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Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
Polynomial dynamical systems are widely used to model and study real phenomena. In biochemistry, they are the preferred choice for modelling the concentration of chemical species in reaction networks with mass-action kinetics. These systems…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
We propose a fast method for the calculation of short-range interactions in molecular dynamics simulations. The so-called random-batch list method is a stochastic version of the classical neighbor-list method to avoid the construction of a…
Predicting protein interactions is one of the more interesting challenges of the post-genomic era. Many algorithms address this problem as a binary classification problem: given two proteins represented as two vectors of features, predict…
This paper addresses the problem of model reduction for dynamical system models that describe biochemical reaction networks. Inherent in such models are properties such as stability, positivity and network structure. Ideally these…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the…
The Paxos distributed consensus algorithm is a challenging case-study for standard, vector-based model checking techniques. Due to asynchronous communication, exhaustive analysis may generate very large state spaces already for small model…
Support vector machine (SVM) is one of the most popular classification algorithms in the machine learning literature. We demonstrate that SVM can be used to balance covariates and estimate average causal effects under the unconfoundedness…
We introduce a fully generalized quiescent chemical reactor system in arbitrary space $\vdim =1,2$ or 3, with $n\in\mathbb{N}$ chemical constituents $\alpha_{i}$, where the character of the numerical solution is strongly determined by the…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
A method to generate reactive trajectories, namely equilibrium trajectories leaving a metastable state and ending in another one is proposed. The algorithm is based on simulating in parallel many copies of the system, and selecting the…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…
Motivated by problems from Chemical Reaction Network Theory, we investigate whether steady state ideals of reversible reaction networks are generated by binomials. We take an algebraic approach considering, besides concentrations of…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
With the increasing interest in robotic synthesis in the context of organic chemistry, the automated extraction of chemical procedures from literature is critical. However, this task remains challenging due to the inherent ambiguity of…