相关论文: Controlling the occurrence sequence of reaction mo…

An intriguing interpretation of the time-evolution of dynamical systems is to view it as a computation that transforms an initial state to a final one. This paradigm has been explored in discrete systems such as cellular automata models,…

Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…

Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…

Finite-dimensional dissipative dynamical systems with multiple time-scales are obtained when modeling chemical reaction kinetics with ordinary differential equations. Such stiff systems are computationally hard to solve and therefore,…

Limit cycles are self-sustained, closed trajectories in phase space representing (un)-stable, periodic behavior in nonlinear dynamical systems. They underpin diverse natural phenomena, from neuronal firing patterns to engineering…

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…

Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…

Simulation models of critical systems often have parameters that need to be calibrated using observed data. For expensive simulation models, calibration is done using an emulator of the simulation model built on simulation output at…

Parametrically modulated optomechanical systems have been recently proposed as a simple and efficient setting for the quantum control of a micromechanical oscillator: relevant possibilities include the generation of squeezing in the…

Spontaneous rhythmic oscillations are widely observed in various real-world systems. In particular, biological rhythms, which typically arise via synchronization of many self-oscillatory cells, often play important functional roles in…

We developed a powerful computational approach to elaborate on onset mechanisms of deterministic chaos due to complex homoclinic bifurcations in diverse systems. Its core is the reduction of phase space dynamics to symbolic binary…

Birhythmicity arises in several physical, biological and chemical systems. Although, many control schemes are proposed for various forms of multistability, only a few exist for controlling birhythmicity. In this paper we investigate the…

Oscillatory chemical reactions are functional components in a variety of biological contexts. In chemistry, the construction and identification of even rudimentary oscillators remain elusive and lack a general framework. Using…

One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of…

The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints such as limited computational resources. As time progresses,…

Synthetic biology is an interdisciplinary field aiming to design biochemical systems with desired behaviors. To this end, molecular controllers have been developed which, when embedded into a pre-existing ambient biochemical network,…

Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…

The dynamics of one species chemical kinetics is studied. Chemical reactions are modelled by means of continuous time Markov processes whose probability distribution obeys a suitable master equation. A large deviation theory is formally…

This paper presents an optimization approach for generating custom manipulator configurations using a proposed unconventional modular library. An end-to-end solution is presented in which the resulting optimal models of the modular…

Multirhythmicity, a form of multistability, in an oscillator is an intriguing phenomenon found across many branches of science. From an application point of view, while the multirhythmicity is sometimes desirable as it presents us with many…