arXiv subjects

Patrick G. Sahrmann

Publications and source records attributed to Patrick G. Sahrmann.

5 recordsLinked to original sources

arXiv2026

Learning Thermal Response Forces: A Method for Extending the Thermodynamic Transferability of Coarse-Grained Models via Machine-Learning

Machine-learned (ML) coarse-grained (CG) models are a promising tool for significantly enhancing the efficiency of molecular simulations by systematically removing degrees of freedom while retaining fidelity to the underlying fine-grained model. The CG potential of mean force (PMF) is inherently dependent on thermodynamic conditions and, hence, a CG force-field (FF) which is trained at one thermodynamic state point is not necessarily accurate at another. We propose, in this work, a novel and data-efficient means of learning temperature dependence into ML CG force-fields via training on the thermal response forces of the PMF. We demonstrate how incorporating these terms into ML CG FFs confers significantly improved transferability for CG water models and demonstrate how this transferability enables accurate and predictive CG dynamics.

physics.chem-ph↗

arXiv2025

Coarse-Graining in Quantum Mechanics: Distinguishable and Indistinguishable Particles

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 on CG modeling of atomistic systems which behave classically, while CG modeling of quantum systems has remained largely unexplored. We present in this work two fundamental advances in particle-based, bottom-up CG theory for systems obeying quantum statistical mechanics. We first expand the bottom-up CG formalism to include indistinguishable quantum particles, including bosons and fermions. We next introduce a variational optimization procedure for CG model parameterization which is founded on the relative entropy minimization (REM) principle and then bridge the classical and quantum REM methods through a semiclassical expansion in terms of the Feynman path centroid. We provide numerical examples of REM CG models of distinguishable and indistinguishable quantum systems, including as examples a harmonically trapped bosonic system and liquid water. The theoretical results presented here constitute a means to accelerate simulating thermal quantum systems ranging from distinguishable particle systems at higher temperatures to quantum indistinguishable particle systems at lower temperatures.

physics.chem-ph↗

arXiv2023

Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Models

Machine learning has recently entered into the mainstream of coarse-grained (CG) molecular modeling and simulation. While a variety of methods for incorporating deep learning into these models exist, many of them involve training neural networks to act directly as the CG force field. This has several benefits, the most significant of which is accuracy. Neural networks can inherently incorporate multi-body effects during the calculation of CG forces, and a well-trained neural network force field outperforms pairwise basis sets generated from essentially any methodology. However, this comes at a significant cost. First, these models are typically slower than pairwise force fields even when accounting for specialized hardware which accelerates the training and integration of such networks. The second, and the focus of this paper, is the need for the considerable amount of data needed to train such force fields. It is common to use 10s of microseconds of molecular dynamics data to train a single CG model, which approaches the point of eliminating the CG models usefulness in the first place. As we investigate in this work, this data-hunger trap from neural networks for predicting molecular energies and forces can be remediated in part by incorporating equivariant convolutional operations. We demonstrate that for CG water, networks which incorporate equivariant convolutional operations can produce functional models using datasets as small as a single frame of reference data, while networks without these operations cannot.

physics.chem-ph↗

arXiv2022

Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models Through Virtual Particles

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 models of biomolecules remains challenging. We demonstrate in this work how virtual particles, CG sites with no atomistic correspondence, can be incorporated into CG models within the context of relative entropy minimization (REM) as latent variables. The methodology presented, variational derivative relative entropy minimization (VD-REM), enables optimization of virtual particle interactions through a gradient descent algorithm aided by machine learning. We apply this methodology to the challenging case of a solvent-free CG model of a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer and demonstrate that introduction of virtual particles captures solvent-mediated behavior and higher-order correlations which REM alone cannot capture in a more standard CG model based only on the mapping of collections of atoms to the CG sites.

physics.chem-ph↗

arXiv2022

Centroid Molecular Dynamics Can Be Greatly Accelerated Through Neural Network Learned Centroid Forces Derived from Path Integral Molecular Dynamics

For nearly the past 30 years, Centroid Molecular Dynamics (CMD) has proven to be a viable classical-like phase space formulation for the calculation of quantum dynamical properties. However, calculation of the centroid effective force remains a significant computational cost and limits the ability of CMD to be an efficient approach to study condensed phase quantum dynamics. In this paper we introduce a neural network-based methodology for first learning the centroid effective force from path integral molecular dynamics data, which is subsequently used as an effective force field to evolve the centroids directly with the CMD algorithm. This method, called Machine-Learned Centroid Molecular Dynamics (ML-CMD) is faster and far less costly than both standard on the fly CMD and ring polymer molecular dynamics (RPMD). The training aspect of ML-CMD is also straightforwardly implemented utilizing the DeepMD software kit. ML-CMD is then applied to two model systems to illustrate the approach: liquid para-hydrogen and water. The results show comparable accuracy to both CMD and RPMD in the estimation of quantum dynamical properties, including the self-diffusion constant and velocity time correlation function, but for significantly reduced overall computational cost.

physics.chem-ph↗