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Coupled molecular-dynamics and finite-element-method simulations for the kinetics of particles subjected to field-mediated forces ; Baroli, Davide ; Bordas, Stéphane et al in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2019), 99(6), A computational approach that couples molecular-dynamics (MD) and the-finite-element-method (FEM) technique is here proposed for the theoretical study of the dynamics of particles subjected to ... [more ▼] A computational approach that couples molecular-dynamics (MD) and the-finite-element-method (FEM) technique is here proposed for the theoretical study of the dynamics of particles subjected to electromechanical forces. The system consists of spherical particles (modeled as micrometric rigid bodies with proper densities and dielectric functions) suspended in a colloidal solution, which flows in a microfluidic channel in the presence of a generic nonuniform variable electric field generated by electrodes. The particles are subjected to external forces (e.g., drag or gravity) which satisfy a particlelike formulation that is typical of the MD approach, along with an electromechanical force that, in turn, requires the three-dimensional self-consistent solutions of correct continuum field equations during the integration of the equations of motion. In the MD-FEM method used in this work, the finite element method is applied to solve the continuum field equations while the MD technique is used for the stepwise explicit integration of the equations of motion. Our work shows the potential of coupled MD-FEM simulations for the study of electromechanical particles and opens a double perspective for implementing (a) MD away from the field of atomistic simulations and (b) the continuum-particle approach to cases where the conventional force evaluation used in MD is not applicable. [less ▲] Detailed reference viewed: 71 (4 UL)Kinetics and thermodynamics of a driven open quantum system Esposito, Massimiliano ; Thingna, Juzar ; in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2017), 96(5), Detailed reference viewed: 200 (5 UL)Elastic properties of the nematic phase in hard ellipsoids of short aspect ratio Heymans, Sven ; Schilling, Tanja in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2017), 96(022708), We present a Monte Carlo simulation study of suspensions of hard ellipsoids of revolution. Based on the spatial fluctuations of the orientational order, we have computed the Frank elastic constants for ... [more ▼] We present a Monte Carlo simulation study of suspensions of hard ellipsoids of revolution. Based on the spatial fluctuations of the orientational order, we have computed the Frank elastic constants for prolate and oblate ellipsoids and compared them to the affine transformation model. The affine transformation model predicts the right order of magnitude of the twist and bend constant but not of the splay constant. In addition, we report the observation of a stable nematic phase at an aspect ratio as low as 2.5. [less ▲] Detailed reference viewed: 124 (7 UL)Stochastic thermodynamics in the strong coupling regime: An unambiguous approach based on coarse graining Strasberg, Philipp ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2017) We consider a classical and possibly driven composite system X ⊗ Y weakly coupled to a Markovian thermal <br /><br /><br /><br /><br /><br />reservoir R so that an unambiguous stochastic thermodynamics ... [more ▼] We consider a classical and possibly driven composite system X ⊗ Y weakly coupled to a Markovian thermal <br /><br /><br /><br /><br /><br />reservoir R so that an unambiguous stochastic thermodynamics ensues for X ⊗ Y . This setup can be equivalently <br /><br /><br /><br /><br /><br />seen as a system X strongly coupled to a non-Markovian reservoir Y ⊗ R. We demonstrate that only in the limit <br /><br /><br /><br /><br /><br />where the dynamics of Y is much faster than X, our unambiguous expressions for thermodynamic quantities, <br /><br /><br /><br /><br /><br />such as heat, entropy, or internal energy, are equivalent to the strong coupling expressions recently obtained in <br /><br /><br /><br /><br /><br />the literature using the Hamiltonian of mean force. By doing so, we also significantly extend these results by <br /><br /><br /><br /><br /><br />formulating them at the level of instantaneous rates and by allowing for time-dependent couplings between X and <br /><br /><br /><br /><br /><br />its environment. Away from the limit where Y evolves much faster than X, previous approaches fail to reproduce <br /><br /><br /><br /><br /><br />the correct results from the original unambiguous formulation, as we illustrate numerically for an underdamped <br /><br /><br /><br /><br /><br />Brownian particle coupled strongly to a non-Markovian reservoir. [less ▲] Detailed reference viewed: 624 (14 UL)Overdamped stochastic thermodynamics with multiple reservoirs ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2016), 94(062148), After establishing stochastic thermodynamics for underdamped Langevin systems in contact with multiple reservoirs, we derive its overdamped limit using timescale separation techniques. The overdamped ... [more ▼] After establishing stochastic thermodynamics for underdamped Langevin systems in contact with multiple reservoirs, we derive its overdamped limit using timescale separation techniques. The overdamped theory is different from the naive theory that one obtains when starting from overdamped Langevin or Fokker-Planck dynamics and only coincides with it in the presence of a single reservoir. The reason is that the coarse-grained fast momentum dynamics reaches a nonequilibrium state, which conducts heat in the presence of multiple reservoirs. The underdamped and overdamped theory are both shown to satisfy fundamental fluctuation theorems. Their predictions for the heat statistics are derived analytically for a Brownian particle on a ring in contact with two reservoirs and subjected to a nonconservative force and are shown to coincide in the long-time limit. [less ▲] Detailed reference viewed: 221 (8 UL)Conservation laws and symmetries in stochastic thermodynamics Polettini, Matteo ; Bulnes Cuetara, Gregory ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2016), 94(052117), Phenomenological nonequilibrium thermodynamics describes how fluxes of conserved quantities, such as matter, energy, and charge, flow from outer reservoirs across a system and how they irreversibly ... [more ▼] Phenomenological nonequilibrium thermodynamics describes how fluxes of conserved quantities, such as matter, energy, and charge, flow from outer reservoirs across a system and how they irreversibly degrade from one form to another. Stochastic thermodynamics is formulated in terms of probability fluxes circulating in the system’s configuration space. The consistency of the two frameworks is granted by the condition of local detailed balance, which specifies the amount of physical quantities exchanged with the reservoirs during single transitions between configurations. We demonstrate that the topology of the configuration space crucially determines the number of independent thermodynamic affinities (forces) that the reservoirs generate across the system and provides a general algorithm that produces the fundamental affinities and their conjugate currents contributing to the total dissipation, based on the interplay between macroscopic conservations laws for the currents and microscopic symmetries of the affinities. [less ▲] Detailed reference viewed: 292 (9 UL)Tightening the uncertainty principle for stochastic currents Polettini, Matteo ; Lazarescu, Alexandre ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2016), 94(052104), We connect two recent advances in the stochastic analysis of nonequilibrium systems: the (loose) uncertainty principle for the currents, which states that statistical errors are bounded by thermodynamic ... [more ▼] We connect two recent advances in the stochastic analysis of nonequilibrium systems: the (loose) uncertainty principle for the currents, which states that statistical errors are bounded by thermodynamic dissipation, and the analysis of thermodynamic consistency of the currents in the light of symmetries. Employing the large deviation techniques presented by Gingrich et al. [Phys. Rev. Lett. 116, 120601 (2016)] and Pietzonka, Barato, and Seifert [Phys. Rev. E 93, 052145 (2016)], we provide a short proof of the loose uncertainty principle, and prove a tighter uncertainty relation for a class of thermodynamically consistent currents J . Our bound involves a measure of partial entropy production, that we interpret as the least amount of entropy that a system sustaining current J can possibly produce, at a given steady state. We provide a complete mathematical discussion of quadratic bounds which allows one to determine which are optimal, and finally we argue that the relationship for the Fano factor of the entropy production rate var σ/mean σ 2 is the most significant realization of the loose bound. We base our analysis both on the formalism of diffusions, and of Markov jump processes in the light of Schnakenberg’s cycle analysis. [less ▲] Detailed reference viewed: 232 (6 UL)Work producing reservoirs: Stochastic thermodynamics with generalized Gibbs ensembles ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2016), 94(020102), We develop a consistent stochastic thermodynamics for environments composed of thermodynamic reservoirs in an external conservative force field, that is, environments described by the generalized or Gibbs ... [more ▼] We develop a consistent stochastic thermodynamics for environments composed of thermodynamic reservoirs in an external conservative force field, that is, environments described by the generalized or Gibbs canonical ensemble. We demonstrate that small systems weakly coupled to such reservoirs exchange both heat and work by verifying a local detailed balance relation for the induced stochastic dynamics. Based on this analysis, we help to rationalize the observation that nonthermal reservoirs can increase the efficiency of thermodynamic heat engines. [less ▲] Detailed reference viewed: 165 (3 UL)Dissipation in small systems: Landau-Zener approach ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2016), 93(062118), We establish a stochastic thermodynamics for a Fermionic level driven by a time-dependent force and interacting with initially thermalized levels playing the role of a reservoir. The driving induces ... [more ▼] We establish a stochastic thermodynamics for a Fermionic level driven by a time-dependent force and interacting with initially thermalized levels playing the role of a reservoir. The driving induces consecutive avoided crossings between system and reservoir levels described within Landau-Zener theory. We derive the resulting system dynamics and thermodynamics and identify energy, work, heat, entropy, and dissipation. Our theory perfectly reproduces the numerically exact quantum work statistics obtained using a two point measurements approach of the total energy and provides an explicit expression for the dissipation in terms of diabatic transitions. [less ▲] Detailed reference viewed: 266 (11 UL)Connectivity percolation in suspensions of attractive square-well spherocylinders Dixit, Mohit ; Meyer, Hugues ; Schilling, Tanja in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2016), (93), 012116 We have studied the connectivity percolation transition in suspensions of attractive square-well spherocylinders by means ofMonte Carlo simulation and connectedness percolation theory. In the 1980s the ... [more ▼] We have studied the connectivity percolation transition in suspensions of attractive square-well spherocylinders by means ofMonte Carlo simulation and connectedness percolation theory. In the 1980s the percolation threshold of slender fibers has been predicted to scale as the fibers’ inverse aspect ratio [Phys. Rev. B 30, 3933 (1984)]. The main finding of our study is that the attractive spherocylinder system reaches this inverse scaling regime at much lower aspect ratios than found in suspensions of hard spherocylinders. We explain this difference by showing that third virial corrections of the pair connectedness functions, which are responsible for the deviation from the scaling regime, are less important for attractive potentials than for hard particles. [less ▲] Detailed reference viewed: 234 (38 UL)Stochastic thermodynamics of hidden pumps Esposito, Massimiliano ; in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2015), 91(5), We show that a reversible pumping mechanism operating between two states of a kinetic network can give rise to Poisson transitions between these two states. An external observer, for whom the pumping ... [more ▼] We show that a reversible pumping mechanism operating between two states of a kinetic network can give rise to Poisson transitions between these two states. An external observer, for whom the pumping mechanism is not accessible, will observe a Markov chain satisfying local detailed balance with an emerging effective force induced by the hidden pump. Due to the reversibility of the pump, the actual entropy production turns out to be lower than the coarse-grained entropy production estimated from the flows and affinities of the resulting Markov chain. Moreover, in presence of a large time scale separation between the fast-pumping dynamics and the slow-network dynamics, a finite current with zero dissipation may be produced. We make use of these general results to build a synthetase-like kinetic scheme able to reversibly produce high free-energy molecules at a finite rate and a rotatory motor achieving 100% efficiency at finite speed. © 2015 American Physical Society. [less ▲] Detailed reference viewed: 154 (7 UL)Exact fluctuation theorem without ensemble quantities Bulnes Cuetara, Gregory ; Esposito, Massimiliano ; in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2014), 1402 Evaluating the entropy production (EP) along a stochastic trajectory requires the knowledge of the system probability distribution, an ensemble quantity notoriously difficult to measure. In this letter ... [more ▼] Evaluating the entropy production (EP) along a stochastic trajectory requires the knowledge of the system probability distribution, an ensemble quantity notoriously difficult to measure. In this letter, we show that the EP of nonautonomous systems in contact with multiple reservoirs can be expressed solely in terms of physical quantities measurable at the single trajectory level with a suitable preparation of the initial condition. As a result, we identify universal energy and particle fluctuation relations valid for any measurement time. We apply our findings to an electronic junction model which may be used to verify our prediction experimentally. [less ▲] Detailed reference viewed: 210 (14 UL)Role of long cycles in excitable dynamics on graphs. Garcia, Guadalupe Clara ; ; et al in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2014), 90(5-1), 052805 Topological cycles in excitable networks can play an important role in maintaining the network activity. When properly activated, cycles act as dynamic pacemakers, sustaining the activity of the whole ... [more ▼] Topological cycles in excitable networks can play an important role in maintaining the network activity. When properly activated, cycles act as dynamic pacemakers, sustaining the activity of the whole network. Most previous research has focused on the contributions of short cycles to network dynamics. Here, we identify the specific cycles that are used during different runs of activation in sparse random graphs, as a basis of characterizing the contribution of cycles of any length. Both simulation and a refined mean-field approach evidence a decrease in the cycle usage when the cycle length increases, reflecting a trade-off between long time for recovery after excitation and low vulnerability to out-of-phase external excitations. In spite of this statistical observation, we find that the successful usage of long cycles, though rare, has important functional consequences for sustaining network activity: The average cycle length is the main feature of the cycle length distribution that affects the average lifetime of activity in the network. Particularly, use of long, rather than short, cycles correlates with higher lifetime, and cutting shortcuts in long cycles tends to increase the average lifetime of the activity. Our findings, thus, emphasize the essential, previously underrated role of long cycles in sustaining network activity. On a more general level, the findings underline the importance of network topology, particularly cycle structure, for self-sustained network dynamics. [less ▲] Detailed reference viewed: 143 (11 UL)Thermodynamics of quantum-jump-conditioned feedback control ; ; et al in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2013), 88(062107), We consider open quantum systems weakly coupled to thermal reservoirs and subjected to quantum feedback operations triggered with or without delay by monitored quantum jumps. We establish a thermodynamic ... [more ▼] We consider open quantum systems weakly coupled to thermal reservoirs and subjected to quantum feedback operations triggered with or without delay by monitored quantum jumps. We establish a thermodynamic description of such systems and analyze how the first and second law of thermodynamics are modified by the feedback. We apply our formalism to study the efficiency of a qubit subjected to a quantum feedback control and operating as a heat pump between two reservoirs. We also demonstrate that quantum feedbacks can be used to stabilize coherences in nonequilibrium stationary states which in some cases may even become pure quantum states. [less ▲] Detailed reference viewed: 249 (6 UL)Entropy-generated power and its efficiency ; ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2013), 88(042105), We propose a simple model for a motor that generates mechanical motion by exploiting an entropic force arising from the topology of the underlying phase space. We show that the generation of mechanical ... [more ▼] We propose a simple model for a motor that generates mechanical motion by exploiting an entropic force arising from the topology of the underlying phase space. We show that the generation of mechanical forces in our system is surprisingly robust to local changes in kinetic and topological parameters. Furthermore, we find that the efficiency at maximum power may show discontinuities. [less ▲] Detailed reference viewed: 177 (6 UL)Diffusion in nonuniform temperature and its geometric analog Polettini, Matteo in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2013), 87 We propose a Langevin equation for systems in an environment with nonuniform temperature. At odds with an older proposal, ours admits a locally Maxwellian steady state, local equipartition holds, and for ... [more ▼] We propose a Langevin equation for systems in an environment with nonuniform temperature. At odds with an older proposal, ours admits a locally Maxwellian steady state, local equipartition holds, and for detailed-balanced (reversible) systems statistical and physical entropies coincide. We describe its thermodynamics, which entails a generalized version of the first law and Clausius's characterization of reversibility. Finally, we show that a Brownian particle constrained into a smooth curve behaves according to our equation, as if experiencing nonuniform temperature. [less ▲] Detailed reference viewed: 154 (5 UL)Finite-time erasing of information stored in fermionic bits Diana, Giovanni ; ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2013) We address the issue of minimizing the heat generated when erasing the information stored in an array of quantum dots in finite time. We identify the fundamental limitations and trade-offs involved in ... [more ▼] We address the issue of minimizing the heat generated when erasing the information stored in an array of quantum dots in finite time. We identify the fundamental limitations and trade-offs involved in this process and analyze how a feedback operation can help improve it [less ▲] Detailed reference viewed: 137 (4 UL)Depletion-interaction effects on the tunneling conductivity of nanorod suspensions ; ; et al in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2013), 88(042140), We study by simulation and theory how the addition of insulating spherical particles affects the conductivity of fluids of conducting rods, modeled by spherocylinders. The electrical connections are ... [more ▼] We study by simulation and theory how the addition of insulating spherical particles affects the conductivity of fluids of conducting rods, modeled by spherocylinders. The electrical connections are implemented as tunneling processes, leading to a more detailed and realistic description than a discontinuous percolation approach. We find that the spheres enhance the tunneling conductivity for a given concentration of rods and that the enhancement increases with rod concentration into the regime where the conducting network is well established. By reformulating the network of rods using a critical path analysis, we quantify the effect of depletion-induced attraction between the rods due to the spheres. Furthermore, we show that our conductivity data are quantitatively reproduced by an effective-medium approximation, which explicitly relates the system tunneling conductance to the structure of the rod-sphere fluid. [less ▲] Detailed reference viewed: 113 (3 UL)Modulated two-level system: Exact work statistics Verley, Gatien ; ; Esposito, Massimiliano in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2013), 88 We consider an open two-level system driven by a piecewise constant periodic field and described by a rate equation with Fermi, Bose, and Arrhenius rates, respectively. We derive an analytical expression ... [more ▼] We consider an open two-level system driven by a piecewise constant periodic field and described by a rate equation with Fermi, Bose, and Arrhenius rates, respectively. We derive an analytical expression for the generating function and large deviation function of the work performed by the field and show that a work fluctuation theorem holds. [less ▲] Detailed reference viewed: 191 (8 UL)Fluctuation theorems and inequalities generalizing the second law of thermodynamics out of equilibrium Verley, Gatien ; in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2012), 86 We present a general framework for systems which are prepared in a nonstationary nonequilibrium state in the absence of any perturbation and which are then further driven through the application of a time ... [more ▼] We present a general framework for systems which are prepared in a nonstationary nonequilibrium state in the absence of any perturbation and which are then further driven through the application of a time-dependent perturbation. By assumption, the evolution of the system must be described by Markovian dynamics. We distinguish two different situations depending on the way the nonequilibrium state is prepared; either it is created by some driving or it results from a relaxation following some initial nonstationary conditions. Our approach is based on a recent generalization of the Hatano-Sasa relation for nonstationary probability distributions. We also investigate whether a form of the second law holds for separate parts of the entropy production and for any nonstationary reference process, a question motivated by the work of M. Esposito et al. [ Phys. Rev. Lett. 104 090601 (2010)]. 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. These detailed fluctuation theorems contain interesting generalizations of the second law of thermodynamics for nonequilibrium systems. [less ▲] Detailed reference viewed: 103 (5 UL) |
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