Related papers: The stochastic evolution of a protocell. The Gille…
A stochastic model for behavioral changes by imitative pair interactions of individuals is developed. `Microscopic' assumptions on the specific form of the imitative processes lead to a stochastic version of the game dynamical equations.…
We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from…
There is great potential to be explored regarding the use of agent-based modelling and simulation as an alternative paradigm to investigate early-stage cancer interactions with the immune system. It does not suffer from some limitations of…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
We study time continuous branching processes with exponentially distributed lifetimes, with two types of cells that proliferate according to binary fission. A range of possible system dynamics are considered, each of which is characterized…
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in various contexts. Here we propose a generative model to capture the dynamics of survival analysis,…
In this paper we analyze the equilibrium properties of a large class of stochastic processes describing the fundamental biological process within bacterial cells, {\em the production process of proteins}. Stochastic models classically used…
We studied the long-term dynamics of evolutionary Swarm Chemistry by extending the simulation length ten-fold compared to earlier work and by developing and using a new automated object harvesting method. Both macroscopic dynamics and…
We present an improvement of the Gillespie Exact Stochastic Simulation Algorithm, which leverages a bitwise representation of variables to perform independent simulations in parallel. We show that the subsequent gain in computational yield…
A machine learning technique is proposed for quantifying uncertainty in power system dynamics with spatiotemporally correlated stochastic forcing. We learn one-dimensional linear partial differential equations for the probability density…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
A new model of crystal growth is presented that describes the phenomena on atomic length and diffusive time scales. The former incorporates elastic and plastic deformation in a natural manner, and the latter enables access to times scales…
Biological living systems in general exhibit complex and diverse dynamics. The latter, in particular, is essential, since diversification increases the odds of survival of an organism while reducing the risk of extinction of the population.…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
A variational lattice model is proposed to define an evolution of sets from a single point (nucleation) following a criterion of "maximization" of the perimeter. At a discrete level, the evolution has a "checkerboard" structure and its…
We consider an exponentially growing population of cells undergoing mutations and ask about the effect of reproductive fluctuations (genetic drift) on its long-term evolution. We combine first step analysis with the stochastic dynamics of a…
The far-from-equilibrium dynamics of glassy systems share important phenomenological traits. A transition is generally observed from a time-homogeneous dynamical regime to an aging regime where physical changes occur intermittently and, on…
Cells achieve size homeostasis by regulating their division timing based on their size, added size, and cell cycle time. Previous research under steady-state conditions demonstrated the robustness of these mechanisms. However, their dynamic…
We investigate the time evolution process of one selected (initially prepared by optical pumping) vibrational molecular state, coupled to all other intra-molecular vibrational states of the same molecule, and also to its environment.…
We study the evolution of interacting groups of agents in two-dimensional geometries. We introduce a microscopic stochastic model that includes floor fields modeling the global flow of individual groups as well as local interaction rules.…