arXiv subjects

Martin Nilsson Jacobi

Publications and source records attributed to Martin Nilsson Jacobi.

23 records · Page 2Linked to original sources

arXiv2007

Using force covariance to derive effective stochastic interactions in dissipative particle dynamics

There exist methods for determining effective conservative interactions in coarse grained particle based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but in the model system we study do not correctly represent transport properties. In this article we suggest the use of force covariance to determine the full functional form of dissipative and stochastic interactions. We show that a combination of the radial distribution function and a force covariance function can be used to determine all interactions in dissipative particle dynamics. Furthermore we use the method to test if the effective interactions in dissipative particle dynamics (DPD) can be adjusted to produce a force covariance consistent with a projection of a microscopic Lennard-Jones simulation. The results indicate that the DPD ansatz may not be consistent with the underlying microscopic dynamics. We discuss how this result relates to theoretical studies reported in the literature.

cond-mat.soft↗

arXiv2007

A method for inferring hierarchical dynamics in stochastic processes

Complex systems may often be characterized by their hierarchical dynamics. In this paper do we present a method and an operational algorithm that automatically infer this property in a broad range of systems; discrete stochastic processes. The main idea is to systematically explore the set of projections from the state space of a process to smaller state spaces, and to determine which of the projections that impose Markovian dynamics on the coarser level. These projections, which we call Markov projections, then constitute the hierarchical dynamics of the system. The algorithm operates on time series or other statistics, so a priori knowledge of the intrinsic workings of a system is not required in order to determine its hierarchical dynamics. We illustrate the method by applying it to two simple processes; a finite state automaton and an iterated map.

nlin.AO↗

arXiv2006

Quotient Manifold Projections and Hierarchical Dynamics

In this paper we explore the mathematical structure of hierarchical organization in smooth dynamical systems. We start by making precise what we mean by a level in a hierarchy, and how the higher le vels need to respect the dynamics on the lower levels. We derive a mathematical construction for identifying distinct levels in a hierarchical dynamics. The construction is expressed through a quotient manifold of the phase space and a Lie group that fulfills certain requirement with respect to the flow. We show that projections up to higher levels can be related to symmetries of the dynamical system. We also discuss how the quotient manifold projections relate to invariant manifolds, invariants of the motion, and Noether's theorem.

math-ph↗

arXiv2005

Quasispecies and recombination

Recombination is introduced into Eigen's theory of quasispecies evolution. Comparing numerical simulations of the rate equations in the non-recombining and recombining cases show that recombination has a strong effect on the error threshold and, for a wide range of mutation rates, gives rise to two stable fixed points in the dynamics. This bi-stability results in the existence of two error thresholds. We prove that, under some assumptions on the fitness landscape but for general crossover probability, a fixed point localized about the sequence with superior fitness is globally stable for low mutation rates.

q-bio.PE↗

arXiv2005

Quasi-Species and Aggregate Dynamics

At an early stage in pre-biotic evolution, groups of replicating molecules must coordinate their reproduction to form aggregated units of selection. Mechanisms that enable this to occur are currently not well understood. In this paper we introduce a deterministic model of primitive replicating aggregates, proto-organisms, that host populations of replicating information carrying molecules. Some of the molecules promote the reproduction of the proto-organism at the cost of their individual replication rate. A situation resembling that of group selection arises. We derive and analytically solve a partial differential equation that describes the system. We find that the relative prevalence of fast and slow replicators is determined by the relative strength of selection at the aggregate level to the selection strength at the molecular level. The analysis is concluded by a preliminary treatment of finite population size effects.

q-bio.PE↗