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Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Diverse physical systems are characterized by their response to small perturbations. Near thermodynamic equilibrium, the fluctuation-dissipation theorem provides a powerful theoretical and experimental tool to determine the nature of…
From a purely operational standpoint, the existence of microbes that can grow under extreme conditions, or "extremophiles", leads to the question of how the molecules making up these microbes can maintain both their structure and function.…
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…
We study the glassy dynamics taking place in dense assemblies of athermal active particles that are driven solely by a nonequilibrium self-propulsion mechanism. Active forces are modeled as an Ornstein-Uhlenbeck stochastic process,…
Critical phenomena in non-equilibrium systems have been studied by means of a wide variety of theoretical and experimental approaches. Mode-coupling, renormalization group, complex Lie algebras and diagrammatic techniques are some of the…
We present a consistent thermodynamic theory for the resonant level model in the wide band limit, whose level energy is driven slowly by an external force. The problem of defining 'system' and 'bath' in the strong coupling regime is…
Phase separating systems that are maintained away from thermodynamic equilibrium via molecular processes represent a class of active systems, which we call active emulsions. These systems are driven by external energy input for example…
Self-organization of kinesin-driven, microtubule-based 3D active fluids relies on the collective dynamics of single microtubules. However, the connection between macroscopic fluid flows and microscopic motion of microtubules remains…
How momentum, energy, and magnetic fields are transported in the presence of macroscopic gradients is a fundamental question in plasma physics. Answering this question is especially challenging for weakly collisional, magnetized plasmas,…
Particle motion at the micro-scale is an incessant tug-of-war between thermal fluctuations and applied forces on one side, and the strong resistance exerted by fluid viscosity on the other. Friction is so strong that completely neglecting…
The past twenty years have seen a resurgence of interest in nonequilibrium thermodynamics, thanks to advances in the theory of stochastic processes and in their thermodynamic interpretation. Fluctuation theorems provide fundamental…
Self-propelled particles include both self-phoretic synthetic colloids and various micro-organisms. By continually consuming energy, they bypass the laws of equilibrium thermodynamics. These laws enforce the Boltzmann distribution in…
First steps towards developing a new perturbation theory for molecular liquids are taken. By choosing a new form of splitting the site-site potential functions between molecules, we will get a set of atomic fluids as the reference system…
A longstanding challenge in nonequilibrium thermodynamics is to predict the emergence of self-organized behaviours and functionalities typical of living matter. Despite the progress with classical complex systems, it remains far from…
Mechanically driven glassy systems and complex fluids exhibit a wealth of rheological behaviors that call for theoretical understanding and predictive modeling. A distinct feature of these nonequilibrium systems is their dynamically…
A simple model for the nonlinear collective transport of interacting particles in a random medium with strong disorder is introduced and analyzed. A finite threshold for the driving force divides the behavior into two regimes characterized…
We derive a new formulation to calculate the excess chemical potential of a fraction of $N_1$ particles interacting with $N_2$ particles of a different species. The excess chemical potential is calculated numerically from first principles…
Far-from-equilibrium phenomena are critical to all natural and engineered systems, and essential to biological processes responsible for life. For over a century and a half, since Carnot, Clausius, Maxwell, Boltzmann, and Gibbs, among many…
Improved understanding of molecular systems has only emphasised the sophistication of networks within the cell. Simultaneously, the advance of nucleic acid nanotechnology, a platform within which reactions can be exquisitely controlled, has…