arXiv subjects

Emanuele Penocchio

Publications and source records attributed to Emanuele Penocchio.

12 recordsLinked to original sources

arXiv2026

Dissipation-Reliability Tradeoff for Stochastic CMOS Bits in Series

Physical instantiations of a bit of information are subject to thermal noise that can trigger unintended bit-flip errors. Bits implemented with CMOS technology typically operate in regimes that reliably suppress these errors with a large supply voltage, but miniaturization and circuit design for implantable biomedical devices motivate error suppression via alternative low-voltage strategies. We present and analyze an error-suppression technique that involves coupling multiple CMOS units into chains, introducing a natural error correction arising from inter-unit correlations. Using tensor networks to numerically solve a stochastic master equation for the CMOS chain, we quantify the dissipation-reliability tradeoff across system sizes that would be intractable with conventional sparse-matrix methods. The calculations show that the typical time for bit-flip errors grows exponentially in the square of the supply voltage but subexponentially with the chain length, a scaling we attribute to a spatially localized, domain-wall-mediated flip rather than a coherent one. While a CMOS chain adds stability compared to a single CMOS unit for a fixed low supply voltage, increasing the supply voltage is a lower-dissipation route to equivalent stability.

cond-mat.stat-mech↗

arXiv2026

A Minimal Thermodynamically Consistent Chemical Oscillator

Inspired by the chemical reaction network considered as the smallest system featuring a Hopf bifurcation and its reversible extension, we introduce an even more minimal reaction network that is thermodynamically consistent and exhibits autonomous oscillations under nonequilibrium driving. The model combines three features that are rarely realized simultaneously in compact oscillator networks: a chemically plausible structure restricted to uni- and bimolecular reactions, reversibility of such reactions, and analytical tractability. The system consists of three internal species coupled to two chemostatted species and still undergoes a supercritical Hopf bifurcation when a chemostat concentration is varied. To analyze the dynamics and thermodynamics near the onset of oscillations, we employ the mathematical technique of normal-form reduction, which allows obtaining a controlled irreversible approximation that preserves the leading phase-space structure of the full reversible network while enabling explicit calculations. This framework provides analytical access to the bifurcation structure and the leading contributions governing thermodynamic observables. Within this setting, we use the onset of oscillations to characterize the thermodynamic response of the system. In particular, we offer an analytical description of key thermodynamic quantities such as the semi-grand Gibbs free energy and the non-conservative work rate, which exhibit a kink-like discontinuity at the Hopf bifurcation. We thus provide an analytical description of a phenomenon previously characterized only through numerical simulations of more complex networks.

cond-mat.stat-mech↗

arXiv2026

It Takes Two to Make a Thing Go Right: Boosting Current in Coupled Motors

Catalysis-driven synthetic molecular motors operate in a loose mechanochemical coupling regime, one in which a decomposition of a fuel molecule does not reliably produce a forward step. In that regime, stochastic backward steps can significantly degrade the motor's current, prompting us to ask whether mechanically coupling multiple such motors can boost their averaged current. By simulating rotaxane-based motors with two classes of models--particle-based nonequilibrium molecular dynamics and jump-diffusion models--we show that current boosts are physically achievable. Our observed boosts, which amplify current by single-digit factors, emerge when coupling between motors can increase the activity, speeding up the rate of both forward and backward steps. In doing so, the bias for preferring forward steps actually degrades, but the lost bias can be largely recovered by raising the fuel concentration, demonstrating a general design strategy: amplify activity through coupling and restore bias through stronger driving.

cond-mat.stat-mech↗

arXiv2025

Coarse Graining Photo-Isomerization Reactions: Thermodynamic Consistency and Implications for Molecular Ratchets

We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions interconverting ground-state species. Crucially, the local detailed balance condition, that constrains reaction kinetics to thermodynamics, remains satisfied throughout the coarse-graining procedures. It applies to the effective photo-isomerization reactions just as it does to the elementary vibronic transitions. We then demonstrate that autonomous photo-driven molecular ratchets operate via the same fundamental mechanism as chemically driven ones. Because the local detailed balance remains satisfied, autonomous photo-driven molecular ratchets, like chemically driven ones, operate exclusively through an information ratchet mechanism. This reveals that their design and optimization should prioritize molecular properties governing the information ratchet mechanism, rather than those influencing energetic bias.

cond-mat.stat-mech↗

arXiv2024

Methods and Conversations in (Post)Modern Thermodynamics

Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic and stochastic chemical reaction networks, metastability, martingales, quantum thermodynamics, and foundational issues.

cond-mat.stat-mech↗

arXiv2023

A [3]-catenane non-autonomous molecular motor model: geometric phase, no-pumping theorem, and energy transduction

We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents nontrivial features due to the two interacting small macrocycles, but is simple enough to be treated analytically in limiting regimes. Among the results obtained, we find a mapping into an equivalent [2]-catenane that reveals the implications of the no-pumping theorem stating that to generate net motion of the small macrocycles, both energies and barriers need to change. In the adiabatic limit (slow driving), we fully characterize the motor's dynamics and show that the net motion of the small macrocycles is expressed as a surface integral in parameter space which corrects previous erroneous results. We also analyze the performance of the motor subjected to a step-wise driving protocols in absence and in presence of an applied load. Optimization strategies for generating large currents and maximizing free-energy transduction are proposed. This simple model provides interesting clues into the working principles of non-autonomous molecular motors and their optimization.

cond-mat.stat-mech↗

arXiv2022

Information Thermodynamics for Deterministic Chemical Reaction Networks

Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance. Here, we expand the scope of information thermodynamics to deterministic bipartite chemical reaction networks, namely, composed of two coupled subnetworks sharing species, but not reactions. We do so by introducing a meaningful notion of mutual information between different molecular features, that we express in terms of deterministic concentrations. This allows us to formulate separate second laws for each subnetwork, which account for their energy and information exchanges, in complete analogy with stochastic systems. We then use our framework to investigate the working mechanisms of a model of chemically-driven self-assembly and an experimental light-driven bimolecular motor. We show that both systems are constituted by two coupled subnetworks of chemical reactions. One subnetwork is maintained out of equilibrium by external reservoirs (chemostats or light sources) and powers the other via energy and information flows. In doing so, we clarify that the information flow is precisely the thermodynamic counterpart of an information ratchet mechanism only when no energy flow is involved.

cond-mat.stat-mech↗

arXiv2022

Sample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump

Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively characterizing the behavior of functional molecules, especially in the presence of bimolecular processes. We present the tools for simulating the jump dynamics both in the macroscopic limit and in the small-volume sample where the numbers of reactive molecules are of the order of few units with an inherently stochastic kinetics. The focus is on how an ideal spatial "compartmentalization" may affect the dynamical features of the tagged molecule. Our general approach is applied to a synthetic light-driven supramolecular pump composed of ring-like and axle-like molecules that dynamically assemble and disassemble, originating an average ring-through-axle directed motion under constant irradiation. In such an example, the dynamical feature of interest is the completion time of direct/inverse cycles of tagged rings and axles. We find a surprisingly strong robustness of the average cycle times with respect to the system's size. This is explained in the presence of rate-determining unimolecular processes, which may, therefore, play a crucial role in stabilizing the behavior of small chemical systems against strong fluctuations in the number of molecules.

physics.chem-ph↗

arXiv2021

Nonequilibrium thermodynamics of light-induced reactions

Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviours. Here, we extend the theory to include incoherent light as a source of free energy. We do so by relying on a local equilibrium assumption to derive the chemical potential of photons relative to the system they interact with. This allows us to identify the thermodynamic potential and the thermodynamic forces driving light-reacting chemical systems out of equilibrium. We use this framework to treat two paradigmatic photochemical mechanisms describing light-induced unimolecular reactions -- namely the adiabatic and diabatic mechanisms -- and highlight the different thermodynamics they lead to. Furthermore, using a thermodynamic coarse-graining procedure, we express our findings in terms of commonly measured experimental quantities such as quantum yields.

cond-mat.stat-mech↗

arXiv2021

Nonequilibrium Thermodynamics of Non-Ideal Chemical Reaction Networks

All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a mean-field approach using activity coefficients. Thermodynamic consistency requires that rate equations do not obey to standard mass-action kinetics, but account for the interactions with concentration dependent kinetic constants. Many features of the ideal formulations are recovered. Crucially, the thermodynamic potential and the forces driving non-ideal chemical systems out of equilibrium are identified. Our theory is general and holds for any mean-field expression of the interactions leading to lower bounded free energies.

cond-mat.stat-mech↗

arXiv2019

Thermodynamic Efficiency in Dissipative Chemistry

Chemical processes in closed systems are poorly controllable since they always relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent experiments in dissipative self-assembly also demonstrated that by opening reaction vessels and steering certain concentrations, an ocean of opportunities for artificial synthesis and energy storage emerges. To navigate it, thermodynamic notions of energy, work and dissipation must be established for these open chemical systems. Here, we do so by building upon recent theoretical advances in nonequilibrium statistical physics. As a central outcome, we show how to quantify the efficiency of such chemical operations and lay the foundation for performance analysis of any dissipative chemical process.

physics.chem-ph↗

arXiv2018

Negative differential response in chemical reactions

Reaction currents in chemical networks usually increase when increasing their driving affinities. But far from equilibrium the opposite can also happen. We find that such negative differential response (NDR) occurs in reaction schemes of major biological relevance, namely, substrate inhibition and autocatalysis. We do so by deriving the full counting statistics of two minimal representative models using large deviation methods. We argue that NDR implies the existence of optimal affinities that maximize the robustness against environmental and intrinsic noise at intermediate values of dissipation. An analogous behavior is found in dissipative self-assembly, for which we identify the optimal working conditions set by NDR.

cond-mat.stat-mech↗