相关论文: Hamiltonian model for multidimensional epistasis

We derive an elegant solution for a two-level system evolving adiabatically under the influence of a driving field with a time-dependent phase, which includes open system effects such as dephasing and spontaneous emission. This solution,…

The East model has a dynamical phase transition between an active (fluid) and inactive (glass) state. We show that this phase transition generalizes to "softened" systems where constraint violations are allowed with small but finite…

Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…

Nonreciprocal interactions in many-body systems lead to time-dependent states, commonly observed in biological, chemical, and ecological systems. The stability of these states in the thermodynamic limit and the critical behavior of the…

We demonstrate that absorbing phase transitions in one dimension may be induced by the dynamics of a single site. As an example we consider a one-dimensional model of diffusing particles, where a single site at the boundary evolves…

A natural example of evolution can be described by a time-dependent two degrees-of-freedom Hamiltonian. We choose the case where initially the Hamiltonian derives from a general cubic potential, the linearised system has frequencies 1 and…

In a recent paper we have introduced several possible inequivalent descriptions of the dynamics and of the transition probabilities of a quantum system when its Hamiltonian is not self-adjoint. Our analysis was carried out in finite…

Defining the extent of epistasis - the non-independence of the effects of mutations - is essential for understanding the relationship of genotype, phenotype, and fitness in biological systems. The applications cover many areas of biological…

Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a…

This paper studies the emergence of multi-stability and hysteresis in those systems that arise, under positive feedback, starting from monotone systems with well-defined steady-state responses. Such feedback configurations appear routinely…

We provide a complete and rigorous description of phase transitions for kinetic models of self-propelled particles interacting through alignment. These models exhibit a competition between alignment and noise. Both the alignment frequency…

Gravitational and electromagnetic interactions are Hamiltonian systems with forces between pairs of particles. We propose an alternative: Hamiltonian dynamics with triplet interactions between point particles. Our system has a potential…

The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving…

The crossing of a transition state in a multidimensional reactive system is mediated by invariant geometric objects in phase space: An invariant hyper-sphere that represents the transition state itself and invariant hyper-cylinders that…

In this study we consider the Hamiltonian approach for the construction of a map for a system with nonlinear resonant interaction, including phase trapping and phase bunching effects. We derive basic equations for a single resonant…

Living systems evolve one mutation at a time, but a single mutation can alter the effect of subsequent mutations. The underlying mechanistic determinants of such epistasis are unclear. Here, we demonstrate that the physical dynamics of a…

A simple model of wave-particle interaction is studied in its self-consistent form, that is, where the particles are allowed to feedback on the waves dynamics. We focus on the configurations of locked solutions (equilibria) and how the…

Two known distinct examples of one-dimensional systems which are known to exhibit a phase transition are critically examined: (A) a lattice model with harmonic nearest-neighbor elastic interactions and an on-site Morse potential, and (B)…

Clonal interference, competition between multiple co-occurring beneficial mutations, has a major role in adaptation of asexual populations. We provide a simple individual based stochastic model of clonal interference taking into account a…

Equilibrium phase transitions are associated with rearrangements of minima of a (Lagrangian) potential. Treatment of non-equilibrium systems requires doubling of degrees of freedom, which may be often interpreted as a transition from the…