Coupled molecular-dynamics and finite-element-method simulations for the kinetics of particles subjected to field-mediated forces

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 ▲]

Elastic properties of the nematic phase in hard ellipsoids of short aspect ratio

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 ▲]

Overdamped stochastic thermodynamics with multiple reservoirs

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 ▲]

Tightening the uncertainty principle for stochastic currents

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 ▲]

Dissipation in small systems: Landau-Zener approach

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 ▲]

Stochastic thermodynamics of hidden pumps

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 ▲]

Role of long cycles in excitable dynamics on graphs.

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 ▲]

Entropy-generated power and its efficiency

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 ▲]

Finite-time erasing of information stored in fermionic bits

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 ▲]

Modulated two-level system: Exact work statistics

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 ▲]