Related papers: Molecular Latent Space Simulators

We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…

The aim of this work is to investigate the use of Incrementally Input-to-State Stable ($\delta$ISS) deep Long Short Term Memory networks (LSTMs) for the identification of nonlinear dynamical systems. We show that suitable sufficient…

Addressing the charged particle beam diagnostics in accelerators poses a formidable challenge, demanding high-fidelity simulations in limited computational time. Machine learning (ML) based surrogate models have emerged as a promising tool…

We derived a number of numerical methods to treat biomolecular systems with multiple time scales. Based on the splitting of the operators associated with the slow-varying and fast-varying forces, new multiple time-stepping (MTS) methods are…

Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…

Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. Such practice is needed in atomistic simulations of complex…

G-Protein Coupled Receptors (GPCRs) are a big family of eukaryotic cell transmembrane proteins, responsible for numerous biological processes. From a practical viewpoint around 34\% of the drugs approved by the US Food and Drug…

It is a challenge to obtain an accurate model of the state-to-state dynamics of a complex biological system from molecular dynamics (MD) simulations. In recent years, Markov State Models have gained immense popularity for computing…

Deep video recognition is more computationally expensive than image recognition, especially on large-scale datasets like Kinetics [1]. Therefore, training scalability is essential to handle a large amount of videos. In this paper, we study…

Markov state models (MSMs) have become a popular approach for investigating the conformational dynamics of proteins and other biomolecules. MSMs are typically built from numerous molecular dynamics simulations by dividing the sampled…

The machine learning approaches are applied in the dynamical simulation of open quantum systems. The long short-term memory recurrent neural network (LSTM-RNN) models are used to simulate the long-time quantum dynamics, which are built…

Maximizing storage performance in geological carbon storage (GCS) is crucial for commercial deployment, but traditional optimization demands resource-intensive simulations, posing computational challenges. This study introduces the…

Structured State Space Models (SSMs), which are at the heart of the recently popular Mamba architecture, are powerful tools for sequence modeling. However, their theoretical foundation relies on a complex, multi-stage process of…

Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations…

In this work, we develop a stochastic matrix product state (stoMPS) approach that combines the MPS technique and Monte Carlo samplings and can be applied to simulate quantum lattice models down to low temperature. In particular, we exploit…

Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…

Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…

Simulating atomic-scale processes, such as protein dynamics and catalytic reactions, is crucial for advancements in biology, chemistry, and materials science. Machine learning force fields (MLFFs) have emerged as powerful tools that achieve…

In this work we investigate approaches to reconstruct generator models from measurements available at the generator terminal bus using machine learning (ML) techniques. The goal is to develop an emulator which is trained online and is…

Multimodal Large Language Models (MLLMs) have demonstrated outstanding performance across a variety of domains. However, training MLLMs is often inefficient, as much of the computation is redundant due to the long input sequences from…