Related papers: Graph-Coarsening for Machine Learning Coarse-grain…
The data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Machine-learned coarse-grained (CG) potentials are fast, but degrade over time when simulations reach under-sampled bio-molecular conformations, and generating widespread all-atom (AA) data to combat this is computationally infeasible. We…
In a recent paper, J. Chem. Phys. 162, 214101 (2025), a novel approach for the rigidification of a molecular cluster was proposed, in which starting with an all-atom (AA) potential, a coarse-grained (CG) potential for the associated cluster…
Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual…
Developing effective coarse grained (CG) approach is a promising way for studying dynamics on large size networks. In the present work, we have proposed a strength-based CG (\sCG) method to study critical phenomena of the Potts model on…
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural…
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available…
Graph coarsening aims to reduce the size of a large graph while preserving some of its key properties, which has been used in many applications to reduce computational load and memory footprint. For instance, in graph machine learning,…
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…
Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…
We consider feature representation learning problem of molecular graphs. Graph Neural Networks have been widely used in feature representation learning of molecular graphs. However, most existing methods deal with molecular graphs…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
A general scheme, which includes constructions of coarse-grained (CG) models, weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of stable states, is presented to detect dynamical and thermodynamical properties in…
Geometric graph neural networks (GNNs) excel at capturing molecular geometry, yet their locality-biased message passing hampers the modeling of long-range interactions. Current solutions have fundamental limitations: extending cutoff radii…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
Finding coarse representations of large graphs is an important computational problem in the fields of scientific computing, large scale graph partitioning, and the reduction of geometric meshes. Of particular interest in all of these fields…
Graph Convolutional Networks (GCNs) are extensively utilized for deep learning on graphs. The large data sizes of graphs and their vertex features make scalable training algorithms and distributed memory systems necessary. Since the…
Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…
A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…
Molecular property calculations are the bedrock of chemical physics. High-fidelity \textit{ab initio} modeling techniques for computing the molecular properties can be prohibitively expensive, and motivate the development of…