Systems with inheritance: dynamics of distributions with conservation of support, natural selection and finite-dimensional asymptotics

If we find a representation of an infinite-dimensional dynamical system as a nonlinear kinetic system with {\it conservation of supports} of distributions, then (after some additional technical steps) we can state that the asymptotics is finite-dimensional. This conservation of support has a {\it quasi-biological interpretation, inheritance} (if a gene was not presented initially in a isolated population without mutations, then it cannot appear at later time). These quasi-biological models can describe various physical, chemical, and, of course, biological systems. The finite-dimensional asymptotic demonstrates effects of {\it ``natural" selection}. The estimations of asymptotic dimension are presented. The support of an individual limit distribution is almost always small. But the union of such supports can be the whole space even for one solution. Possible are such situations: a solution is a finite set of narrow peaks getting in time more and more narrow, moving slower and slower. It is possible that these peaks do not tend to fixed positions, rather they continue moving, and the path covered tends to infinity at $t \rightarrow \infty$. The {\it drift equations} for peaks motion are obtained. Various types of stability are studied. In example, models of cell division self-synchronization are studied. The appropriate construction of notion of typicalness in infinite-dimensional spaces is discussed, and the ``completely thin" sets are introduced

Selection theorem for systems with inheritance

The problem of finite-dimensional asymptotics of infinite-dimensional dynamic systems is studied. A non-linear kinetic system with conservation of supports for distributions has generically finite-dimensional asymptotics. Such systems are apparent in many areas of biology, physics (the theory of parametric wave interaction), chemistry and economics. This conservation of support has a biological interpretation: inheritance. The finite-dimensional asymptotics demonstrates effects of "natural" selection. Estimations of the asymptotic dimension are presented. After some initial time, solution of a kinetic equation with conservation of support becomes a finite set of narrow peaks that become increasingly narrow over time and move increasingly slowly. It is possible that these peaks do not tend to fixed positions, and the path covered tends to infinity as t goes to infinity. The drift equations for peak motion are obtained. Various types of distribution stability are studied: internal stability (stability with respect to perturbations that do not extend the support), external stability or uninvadability (stability with respect to strongly small perturbations that extend the support), and stable realizability (stability with respect to small shifts and extensions of the density peaks). Models of self-synchronization of cell division are studied, as an example of selection in systems with additional symmetry. Appropriate construction of the notion of typicalness in infinite-dimensional space is discussed, and the notion of "completely thin" sets is introduced. Key words: Dynamics; Attractor; Evolution; Entropy; Natural selectionComment: 46 pages, the final journal versio

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page

One-dimensional hydrodynamic model generating a turbulent cascade

As a minimal mathematical model generating cascade analogous to that of the Navier-Stokes turbulence in the inertial range, we propose a one-dimensional partial-differential-equation model that conserves the integral of the squared vorticity analogue (enstrophy) in the inviscid case. With a large-scale forcing and small viscosity, we find numerically that the model exhibits the enstrophy cascade, the broad energy spectrum with a sizable correction to the dimensional-analysis prediction, peculiar intermittency and self-similarity in the dynamical system structure.Comment: 5 pages, 4 figure

Conditional ergodicity in infinite dimension

The goal of this paper is to develop a general method to establish conditional ergodicity of infinite-dimensional Markov chains. Given a Markov chain in a product space, we aim to understand the ergodic properties of its conditional distributions given one of the components. Such questions play a fundamental role in the ergodic theory of nonlinear filters. In the setting of Harris chains, conditional ergodicity has been established under general nondegeneracy assumptions. Unfortunately, Markov chains in infinite-dimensional state spaces are rarely amenable to the classical theory of Harris chains due to the singularity of their transition probabilities, while topological and functional methods that have been developed in the ergodic theory of infinite-dimensional Markov chains are not well suited to the investigation of conditional distributions. We must therefore develop new measure-theoretic tools in the ergodic theory of Markov chains that enable the investigation of conditional ergodicity for infinite dimensional or weak-* ergodic processes. To this end, we first develop local counterparts of zero-two laws that arise in the theory of Harris chains. These results give rise to ergodic theorems for Markov chains that admit asymptotic couplings or that are locally mixing in the sense of H. F\"{o}llmer, and to a non-Markovian ergodic theorem for stationary absolutely regular sequences. We proceed to show that local ergodicity is inherited by conditioning on a nondegenerate observation process. This is used to prove stability and unique ergodicity of the nonlinear filter. Finally, we show that our abstract results can be applied to infinite-dimensional Markov processes that arise in several settings, including dissipative stochastic partial differential equations, stochastic spin systems and stochastic differential delay equations.Comment: Published in at http://dx.doi.org/10.1214/13-AOP879 the Annals of Probability (http://www.imstat.org/aop/) by the Institute of Mathematical Statistics (http://www.imstat.org