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All sources NASA NTRS DOE OSTI

DOE OSTI2025

Key Factors in Semi-Generic Coarse-Grained Modeling of Solid Polymer Electrolytes

Given the long length and time scales of interest and strong interactions present in solid polymer electrolytes, coarse-grained molecular models can be useful in understanding the molecular basis of their structure and transport properties. Rather than representing atoms individually, coarse-grained models use beads representing groups of atoms, making the system simpler and more efficient. Generic coarse-grained models, that are not built based on matching a particular atomistic system, can provide insight into the important physical considerations that apply across different chemical systems, though it can be unclear how to best match to experimental systems and capture relevant experimental behaviors with as simple of a model as possible. Here, we build on generic bead-spring models, but use stiff angle potentials, set different bead properties for different polymer types, and include additional ion parameters, creating a semi-generic coarse-grained model that can map more specifically to polymers and copolymers with different chain architectures, component glass transition temperatures, and ion solvation behaviors. We set most parameters with basic homopolymer data such as glass transition temperatures, Kuhn length, density, and dielectric constant, with further adjustment based on data from the polymer electrolyte system. We specifically model polystyrene-block-poly(oligo-oxyethylene methyl ether methacrylate) (PS-b-POEM) with lithium triflate salt, considering the POEM to be made of a poly(methylmethacrylate) backbone with poly(ethylene oxide) side chains. Solvation of ions is accounted for by additional polymer-ion interactions of the form -S/r4, plus additional lithium-polymer Lennard-Jones interactions. We find these potentials have different effects and discuss strategies for setting these parameters.

Zhang, Yuanhao↗

NASA NTRS2010

Measuring Crack Length in Coarse Grain Ceramics

Due to a coarse grain structure, crack lengths in precracked spinel specimens could not be measured optically, so the crack lengths and fracture toughness were estimated by strain gage measurements. An expression was developed via finite element analysis to correlate the measured strain with crack length in four-point flexure. The fracture toughness estimated by the strain gaged samples and another standardized method were in agreement.

Salem, Jonathan A.↗

DOE OSTI2024

Surface Variability Mapping and Roughness Analysis of the Moon Using a Coarse–Graining Decomposition

The lunar surface contains a wide variety of topographic shapes and features, each with different distributions and scales, and any analysis technique to objectively measure roughness must respect these qualities. Coarse-graining is a naturally scale-dependent filtering technique that preserves scale-dependent symmetries and produces coarse elevation maps that gradually erase the smaller features from the original topography. In this study of the lunar surface, we present two surface variability metrics obtained from coarse-graining lunar topography: fine elevation and coarse curvature. Both metrics are isotropic, deterministic, slope-independent, and coordinate-agnostic. Fine (detrended) elevation is acquired by subtracting the coarse elevation from the original topography and contains features that are smaller than the coarse-graining length-scale. Coarse curvature is the Laplacian of coarsened topography, and naturally quantifies the curvature at any scale and indicates whether a location is elevated or depressed relative to its neighborhood at that scale. We find that highlands and maria have distinct roughness characteristics at all length-scales. Our topographic spectra reveal four scale-breaks that mark characteristic shifts in surface roughness: 100, 300, 1,000, and 4,000 km. Comparing fine elevation distributions between maria and highlands, we show that maria fine elevation is biased toward smaller-magnitude elevations and that the maria–highland discrepancies are more pronounced at larger length-scales. Here, we also provide local examples of selected regions to demonstrate that these metrics can successfully distinguish geological features of different length-scales.

58 GEOSCIENCES↗

DOE OSTI2026

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

Computational Engineering, Finance, and Science (c↗

DOE OSTI2023

Arbitrarily accurate, nonparametric coarse graining with Markov renewal processes and the Mori–Zwanzig formulation

Stochastic dynamics, such as molecular dynamics, are important in many scientific applications. However, summarizing and analyzing the results of such simulations is often challenging due to the high dimension in which simulations are carried out and, consequently, due to the very large amount of data that are typically generated. Coarse graining is a popular technique for addressing this problem by providing compact and expressive representations. Coarse graining, however, potentially comes at the cost of accuracy, as dynamical information is, in general, lost when projecting the problem in a lower-dimensional space. This article shows how to eliminate coarse-graining error using two key ideas. First, we represent coarse-grained dynamics as a Markov renewal process. Second, we outline a data-driven, non-parametric Mori–Zwanzig approach for computing jump times of the renewal process. Numerical tests on a small protein illustrate the method.

36 MATERIALS SCIENCE↗

DOE OSTI2021

DynPaC: Coarse-Grained, Dynamic, and Partially Reconfigurable Array for Streaming Applications

Coarse-grained reconfigurable arrays (CGRAs) provide higher flexibility than application-specific integrated circuits (ASICs) and higher efficiency than fine-grained reconfigurable devices such as Field Programmable Gate Arrays (FPGAs). However, CGRAs are generally designed to support offloading of a single kernel. While their design, based on communicating functional units, appears to naturally suit streaming applications composed of multiple cooperating kernels, current approaches only statically partition the resources across kernels. However, streaming applications often are data-dependent, leading to variable kernel execution times depending on the input data and impacting the throughput of the entire pipeline if resources are statically allocated. Therefore, in this paper, we discuss the design of DynPaC — a coarse-grained, dynamically, and partially reconfigurable array for data-dependent streaming applications. We discuss the required software and hardware components to manage partial dynamic reconfiguration. We demonstrate that by supporting partial dynamic reconfiguration, we can obtain an average speedup of 1.44X for a representative set of applications w.r.t. static partitioning, with a limited area overhead (6.4% of the entire chip).

Tan, Cheng↗

DOE OSTI2019

A multi-scale experimental investigation of flow properties in coarse-grained hydrate reservoirs during production (Final Scientific/Technical Report)

In this project, “A multi-scale experimental investigation of flow properties in coarse-grained hydrate reservoirs during production” we explored the relative permeability and dissipation behavior of hydrate-bearing coarse-grained sediment at the core scale and we observed the formation and dissociation of these materials at the pore scale with micro-CT and Raman experiments. The 3-year project results inform reservoir simulation efforts, critical to determining the viability of the coarse-grained hydrate reservoir as an energy resource. We performed the first 3 phase relative permeability experiments in a hydrate-bearing medium using the steady state method (gas and water flow in the presence of hydrate). Results support a model where water is the most wetting phase, hydrate is the intermediate wetting phase, and gas is the least wetting phase. This model can be used to predict relative permeability of gas and water in the presence of hydrate. We showed that when hydrate dissociates, it does so at a pressure and temperature predicted for fresh water (no salinity) conditions. At the scale of a grid block, reservoir simulation models should assume that hydrate dissociates at the freshwater phase boundary. We observed that the chemistry and the pore habit of methane hydrates change dramatically over the timescales of experiments (hours to weeks). It takes weeks to months for hydrates to evolve from a non-stoichiometric to stoichiometric compound with 3:1 large cage vs small cage occupancy. We documented hydrates forming initially in small clayey silt surfaces but gradually concentrated in large pores in sand-sized sediment.

03 NATURAL GAS↗

DOE OSTI2023

Metasomatic alteration of coarse‐grained igneous calcium‐aluminum‐rich inclusions from CK3 carbonaceous chondrites

Abstract We report on the primary and secondary mineralogies of three coarse‐grained igneous calcium‐aluminum‐rich inclusions (CAIs) (Compact Type A [CTA], Type B [B], and forsterite‐bearing type B [FoB]) from the Northwest Africa (NWA) 5343 (CK3.7) and NWA 4964 (CK3.8) carbonaceous chondrites, compare them with the mineralogy of igneous CAIs from the Allende (CV3.6) chondrite, and discuss the nature of the alteration processes that affected the CK and CV CAIs. The primary mineralogy and mineral chemistry of the CK3 CAIs studied are similar to those from Allende; however, primary melilite and anorthite are nearly completely absent. Although the secondary minerals identified in CK CAIs (Al‐diopside, andradite, Cl‐apatite, clintonite, forsterite, ferroan olivine, Fe,Ni‐sulfides, grossular, ilmenite, magnetite, plagioclase, spinel, titanite, and wadalite) occur also in the Allende CAIs, there are several important differences: (i) In addition to melilite and anorthite, which are nearly completely replaced by secondary minerals, the alteration of CK CAIs also affected high‐Ti pyroxenes (fassaite and grossmanite) characterized by high Ti 3+ /Ti 4+ ratio and spinel. These pyroxenes are corroded and crosscut by veins of Fe‐ and Ti‐bearing grossular, Fe‐bearing Al,Ti‐diopside, titanite, and ilmenite. Spinel is corroded by Fe‐bearing Al‐diopside and grossular. (ii) The secondary mineral assemblages of grossular + monticellite and grossular + wollastonite, commonly observed in the Allende CAIs, are absent; the Fe‐bearing grossular + Fe‐bearing Al‐diopside ± Fe,Mg‐spinel, Fe‐bearing grossular + Fe,Mg‐olivine ± Fe,Mg‐spinel, and Ca,Na‐plagioclase + Fe‐bearing Al‐diopside + Fe‐bearing grossular assemblages are present instead. These mineral assemblages are often crosscut by veins of Fe‐bearing Al‐diopside, Fe,Mg‐olivine, Fe,Mg‐spinel, and Ca,Na‐plagioclase. The coarse‐grained secondary grossular and Al‐diopside often show multilayered chemical zoning with distinct compositional boundaries between the layers; the abundances of Fe and Ti typically increase toward the grain edges. (iv) Sodium‐rich secondary minerals, nepheline and sodalite, commonly observed in the peripheral portions of the Allende CAIs, are absent; Ca,Na‐plagioclase is present instead. We conclude that coarse‐grained igneous CAIs from CK3.7–3.8 s and Allende experienced an open‐system multistage metasomatic alteration in the presence of an aqueous solution–infiltration metasomatism. This process resulted in localized mobilization of all major rock‐forming elements: Si, Ca, Al, Ti, Mg, Fe, Mn, Na, K, and Cl. The metasomatic alteration of CK CAIs is more advanced and occurred under higher temperature and higher oxygen fugacity than that of the Allende CAIs.

Geochemistry & Geophysics↗

DOE OSTI2020

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Coarse-graining Hamiltonian systems using WSINDy

Abstract Weak form equation learning and surrogate modeling has proven to be computationally efficient and robust to measurement noise in a wide range of applications including ODE, PDE, and SDE discovery, as well as in coarse-graining applications, such as homogenization and mean-field descriptions of interacting particle systems. In this work we extend this coarse-graining capability to the setting of Hamiltonian dynamics which possess approximate symmetries associated with timescale separation. A smooth $$\varepsilon$$ ε -dependent Hamiltonian vector field $$X_\varepsilon$$ X ε possesses an approximate symmetry if the limiting vector field $$X_0=\lim _{\varepsilon \rightarrow 0}X_\varepsilon$$ X 0 = lim ε → 0 X ε possesses an exact symmetry. Such approximate symmetries often lead to the existence of a Hamiltonian system of reduced dimension that may be used to efficiently capture the dynamics of the symmetry-invariant dependent variables. Deriving such reduced systems, or approximating them numerically, is an ongoing challenge. We demonstrate that WSINDy can successfully identify this reduced Hamiltonian system in the presence of large perturbations imparted in the $$\varepsilon >0$$ ε > 0 regime, while remaining robust to extrinsic noise. This is significant in part due to the nontrivial means by which such systems are derived analytically. WSINDy naturally preserves the Hamiltonian structure by restricting to a trial basis of Hamiltonian vector fields. The methodology is computationally efficient, often requiring only a single trajectory to learn the global reduced Hamiltonian, and avoiding forward solves in the learning process. In this way, we argue that weak-form equation learning is particularly well-suited for Hamiltonian coarse-graining. Using nearly-periodic Hamiltonian systems as a prototypical class of systems with approximate symmetries, we show that WSINDy robustly identifies the correct leading-order system, with dimension reduced by at least two, upon observation of the relevant degrees of freedom. While our main contribution is computational, we also provide a contribution to the literature on averaging theory by proving that first-order averaging at the level of vector fields preserves Hamiltonian structure in nearly-periodic Hamiltonian systems. This provides theoretical justification for our approach as WSINDy’s computations occur at the level of Hamiltonian vector fields. We illustrate the efficacy of our proposed method using physically relevant examples, including coupled oscillator dynamics, the Hénon–Heiles system for stellar motion within a galaxy, and the dynamics of charged particles.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Trace element geochemistry of coarse-grained angrites from Northwest Africa: Implications for their petrogenesis on the angrite parent body

The angrites are a class of achondrites that encompass a wide range of igneous textures from quenched, volcanic, and subvolcanic stones to slowly cooled, plutonic rocks. The compositions of the various geochemical reservoirs generating this variety of rocks have not been investigated fully because historically the numbers and masses of angrites available for study have been quite small. However, the rapid increase in meteorites from Northwest Africa (NWA) has enabled a renewed opportunity for such an investigation. In particular, three samples, NWA 2999, 4590, and 4801, have provided a new window into our understanding of the origin and petrogenesis of the coarse-grained (plutonic) angrites. We report here the trace element abundances in individual mineral grains of pyroxene, plagioclase, olivine/kirschsteinite, and phosphate and in the whole-rock samples. We utilize these data to constrain the petrogenetic history of each of these samples on the angrite parent body (e.g., parental melt compositions and oxygen fugacity conditions) and assess genetic relationships to previously investigated angrites. The trace element abundances in each of the three coarse-grained angrites studied here indicate a unique history for each. The observed trace element abundances and patterns in NWA 2999 show similarities with previously studied fine-grained, volcanic angrites and potentially indicate a common geochemical source reservoir, even though NWA 2999 is temporally distinct from the volcanic angrites. In contrast, NWA 4590 has trace element characteristics analogous to other coarse-grained angrites (e.g., Lewis Cliff [LEW] 86010), suggesting that these samples originated from geochemically similar source reservoirs. The third angrite, NWA 4801, exhibits geochemical characteristics most similar to the plutonic, coarse-grained angrites, but also appears to have some affinities in its trace element characteristics to the volcanic, fine-grained angrites. This suggests that NWA 4801 may represent a petrogenetic link between two distinct geochemical reservoirs on the angrite parent body. In aggregate, the trace element distributions in these three plutonic angrites suggest that while they may have originated up to several million years after the fine-grained angrites, they sampled a range of source reservoirs on the angrite parent body. Here, some of these source reservoirs were likely similar to those of the fine-grained angrites, but others had distinct geochemical characteristics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Peridynamic Model for Single-Layer Graphene Obtained from Coarse Grained Bond Forces

An ordinary state-based peridynamic material model is proposed for single sheet graphene. The model is calibrated using coarse grained molecular dynamics simulations. The coarse graining method allows the dependence of bond force on bond length to be determined, including the horizon. The peridynamic model allows the horizon to be rescaled, providing a multiscale capability and allowing for substantial reductions in computational cost compared with molecular dynamics. The calibrated peridynamic model is compared to experimental data on the deflection and perforation of a graphene monolayer by an atomic force microscope probe.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Development and testing of coarse-grained models for ultrasonic simulations of cast austenitic stainless steel

Ultrasonic inspection of cast austenitic stainless steel (CASS) in the nuclear industry is particularly challenging because of sound field scatter and attenuation caused by the coarse-grained microstructure. Modeling and simulation are important tools in ultrasonic testing, as they can be used to help address key aspects of inspections, such as developing new probe designs, predicting inspection reliability, and testing phased-array focal laws. However, developing a useful and reliable CASS model is challenging due to the many grain interfaces and crystalline orientations that must be captured. We demonstrate a method of creating a realistic CASS model that is usable in CIVA, a commercially available modeling and simulation software platform. Using polished and chemically etched sections, we generate models of a coarse-grained equiaxed specimen and a columnar specimen. We also test an alternative method of generating a coarse-grained model using Voronoi regions. We qualitatively compare sound field scatter and quantitatively compare sound field attenuation and beam partitioning in simulated sound fields to those of laboratory-measured sound fields. Results show that the Voronoi models perform as well as or better than the models based on actual grain morphology. Here we also show that model-to-model randomness in Voronoi grain structure can impact the magnitude of a simulated echo response by a factor of two or more. Although CASS models are potentially a good depiction of reality for a given scenario, they should not be considered representative since CASS morphology can change significantly from specimen to specimen or within the same specimen.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Coarse-grained methods for heterogeneous vesicles with phase-separated domains: Elastic mechanics of shape fluctuations, plate compression, and channel insertion

We develop coarse-grained particle approaches for studying the elastic mechanics of vesicles with heterogeneous membranes having phase-separated domains. We perform simulations both of passive shape fluctuations and of active systems where vesicles are subjected to compression between two plates or subjected to insertion into narrow channels. Analysis methods are developed for mapping particle configurations to continuum fields with spherical harmonics representations. Heterogeneous vesicles are found to exhibit rich behaviors where the heterogeneity can amplify surface two-point correlations, reduce resistance during compression, and augment vesicle transport times in channels. The developed methods provide general approaches for characterizing the mechanics of coarse-grained heterogeneous systems taking into account the roles of thermal fluctuations, geometry, and phase separation.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1994

A constraint-logic based implementation of the coarse-grained approach to data acquisition scheduling of the International Ultraviolet Explorer orbiting observatory

The International Ultraviolet Explorer (IUE) satellite observatory has been in operation continuously since 1978. It typically carries out several thousand observations per year for over a hundred different science projects. These observations, which can occur in one of four different data-taking modes, fall under several satellite-related constraints and many other constraints which derive from the science goals of the projects being undertaken. One strategy which has made the scheduling problem tractable has been that of 'coarse-graining' the time into discrete blocks of equal size (8 hours), each of which is devoted to a single science program, and each of which is sufficiently long for several observations to be carried out. We call it 'coarse-graining' because the schedule is done at a 'coarse' level which ignores fine structure; i.e., no attempt is made to plan the sequence of observations occurring within each time block. We have incorporated the IUE's coarse-grained approach in new software which examines the science needs of the observations and produces a limited set of alternative schedules which meet all of the instrument and science-related constraints. With this algorithm, the IUE can still be scheduled by a single person using a standard workstation, as it has been. We believe that this software could could be adapted to a more complex mission while retaining the IUE's high flexibility and efficiency and scientific return of future satellite missions.

Mccollum, Bruce↗

DOE OSTI2023

Towards a unified nonlocal, peridynamics framework for the coarse-graining of molecular dynamics data with fractures

Molecular dynamics (MD) has served as a powerful tool for designing materials with reduced reliance on laboratory testing. However, the use of MD directly to treat the deformation and failure of materials at the mesoscale is still largely beyond reach. In this work, we propose a learning framework to extract a peridynamics model as a mesoscale continuum surrogate from MD simulated material fracture data sets. Firstly, we develop a novel coarse-graining method, to automatically handle the material fracture and its corresponding discontinuities in the MD displacement data sets. Inspired by the weighted essentially non-oscillatory (WENO) scheme, the key idea lies at an adaptive procedure to automatically choose the locally smoothest stencil, then reconstruct the coarse-grained material displacement field as the piecewise smooth solutions containing discontinuities. Then, based on the coarse-grained MD data, a two-phase optimization-based learning approach is proposed to infer the optimal peridynamics model with damage criterion. In the first phase, we identify the optimal nonlocal kernel function from the data sets without material damage to capture the material stiffness properties. Then, in the second phase, the material damage criterion is learnt as a smoothed step function from the data with fractures. As a result, a peridynamics surrogate is obtained. As a continuum model, our peridynamics surrogate model can be employed in further prediction tasks with different grid resolutions from training, and hence allows for substantial reductions in computational cost compared with MD. We illustrate the efficacy of the proposed approach with several numerical tests for the dynamic crack propagation problem in a single-layer graphene. Our tests show that the proposed data-driven model is robust and generalizable, in the sense that it is capable of modeling the initialization and growth of fractures under discretization and loading settings that are different from the ones used during training.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Coarse-Grained Density Functional Theory Predictions via Deep Kernel Learning

Scalable electronic predictions are critical for soft materials design. Recently, the Electronic Coarse-Graining (ECG) method was introduced to renormalize all-atom quantum chemical (QC) predictions to coarse-grained (CG) resolutions using deep neural networks (DNNs). While DNNs can learn complex representations that prove challenging for kernel-based methods, they are susceptible to overfitting and the overconfidence of uncertainty estimations. Here, we develop ECG within a GPU-accelerated Deep Kernel Learning (DKL) framework to enable CG QC predictions using range-separated hybrid density functional theory (DFT), obtaining a 107 speedup relative to naive all-atom QC. By treating the predicted electronic properties as random Gaussian Processes, DKL incorporates CG mapping degeneracy by learning the distribution of electronic energies as a function of CG configuration. DKL-ECG accurately reproduces molecular orbital energies from range-separated DFT while facilitating efficient training via active learning using the uncertainties provided by DKL. Further, we show that while active learning algorithms enable efficient sampling of a more diverse configurational space relative to random sampling, all explored query methods exhibit comparable performance for the examined system. We attribute this result to the significant overlap of the feature space and output property distributions across multiple temperatures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗