Related papers: Biological implications of dynamical phases in non…
In this paper we investigate equilibria of continuous differential equation models of network dynamics. The motivation comes from gene regulatory networks where each directed edge represents either down- or up-regulation, and is modeled by…
An analytical characterization of thermodynamically rational agent behaviour is obtained for a simple, yet non--trivial example of a ``Maxwell's demon" operating with partial information. Our results provide the first fully transparent…
We show that the dynamics of simple disordered models, like the directed Trap Model and the Random Energy Model, takes place at a coexistence point between active and inactive dynamical phases. We relate the presence of a dynamic phase…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
A demonic being, introduced by Maxwell, to miraculously create thermal non-equilibrium and violate the Second law of thermodynamics, has been among the most intriguing and elusive wishful concepts for over 150 years. Maxwell and his…
Life is characterized by a myriad of complex dynamic processes allowing organisms to grow, reproduce, and evolve. Physical approaches for describing systems out of thermodynamic equilibrium have been increasingly applied to living systems,…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they…
Our work analyzes the potential of ion traps for the experimental simulation of non-equilibrium phase transitions observed in certain spin-chain models which can be mapped to free-fermion systems. In order to make the dynamics more…
We study the dynamics of many charges interacting with the Maxwell field. The particles are modeled by means of non-negative distribution functions $f^+$ and $f^-$ representing two species of charged matter with positive and negative…
Key features of biological activity can often be captured by transitions between a finite number of semi-stable states that correspond to behaviors or decisions. We present here a broad class of dynamical systems that are ideal for modeling…
Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are…
The dynamic range measures the capacity of a system to discriminate the intensity of an external stimulus. Such an ability is fundamental for living beings to survive: to leverage resources and to avoid danger. Consequently, the larger is…
As a first step toward realizing a dynamical system that evolves while spontaneously determining its own rule for time evolution, function dynamics (FD) is analyzed. FD consists of a functional equation with a self-referential term, given…
A thermodynamic phase transition denotes a drastic change of state of a physical system due to a continuous change of thermodynamic variables, as for instance pressure and temperature. The classical van der Waals equation of state is the…
Control schemes for dynamical systems typically involve stabilizing unstable periodic orbits. In this paper we introduce a new paradigm of control that involves `trapping' the dynamics arbitrarily close to any desired trajectory. This is…
We propose a new way of looking at the quantum Maxwell's demon problem in terms of conditional action. A "conditional action" on a system is a unitary time evolution, selected according to the result of a previous measurement, which can…
Dinuclear systems that occur in the post-saddle to scission stage in nuclear fission process are special transient formations. The diabatic evolution at this stage is studied using the methods of non-equilibrium thermodynamics. A novel…