Related papers: Understanding Reaction Mechanisms from Start to Fi…
We present flow matching for reaction coordinates (FMRC), a novel deep learning algorithm designed to identify optimal reaction coordinates (RC) in biomolecular reversible dynamics. FMRC is based on the mathematical principles of…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
We consider the application of Kramers theory to the microscopic calculation of rates of conformational transitions of macromolecules. The main difficulty in such an approach is to locate the transition state in a huge configuration space.…
Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Contact-based motion planning for manipulation, object exploration or balancing often requires finding sequences of fixed and sliding contacts and planning the transition from one contact in the environment to another. However, most…
A chemical reaction mechanism (CRM) is a sequence of molecular-level events involving bond-breaking/forming processes, generating transient intermediates along the reaction pathway as reactants transform into products. Understanding such…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…
In a molecular communication network, transmitters may encode information in concentration or frequency of signalling molecules. When the signalling molecules reach the receivers, they react, via a set of chemical reactions or a molecular…
In this note we propose a method based on artificial neural network to study the transition between states governed by stochastic processes. In particular, we aim for numerical schemes for the committor function, the central object of…
The path decomposition expansion represents the propagator of the irreversible reaction as a convolution of the first-passage, last-passage and rebinding time probability densities. Using path integral technique, we give an elementary, yet…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These…
We study the qualitative behavior of a model to represent local regulation in a metabolic network. The model is based on the end-product control structure introduced in [A. Goelzer, F. Bekkal Brikci, I. Martin-Verstraete et al., BMC Syst…
The stacking problem is approached by computational mechanics, using an Ising next nearest neighbor model. Computational mechanics allows to treat the stacking arrangement as an information processing system in the light of a symbol…
We present COmpetitive Mechanisms for Efficient Transfer (COMET), a modular world model which leverages reusable, independent mechanisms across different environments. COMET is trained on multiple environments with varying dynamics via a…