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There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…
We propose a supervised machine learning algorithm, decision trees, to analyze molecular dynamics output. The approach aims to identify the predominant geometric features which correlate with trajectories that transition between two…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
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.…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
Using movement primitive libraries is an effective means to enable robots to solve more complex tasks. In order to build these movement libraries, current algorithms require a prior segmentation of the demonstration trajectories. A…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
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…
The expansiveness of compositional phase space is too vast to fully search using current theoretical tools for many emergent problems in condensed matter physics. The reliance on a deep chemical understanding is one method to identify local…
Adaptive cognition requires structured internal models of objects and their relations. Predictive neural networks are often proposed to learn such world models, but how these are instantiated and how they support prediction remain unclear.…
We present a continuation method that entails generating a sequence of transition probability density functions from the prior to the posterior in the context of Bayesian inference for parameter estimation problems. The characterization of…
Sequential recommendation requires the recommender to capture the evolving behavior characteristics from logged user behavior data for accurate recommendations. However, user behavior sequences are viewed as a script with multiple ongoing…
Guidance provides a simple and effective framework for posterior sampling by steering the generation process towards the desired distribution. When modeling discrete data, existing approaches mostly focus on guidance with the first-order…
Improvements in computational and experimental capabilities are rapidly increasing the amount of scientific data that is routinely generated. In applications that are constrained by memory and computational intensity, excessively large…
Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…
Knowledge Distillation is becoming one of the primary trends among neural network compression algorithms to improve the generalization performance of a smaller student model with guidance from a larger teacher model. This momentous rise in…
We briefly review simulation schemes for the investigation of rare transitions and we resume the recently introduced Transition Interface Sampling, a method in which the computation of rate constants is recast into the computation of fluxes…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…