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We propose a dynamic mechanism of a molecular machine for energy conversion, by considering a simple model describing the dynamics of two components, the head and the chain. After injection of energy to the head region, the energy is stored…
Thermodynamic selection is an indirect competition between agents feeding on the same energy resource and obeying the laws of thermodynamics. We examine scenarios of this selection, where the agent is modeled as a heat-engine coupled to two…
Cooperation is usually represented as a Prisoner's Dilemma game. Although individual self-interest may not favour cooperation, cooperation can evolve if, for example, players interact multiple times adjusting their behaviour accordingly to…
We consider the problem of efficiently performing simulation and inference for stochastic kinetic models. Whilst it is possible to work directly with the resulting Markov jump process, computational cost can be prohibitive for networks of…
The classical theory of chemical reactions can be understood in terms of diffusive barrier crossing, where the rate of a reaction is determined by the inverse of the mean first passage time (FPT) to cross a free energy barrier. Whenever a…
The widespread deployment of Machine Learning systems everywhere raises challenges, such as dealing with interactions or competition between multiple learners. In that goal, we study multi-agent sequential decision-making by considering…
In many stochastic simulations of biochemical reaction networks, it is desirable to ``coarse-grain'' the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed,…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by periodically updating the system with a Metropolis criteria, where the integration step is…
We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Reactive synthesis is a framework for modeling and automatically synthesizing strategies in robotics, typically through computing a \emph{winning} strategy in a 2-player game between the robot and the environment. Winning strategies,…
We study environments in which agents are randomly matched to play a Prisoner's Dilemma, and each player observes a few of the partner's past actions against previous opponents. We depart from the existing related literature by allowing a…
We consider several multiscale-in-time kinetic Monte Carlo models, in which some variables evolve on a fast time scale, while the others evolve on a slow time scale. In the first two models we consider, a particle evolves in a…
A co-polycondensation reaction is discussed analytically and by Monte-Carlo simulations where two reactive units compete for reactions with an alternating third reactive unit, whereby irreversible reactions replace bonds which are able to…
Natural behavior consists of dynamics that are complex and unpredictable, especially when trying to predict many steps into the future. While some success has been found in building representations of behavior under constrained or…
We consider decision problems under uncertainty where the options available to a decision maker and the resulting outcome are related through a causal mechanism which is unknown to the decision maker. We ask how a decision maker can learn…
Roulette-wheel selection is a frequently used method in genetic and evolutionary algorithms or in modeling of complex networks. Existing routines select one of N individuals using search algorithms of O(N) or O(log(N)) complexity. We…
We apply tools from real algebraic geometry to the problem of multistationarity of chemical reaction networks. A particular focus is on the case of reaction networks whose steady states admit a monomial parametrization. For such systems we…
To ensure that a robot is able to accomplish an extensive range of tasks, it is necessary to achieve a flexible combination of multiple behaviors. This is because the design of task motions suited to each situation would become increasingly…