Related papers: Reaction Coordinates for Conformational Transition…

A classical coulombic correlation functional in one-loop (1L) and local-density-approximation (LDA) is derived for electrolyte solutions, starting from a first-principles many-body partition function. The 1L-LDA functional captures…

Researchers in the behavioral and social sciences use linear discriminant analysis (LDA) for predictions of group membership (classification) and for identifying the variables most relevant to group separation among a set of continuous…

Large Language Models (LLMs) demonstrate exceptional performance across diverse tasks by leveraging pre-trained (i.e., parametric) and external (i.e., contextual) knowledge. While substantial efforts have been made to enhance the…

Adaptive multilevel splitting algorithms have been introduced rather recently for estimating tail distributions in a fast and efficient way. In particular, they can be used for computing the so-called reactive trajectories corresponding to…

Interpretable reaction coordinates are essential for understanding rare conformational transitions in molecular dynamics. The Atomistic Mechanism Of Rare Events in Molecular Dynamics (AMORE-MD) framework enhances interpretability of…

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…

Trajectory mutual information is frequently used to quantify information transfer in biochemical systems. Tractable solutions of the trajectory mutual information can be obtained via the widely used Linear-Noise Approximation (LNA) using…

Suggestion of modifications of finite-dimensional QED models are proposed for interpreting chemical reactions in terms of artificial atoms and molecules on quantum dots placed in optical cavities. Moving both photons and atoms is possible…

Molecule- and particle-based simulations provide the tools to test, in microscopic detail, the validity of classical nucleation theory. In this endeavour, determining nucleation mechanisms and rates for phase separation requires an…

We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective…

Effectively integrating molecular graph structures with Large Language Models (LLMs) is a key challenge in drug discovery. Most existing multi-modal alignment methods typically process these structures by fine-tuning the LLM or adding a…

We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…

Large language models (LLMs) have achieved substantial advances in logical reasoning, yet they continue to lag behind human-level performance. In-context learning provides a viable solution that boosts the model's performance via prompting…

A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…

Large Language Models (LLMs) have significantly advanced molecular discovery, but existing multimodal molecular architectures fundamentally rely on autoregressive (AR) backbones. This strict left-to-right inductive bias is sub-optimal for…

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…

Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…

Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…

In this work we introduce an Autoencoder for molecular conformations. Our proposed model converts the discrete spatial arrangements of atoms in a given molecular graph (conformation) into and from a continuous fixed-sized latent…

General-purpose large language models (LLMs) are increasingly deployed in verticals such as telecommunications, where adaptation is hindered by scarce, low-information-density corpora and tight mobile/edge constraints. We propose Data…