相关论文: Identification of simple reaction coordinates from…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
We develop an efficient method to calculate probabilities of large deviations from the typical behavior (rare events) in reaction--diffusion systems. The method is based on a semiclassical treatment of underlying "quantum" Hamiltonian,…
The Jacobian matrix of a dynamic system and its principal minors play a prominent role in the study of qualitative dynamics and bifurcation analysis. When interpreting the Jacobian as an adjacency matrix of an interaction graph, its…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
We present our SageMath package elementary_vectors for computing elementary and sign vectors of real subspaces. In this setting, elementary vectors are support-minimal vectors that can be determined from maximal minors of a real matrix…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
Nuclear reactions govern major aspects of the chemical evolution od galaxies and stars. Analytic study of the reaction rates and reaction probability integrals is attempted here. Exact expressions for the reaction rates and reaction…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes…
Accurate structural analysis is essential to gain physical knowledge and understanding of atomic-scale processes in materials from atomistic simulations. However, traditional analysis methods often reach their limits when applied to…
We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation single- and double-ended transition-state optimization algorithms - the freezing string and Berny optimization…
The relationship between the shape of a molecule and its chemical reactivity is a central tenet in chemistry. However, the influence of the molecular geometry on reactivity can be subtle and result from several opposing effects. Using a…
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to…
Chemical reaction network is an important method for modeling and exploring complex biological processes, bio-chemical interactions and the behavior of different dynamics in system biology. But, formulating such reaction kinetics takes…
The effective equations of motion for a point charged particle taking account of radiation reaction are considered in various space-time dimensions. The divergencies steaming from the pointness of the particle are studied and the effective…
The theory of chemical kinetics form the basis to describe the dynamics of chemical systems. Owing to physical and thermodynamic constraints, chemical reaction systems possess various structures, which can be utilized to characterize…
A central concern of molecular dynamics simulations are the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system, and have generally been calculated using either predefined…
In this work we revisit the classic problem of homogeneous nucleation of a liquid droplet in a supersaturated vapor phase. We consider this at different extents of the driving force, which here is the extent of supersaturation, and…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…