗

arXiv2015

A biophysical model of cell evolution after cytotoxic treatments: damage, repair and cell response

We present a theoretical agent-based model of cell evolution under the action of cytotoxic treatments, such as radioteraphy or chemoteraphy. The major features of cell cycle and proliferation, cell damage and repair, and chemical diffusion are included. Cell evolution is based on a discrete Markov chain, with cells stepping along a sequence of discrete internal states from 'normal' to 'inactive'. Probabilistic laws are introduced for each type of event a cell can undergo during its life cycle: duplication, arrest, apoptosis, senescence, damage, healing. We adjust the model parameters on a series of cell irradiation experiments, carried out in a clinical LINAC at 20 MV, in which the damage and repair kinetics of single- and double-strand breaks are followed. Two showcase applications of the model are then presented. In the first one, we reconstruct the cell survival curves from a number of published low- and high-dose irradiation experiments. We reobtain a very good description of the data without assuming the well-known linear-quadratic model, but instead including a variable DSB repair probability, which is found to spontaneously saturate with an exponential decay at increasingly high doses. As a second test, we attempt to simulate the two extreme possibilities of the so-called 'bystander' effect in radiotherapy: the 'local' effect versus a 'global' effect, respectively activated by the short-range or long-range diffusion of some factor, presumably secreted by the irradiated cells. Even with an oversimplified simulation, we could demonstrate a sizeable difference in the proliferation rate of non-irradiated cells, the proliferation acceleration being much larger for the global than the local effect, for relatively small fractions of irradiated cells in the colony.

q-bio.CB↗

arXiv2015

High Conductance Ratio in Molecular Optical Switching of Functionalized Nanoparticle Self-Assembled Nanodevices

Self-assembled functionalized nano particles are at the focus of a number of potential applications, in particular for molecular scale electronics devices. Here we perform experiments of self-assembly of 10 nm Au nano particles (NPs), functionalized by a dense layer of azobenzene-bithiophene (AzBT) molecules, with the aim of building a light-switchable device with memristive properties. We fabricate planar nanodevices consisting of NP self-assembled network (NPSANs) contacted by nanoelectrodes separated by interelectrode gaps ranging from 30 to 100 nm. We demonstrate the light-induced reversible switching of the electrical conductance in these AzBT NPSANs with a record on/off conductance ratio up to 620, an average value of ca. 30 and with 85% of the devices having a ratio above 10. Molecular dynamics simulation of the structure and dynamics of the interface between molecular monolayers chemisorbed on the nano particle surface are performed and compared to the experimental findings. The properties of the contact interface are shown to be strongly correlated to the molecular conformation which in the case of AzBT molecules, can reversibly switched between a cis and a trans form by means of light irradiations of well-defined wavelength. Molecular dynamics simulations provide a microscopic explanation for the experimental observation of the reduction of the on/off current ratio between the two isomers, compared to experiments performed on flat self-assembled monolayers contacted by a conducting cAFM tip.

cond-mat.mes-hall↗

arXiv2013

Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.

physics.bio-ph↗

arXiv2012

Theory and Monte Carlo simulations for the stretching of flexible and semi-flexible single polymer chains under external fields

Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many results can be thereby obtained for specific kinds of polymers and specific geometries. In this work we describe the non-uniform stretching of a single, non-branched polymer molecule by an external field (e.g. fluid in uniform motion, or uniform electric field) by a universal physical framework which leads to general conclusions on different types of polymers. We derive analytical results both for the freely-jointed chain and the worm-like chain models based on classical statistical mechanics. Moreover, we provide a Monte Carlo numerical analysis of the mechanical properties of flexible and semi-flexible polymers anchored at one end. The simulations confirm the analytical achievements, and moreover allow to study the situations where the theory can not provide explicit and useful results. In all cases we evaluate the average conformation of the polymer and its fluctuation statistics as a function of the chain length, bending rigidity and field strength.

physics.bio-ph↗

arXiv2012

Theory of single-molecule experiments in the overstretching force regime

We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and constant-displacement (Helmholtz) formulations of single molecule stretching experiments are shown to converge in the thermodynamic limit. Monte Carlo simulations of continuous three dimensional polymers of variable length are carried out, based on this formulation. We demonstrate that the experimental force-extension curves for short and long chain polymers are described by a unique universal model, despite the differences in chemistry and rate-dependence of transition forces.

physics.bio-ph↗

arXiv2011

Molecular dynamics simulation of the recrystallization of amorphous Si layers: Comprehensive study of the dependence of the recrystallization velocity on the interatomic potential

The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The amorphous on crystalline stack is annealed afterward on a wide range of temperature and time using five different interatomic potentials: Stillinger-Weber, Tersoff, EDIP, SW115, and Lenosky. The simulations are exploited to systematically extract the recrystallization velocity. A strong dependency of the results on the interatomic potential is evidenced and explained by the capability of some potentials (Tersoff and SW115) to correctly handle the amorphous structure, while other potentials (Stillinger-Weber, EDIP, and Lenosky) lead to the melting of the amorphous. Consequently, the interatomic potentials are classified according to their ability to simulate the solid or the liquid phase epitaxy.

physics.comp-ph↗