Related papers: Simulation Of Reaction Systems By The Strictly Min…
Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the…
This paper proposes a novel methodology for addressing the simulation-reality gap for multi-robot swarm systems. Rather than immediately try to shrink or `bridge the gap' anytime a real-world experiment failed that worked in simulation, we…
Properties of reaction zones resulting from A+B -> C type reaction-diffusion processes are investigated by analytical and numerical methods. The reagents A and B are separated initially and, in addition, there is an initial macroscopic…
Trying to identify the entropy production within a cell has been part of debates and studies in the last century. First the idea was to make a resemblance of a cell with a Carnot engine, which is the most thermodynamically perfect machine.…
Feedback optimization algorithms compute inputs to a system using real-time output measurements, which helps mitigate the effects of disturbances. However, existing work often models both system dynamics and computations in either discrete…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these…
Reaction-diffusion models have been used over decades to study biological systems. In this context, evolution equations for probability distribution functions and the associated stochastic differential equations have nowadays become…
This paper presents an investigation of the notion of reaction time in some synchronous systems. A state-based description of such systems is given, and the reaction time of such systems under some classic composition primitives is studied.…
Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…
Many mathematical models for biological phenomena, such as the spread of diseases, are based on reaction-diffusion equations for densities of interacting cell populations. We present a consistent derivation of reaction-diffusion equations…
Multi-component quantum systems in strong interaction with their environment are receiving increasing attention due to their importance in a variety of contexts, ranging from solid state quantum information processing to the quantum…
Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on…
This is a short note with some (very elementary) remarks concerning realization theory and the choice of inputs for identifying systems. Its goal is to bring some of these facts to the attention of the systems biology community.
Understanding realistic complex systems requires confronting significant conceptual, theoretical and experimental limitations rooted in the persistence of views that originated in the mechanics of simple moving bodies. We define the…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy…
Q-conditional symmetries (nonclassical symmetries) for a general class of two-component reaction-diffusion systems with constant diffusivities are studied. Using the recently introduced notion of Q-conditional symmetries of the first type…
The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in…
The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…