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Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
A self-replicating system where the elements belonging to a solution category can replicate themselves by copying their own informations, is considered. The information carried by each element is defined by an element of all the n multiple…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
We investigate the equilibration of an isolated macroscopic quantum system in the sense that deviations from a steady state become unmeasurably small for the overwhelming majority of times within any sufficiently large time interval. The…
We propose quantization relationships which would let us describe and solution problems originated by conflicting or cooperative behaviors among the members of a system from the point of view of quantum mechanical interactions. The quantum…
We consider the numerical solution of coupled volume-surface reaction-diffusion systems having a detailed balance equilibrium. Based on the conservation of mass, an appropriate quadratic entropy functional is identified and an…
The entropy production rate associated with broken time-reversal symmetry provides an essential characterization of nanosystems out of equilibrium, from driven colloidal particles to molecular motors. Limited access to the dynamical states…
We investigate the behaviour of randomly cross-linked (co)polymer blends using a combination of replica theory and large-scale molecular dynamics simulations. In particular, we derive the analogue of the random phase approximation for…
Equilibrium statistical mechanics provides a robust framework for characterizing phase transitions in systems whose microsopic dynamics are time-reversible. Efforts to develop and validate theoretical frameworks for time-irreversible,…
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…
We consider an arbitrary quantum system coupled non perturbatively to a large arbitrary and fully quantum environment. In [G. Ithier and F. Benaych-Georges, Phys. Rev. A 96, 012108 (2017)] the typicality of the dynamics of such an embedded…
The dynamics of phase transitions plays a crucial r\^ole in the so-called interface between high energy particle physics and cosmology. Many of the interesting results generated during the last fifteen years or so rely on simplified…
In this work, we propose a composite pulses scheme by modulating phases to achieve high fidelity population transfer in three-level systems. To circumvent the obstacle that not enough variables are exploited to eliminate the systematic…
We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise…
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…
Although a number of studies have shown that natural and laboratory populations initially well-adapted to their environment can evolve rapidly when conditions suddenly change, the dynamics of rapid adaptation are not well understood. Here a…
We study the nonequilibrium dynamics of a many-body bosonic system on a lattice, subject to driving and dissipation. The time-evolution is described by a master equation, which we treat within a generalized Gutzwiller mean field…
It has been recently observed that the dynamical properties of mass action systems arising from many models of biochemical reaction networks can be derived by considering the corresponding properties of a related generalized mass action…
To describe the nonequilibrium states of a system we introduce a new thermodynamic parameter - the lifetime of a system. The statistical distributions which can be obtained out of the mesoscopic description characterizing the behaviour of a…