Related papers: Identification of simple reaction coordinates from…
We use the formalism of Geometrothermodynamics to describe chemical reactions in the context of equilibrium thermodynamics. Any chemical reaction in a closed system is shown to be described by a geodesic in a $2-$dimensional manifold that…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet,…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
We propose a method to study the thermodynamic behaviour of small systems beyond the weak coupling and Markovian approximation, which is different in spirit from conventional approaches. The idea is to redefine the system and environment…
We propose a direct optimization framework for learning reduced and sparse chemical reaction networks (CRNs) from time-series trajectory data. In contrast to widely used indirect methods-such as those based on sparse identification of…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
A modification of the Adaptive Biasing Force method is introduced, in which the free energy is approximated by a sum of tensor products of one-dimensional functions. This enables to handle a larger number of reaction coordinates than the…
The choice of vibrational coordinates is crucial for the accuracy, efficiency, and interpretability of molecular vibrational dynamics and spectra calculations. We explore the recently proposed normalizing-flow vibrational coordinates, which…
A major challenge in nonadiabatic molecular dynamics is to automatically and objectively identify the key reaction coordinates that drive molecules toward distinct excited-state decay channels. Traditional manual analyses are inefficient…
Moment dynamics in stochastic chemical kinetics often involve an infinite chain of coupled equations, where lower-order moments depend on higher-order ones, making them analytically intractable. Moment bounding via semidefinite programming…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
A wide variety of real life complex networks are prohibitively large for modeling, analysis and control. Understanding the structure and dynamics of such networks entails creating a smaller representative network that preserves its relevant…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
In this work, we introduce a flow based machine learning approach, called reaction coordinate (RC) flow, for discovery of low-dimensional kinetic models of molecular systems. The RC flow utilizes a normalizing flow to design the coordinate…
The reaction-diffusion master equation (RDME) is commonly used to model processes where both the spatial and stochastic nature of chemical reactions need to be considered. We show that the RDME in many cases is inconsistent with a…