Related papers: Computing reaction rates in bio-molecular systems …
We study a system of self-propelled disks that perform run-and-tumble motion, where particles can adopt more than one internal state. One of those internal states can be transmitted to another particle if the particle carrying this state…
We study the effects of fast spatial movement of molecules on the dynamics of chemical species in a spatially heterogeneous chemical reaction network using a compartment model. The reaction networks we consider are either single- or…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
Our knowledge about the "cold" Universe often relies on molecular spectra. A general property of such spectra is that the energy level populations are rarely at local thermodynamic equilibrium. Solving the radiative transfer thus requires…
We study the decay process for the reaction-diffusion process of three species on the small-world network. The decay process is manipulated from the deterministic rate equation of three species in the reaction-diffusion system. The particle…
A general framework for the simulation of reaction-diffusion systems with probabilistic cellular automata is presented. The basic reaction probabilities of the chemical model translate directly into the transition rules of the automaton,…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…
Reaction coordinates (RCs) are low-dimensional representations of complex dynamical systems that capture their long-term dynamics. In this work, we focus on the criteria of lumpability and decomposability, previously established for…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
Biochemical reaction systems may be viewed as discrete event processes characterized by a number of states and state transitions. These systems may be modeled as state transition systems with transitions representing individual reaction…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
Reaction-diffusion models are common in many areas of statistical physics, where they describe the late-time dynamics of chemical reactions. Using a Bose gas representation, which maps the real-time dynamics of the reactants to the…
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…
A non-conventional approach to calculating reactions in quantum mechanics is presented. Reaction observables are obtained with bound state calculation techniques. The accuracy of the method to calculate few-nucleon response functions is…
The power-law TST reaction rate coefficient for an elementary bimolecular reaction is studied when the reaction takes place in a nonequilibrium system with power-law distributions. We derive a generalized TST rate coefficient, which not…
The relationship between components of biochemical network and the resulting dynamics of the overall system is a key focus of computational biology. However, as these networks and resulting mathematical models are inherently complex and…