Related papers: Hessian Matching for Machine-Learned Coarse-Graine…
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…
Coarse-grained models have proven helpful for simulating complex systems over long timescales to provide molecular insights into various processes. Methodologies for systematic parameterization of the underlying energy function, or force…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Modeling complex systems that evolve toward equilibrium distributions is important in various physical applications, including molecular dynamics and robotic control. These systems often follow the stochastic gradient descent of an…
Brute-force simulations for dynamics on very large networks are quite expensive. While phenomenological treatments may capture some macroscopic properties, they often ignore important microscopic details. Fortunately, one may be only…
We present a novel learning framework that consistently embeds underlying physics while bypassing a significant drawback of most modern, data-driven coarse-grained approaches in the context of molecular dynamics (MD), i.e., the availability…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Coarse graining (CG) enables the investigation of molecular properties for larger systems and at longer timescales than the ones attainable at the atomistic resolution. Machine learning techniques have been recently proposed to learn CG…
Machine-learned coarse-grained (MLCG) molecular dynamics is a promising option for modeling biomolecules. However, MLCG models currently require large amounts of data from reference atomistic molecular dynamics or substantial computation…
Coarse-grained (CG) modeling enables molecular simulations to reach time and length scales inaccessible to fully atomistic methods. For classical CG models, the choice of mapping, that is, how atoms are grouped into CG sites, is a major…
For training fully-connected neural networks (FCNNs), we propose a practical approximate second-order method including: 1) an approximation of the Hessian matrix and 2) a conjugate gradient (CG) based method. Our proposed approximate…
This work studies a composite minimization problem involving a differentiable function q and a nonsmooth function h, both of which may be nonconvex. This problem is ubiquitous in signal processing and machine learning yet remains…
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…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
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…
We utilize connections between molecular coarse-graining approaches and implicit generative models in machine learning to describe a new framework for systematic molecular coarse-graining (CG). Focus is placed on the formalism encompassing…