相关论文: How to Differentiate Collective Variables in Free …

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

In modern day simulations of many-body systems much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CV) or reaction coordinates. A vast array of…

In recent years, deep generative models for graphs have been used to generate new molecules. These models have produced good results, leading to several proposals in the literature. However, these models may have troubles learning some of…

Neural language models can be successfully trained on source code, leading to applications such as code completion. However, their versatile autoregressive self-supervision objective overlooks important global sequence-level features that…

In this paper, we present a new R package COREclust dedicated to the detection of representative variables in high dimensional spaces with a potentially limited number of observations. Variable sets detection is based on an original graph…

Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…

Conditional Variational AutoEncoder (CVAE) effectively increases the diversity and informativeness of responses in open-ended dialogue generation tasks through enriching the context vector with sampled latent variables. However, due to the…

In an era of widespread influence of Natural Language Processing (NLP), there have been multiple research efforts to supplant traditional manual coding techniques with automated systems capable of generating solutions autonomously. With…

Instantaneous quantum computing is a sub-universal quantum complexity class, whose circuits have proven to be hard to simulate classically in the Discrete-Variable (DV) realm. We extend this proof to the Continuous-Variable (CV) domain by…

The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase…

We present a way to combine Vlasov and two-fluid codes for the simulation of a collisionless plasma in large domains while keeping full information of the velocity distribution in localized areas of interest. This is made possible by…

Sampling complex free energy surfaces is one of the main challenges of modern atomistic simulation methods. The presence of kinetic bottlenecks in such surfaces often renders a direct approach useless. A popular strategy is to identify a…

Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents with predefined tools, enabling chemists to express…

Large language models face significant computational bottlenecks during inference due to the expensive output layer computation over large vocabularies. We present CSV-Decode, a novel approach that uses geometric upper bounds to construct…

Path-like collective variables can be very effective for accurately modeling complex biomolecular processes in molecular dynamics simulations. Recently, we introduced DeepLNE, a machine learning-based path-like CV that provides a…

An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++…

A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1,1) x…

The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule…

Optimization of beamlines and lattices is a common problem in accelerator physics, which is usually solved with semi-analytical methods and numerical optimization routines. However, these are usually of the gradient-free or…

The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…