Related papers: Verifying Chemical Reaction Network Implementation…
Network inference is a rapidly advancing field, with new methods being proposed on a regular basis. Understanding the advantages and limitations of different network inference methods is key to their effective application in different…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
We use categorical methods to define a new flavor of Petri nets where transitions can only fire a limited number of times, specified by a quantity that we call mana. We do so with chemistry in mind, looking at ways of modelling the behavior…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
With the aim of establishing a framework to efficiently perform the practical application of quantum chemistry simulation on near-term quantum devices, we envision a hybrid quantum--classical framework for leveraging problem decomposition…
Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…
Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…
A key step in the origin of life is the emergence of a primitive metabolism. This requires the formation of a subset of chemical reactions that is both self-sustaining and collectively autocatalytic. A generic theory to study such processes…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…
The Flow Decomposition problem, which asks for the smallest set of weighted paths that "covers" a flow on a DAG, has recently been used as an important computational step in transcript assembly. We prove the problem is in FPT when…
Mass-action kinetics is frequently used in systems biology to model the behaviour of interacting chemical species. Many important dynamical properties are known to hold for such systems if they are weakly reversible and have a low…
We present herein an extension of an algebraic statistical method for inferring biochemical reaction networks from experimental data, proposed recently in [3]. This extension allows us to analyze reaction networks that are not necessarily…
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…
While the field of first-principles explorations into chemical reaction space has been continuously growing, the development of strategies for analyzing resulting chemical reaction networks (CRNs) is lagging behind. A CRN consists of…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…