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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗
DOE OSTI2023

Reinforcement learning based hybrid bond-order coarse-grained interatomic potentials for exploring mesoscale aggregation in liquid–liquid mixtures

Exploring mesoscopic physical phenomena has always been a challenge for brute-force all-atom molecular dynamics simulations. Although recent advances in computing hardware have improved the accessible length scales, reaching mesoscopic timescales is still a significant bottleneck. Coarse-graining of all-atom models allows robust investigation of mesoscale physics with a reduced spatial and temporal resolution but preserves desired structural features of molecules, unlike continuum-based methods. Here, we present a hybrid bond-order coarse-grained forcefield (HyCG) for modeling mesoscale aggregation phenomena in liquid–liquid mixtures. The intuitive hybrid functional form of the potential offers interpretability to our model, unlike many machine learning based interatomic potentials. We parameterize the potential with the continuous action Monte Carlo Tree Search (cMCTS) algorithm, a reinforcement learning (RL) based global optimizing scheme, using training data from all-atom simulations. The resulting RL-HyCG correctly describes mesoscale critical fluctuations in binary liquid–liquid extraction systems. cMCTS, the RL algorithm, accurately captures the mean behavior of various geometrical properties of the molecule of interest, which were excluded from the training set. The developed potential model along with the RL-based training workflow could be applied to explore a variety of other mesoscale physical phenomena that are typically inaccessible to all-atom molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Effect of Initial Microstructure on the Toughness of Coarse-Grained Heat-Affected Zone in a Microalloyed Steel

Toughness of the coarse-grained-heat-affected-zone (CGHAZ) strongly depends on the prior austenite grain size. The prior austenite grain size is affected not only by chemical composition, thermal cycle, and dissolution of second-phase particles, but also by the initial microstructure. The effect of base metal microstructure (ferrite/pearlite obtained by air cooling and martensite obtained by water-quenching) on Charpy impact toughness of the CGHAZ has been investigated for different heat inputs for high-heat input welding of a microalloyed steel. A welding thermal cycle with a heat input of 100 kJ/cm and 400 kJ/cm were simulated on the MMS-300 system. Despite a similar microstructure in the CGHAZ of both the base metals, the average Charpy impact energy for the air-cooled base metal was found to be higher than the water-quenched base metal. Through thermo-kinetic simulations, it was found that a higher enrichment of Mn/C at the ferrite/austenite transformation interface of the CGHAZ of water-quenched base metal resulted in stabilizing austenite at a lower A1 temperature, which resulted in a coarser austenite grain size and eventually lowering the toughness of the CGHAZ.

36 MATERIALS SCIENCE↗
NASA NTRS1987

Chondrules, matrix and coarse-grained chondrule rims in the Allende meteorite - Origin, interrelationships, and possible precursor components

INAA and broad-beam EMPA are used to determine the bulk compositions of 20 chondrules, 13 coarse-grained chondrule rims, and one nonporphyritic CV chondrule (NPCVC) from CV3 Allende (and of one NPCVC each from Leoville and Vigarano). The data are presented in extensive tables and graphs and analyzed in detail. Five probable chondrule precursor components are deduced, and the solar-nebula processes giving rise to them (and probably to the coarse-grained rims as well) are discussed. It is suggested that the formation of the rimmed chondrules involved nebular reheating in space, after the accretion of dusty coatings.

Rubin, Alan E.↗
DOE OSTI2023

Spatio–Temporal Coarse–Graining Decomposition of the Global Ocean Geostrophic Kinetic Energy

We expand on a recent determination of the first global energy spectrum of the ocean’s surface geostrophic circulation using a coarse-graining (CG) method. We compare spectra from CG to those from spherical harmonics by treating land in a manner consistent with the boundary conditions. While the two methods yield qualitatively consistent domain-averaged results, spherical harmonics spectra are too noisy at gyre-scales (> 1000 km). More importantly, spherical harmonics are inherently global and cannot provide local information connecting scales with currents geographically. CG shows that the extra-tropics mesoscales (100–500 km) have a root-mean-square (rms) velocity of ~15 cm/s, which increases to ~30–40 cm/s locally in the Gulf Stream and Kuroshio and to ~16–28 cm/s in the ACC. There is notable hemispheric asymmetry in mesoscale energy-per-area, which is higher in the north due to continental boundaries. We estimate that ≈25–50% of total geostrophic energy is at scales smaller than 100 km, and is un(der)-resolved by pre-SWOT satellite products. Spectra of the time-mean circulation show that most of its energy (up to 70%) resides in stationary eddies with characteristic scales smaller than (< 500 km). This highlights the preponderance of ‘standing’ small-scale structures in the global ocean due to the temporally coherent forcing by boundaries. By coarse-graining in space and time, we compute the first spatio-temporal global spectrum of geostrophic circulation from AVISO and NEMO. These spectra show that every length-scale evolves over a wide range of time-scales with a consistent peak at ≈200 km and ≈2–3 weeks.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1982

An estimate of atmospheric contamination of Allende coarse-grained inclusion 3529Z

Studies conducted by Zaikowski and Schaeffer (1979) have shown that minerals can take up rare gases when exposed to the atmosphere. Herzog et al. (1980) have conducted a laser microprobe study of coarse-grained Ca-Al-rich inclusions from the Allende meteorite. The amount of Ar-40 found in the Allende minerals is less than the equilibrium amount found for a synthetic serpentine by Zaikowski and Schaeffer. The present investigation has the objective to obtain a better estimate for the absorption of atmospheric argon by the minerals in Allende. Ar-38 was used as a tracer to investigate the diffusion of argon into a coarse-grained Ca-Al-rich inclusion from Allende. On the basis of the results obtained in the current investigation, it is believed that atmospheric contamination is not the cause for the extra argon and the above 4.55 G.y. ages in the case of the considered Allende inclusion.

Warasila, R.↗
DOE OSTI2026

Temporal Coarse Graining for Classical Stochastic Noise in Quantum Systems

Simulations of quantum systems with Hamiltonian classical stochastic noise can be challenging when the noise exhibits temporal correlations over a multitude of time scales, such as for 1/f noise in solid-state quantum information processors. Here we present an approach for simulating Hamiltonian classical stochastic noise that performs temporal coarse-graining by effectively integrating out the high-frequency components of the noise. We focus on the case where the stochastic noise can be expressed as a sum of Ornstein-Uhlenbeck processes. Temporal coarse-graining is then achieved by conditioning the stochastic process on a coarse realization of the noise, expressing the conditioned stochastic process in terms of a sum of smooth, deterministic functions and bridge processes with boundaries fixed at zero, and performing the ensemble average over the bridge processes. For Ornstein-Uhlenbeck processes, the deterministic components capture all dependence on the coarse realization, and the stochastic bridge processes are not only independent but taken from the same distribution with correlators that can be expressed analytically, allowing the associated noise propagators to be precomputed once for all simulations. This combination of noise trajectories on a coarse time grid and ensemble averaging over bridge processes has practical advantages, such as a simple concatenation rule, that we highlight with numerical examples.

Albash, Tameem [Sandia National Lab. (SNL-NM), Alb↗
DOE OSTI2023

Isolating Chemical Reaction Mechanism as a Variable with Reactive Coarse-Grained Molecular Dynamics: Step-Growth versus Chain-Growth Polymerization

Here we present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often group multiple atoms into a single “coarse-grained” interaction site, which leads to a loss of chemical resolution. In this work we convert this shortcoming into a feature and use identical coarse-grained models to represent molecules that share nonreactive characteristics but react by different mechanisms. As a proof of concept, we use this approach to simulate and investigate distinct, yet similar, trifunctional isocyanurate resin formulations that polymerize by either chain- or step-growth. Because the underlying molecular mechanics of these models are identical, all emergent differences are a function of the reaction mechanism only. We find that the microscopic morphologies resemble related all-atom simulations and that simulated mechanical testing reasonably agrees with experiment.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Coarse-grained fixed-point tensor networks and holographic reflected entropy in 3D gravity

We use the framework of fixed-point BCFT tensor networks to present a microscopic CFT derivation of the correspondence between reflected entropy (RE) and entanglement wedge cross section (EW) in AdS 3 /CFT 2 , for both bipartite and multipartite settings. These fixed-point tensor networks, obtained by triangulating Euclidean CFT path integrals, allow us to explicitly construct the canonical purification via cutting-and-gluing CFT path integrals. Employing modular flow in the large-c limit, we demonstrate that these intrinsic CFT manipulations reproduce bulk geometric prescriptions, without assuming the AdS/CFT dictionary. The emergence of bulk geometry is traced to coarse-graining over heavy states in the large-c limit. Universal coarse-grained BCFT data for compact 2D CFTs, through the relation to Liouville theory with ZZ boundary conditions, yields hyperbolic geometry on the Cauchy slice. The corresponding averaged replica partition functions reproduce all candidate EWs, arising from different averaging patterns, with the dominant one providing the correct RE and EW. In this way, many heuristic tensor-network intuitions in toy models are made precise and established directly from intrinsic CFT data.

AdS-CFT correspondence↗
NASA NTRS1979

Consortium breccia 73255 - Genesis and history of two coarse-grained 'norite' clasts

A study of two clasts of coarse-grained anorthositic-noritic-troctolitic-suite norites from the fragment-laden melt rock 73255 is presented. Both clasts are igneous rocks crystallized from melts that were probably internally generated; clast 27,80 is a cumulate, and the parent magmas of both rocks probably crystallized below the lunar surface. Despite similar history, the parent rocks of the two clasts appear to be derived from distinct magma types: the 27,80 is characterized by plagioclase and orthopyroxene as the major constituents and by a high K, Nb, and Zr content, while the 27,45 type also contains augite and has a low content of K, Nb, and Zr.

James, O. B.↗
DOE OSTI2024

Molecular Dynamics Study of the Effect of Grafting Density on Ion Diffusivity in a MARTINI Coarse-Grained Strong Polyelectrolyte Brush

Because surface-grafted polyelectrolyte brushes (PEBs) are responsive to external stimuli, such as electric fields and ionic strength, PEBs are attractive for applications ranging from drug delivery to separation technologies. Essential to PEB utilization is understanding how critical parameters like grafting density (σ) impact the PEB structure and the dynamics of the PEB and counterions. To study the effect of σ on PEB and the counterion structure and dynamics, we fine-tune a coarse-grained model that retains the chemical specificity of a strong polyelectrolyte, poly[(2-(methacryloyloxy)ethyl) trimethylammonium chloride] (PMETAC), using the MARTINI force field. Using “salt-free” conditions where the counterion concentration balances the charge on the brush, we build coarse-grained (CG) molecular dynamics simulations for MARTINI PMETAC brushes (N = 150 monomers; M W = 31.2 kg/mol) at experimentally relevant values of σ = 0.05, 0.10, 0.20, and 0.40 chains/nm 2 . Using 5 μs simulations, we investigate the effects of grafting density on the PEB structure, ion dissociation dynamics, polymer mobility, and counterion diffusivity. Results show that competition between electrostatic interactions, steric hindrance, and polymer mobility controls counterion diffusivity. Finally, the interplay of these factors leads to diffusivity that depends non-monotonically on σ, with counterion diffusivity peaking at an intermediate σ = 0.10 chains/nm 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Understanding Viscoelasticity of an Entangled Silicone Copolymer via Coarse-Grained Molecular Dynamics Simulations

Entangled dynamics is important for understanding rheological properties of long-chain polymers. For entangled homopolymers, the classic tube-reptation model and its refinements have been successfully applied to quantify properties like diffusion coefficient and zero-rate viscosity. However, the application of such models to copolymers has been limited despite scientific and industrial importance. Here, we study the entangled melt dynamics of poly(dimethyl-co-diphenyl)siloxane random copolymer for a range of mean-composition-ratio ϕ of the diphenyl component via long-term molecular dynamics simulation with a recently developed coarse-grained model. We found that the segmental relaxation is heterogeneous at the monomeric level because of compositional fluctuations. However, at the chain-entanglement level and higher length scales, the viscoelastic response is homogeneous with compositional dependence only through the overall diphenyl fraction ϕ. The relaxation modulus of the entangled copolymer melt conforms to the Likhtman–McLeish model, and the viscosity predicted using our current coarse-grained parameters is in good quantitative agreement with experimental data.

Copolymers↗
DOE OSTI2021

Transfer learning of memory kernels for transferable coarse-graining of polymer dynamics

The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of polymer solutions. The CG model is based on the generalized Langevin equation, where the memory kernel plays the critical role in determining the dynamics in all time scales. Thus, we propose methods for transfer learning of memory kernels. The key ingredient of our methods is Gaussian process regression. By integration with the model order reduction via proper orthogonal decomposition and the active learning technique, the transfer learning can be practically efficient and requires minimum training data. Through two example polymer solution systems, we demonstrate the accuracy and efficiency of the proposed transfer learning methods in the construction of transferable memory kernels. The transferability allows for out-of-sample predictions, even in the extrapolated domain of parameters. Built on the transferable memory kernels, the CG models can reproduce the dynamic properties of polymers in all time scales at different thermodynamic conditions (such as temperature and solvent viscosity) and for different systems with varying concentrations and lengths of polymers.

Ma, Zhan↗
DOE OSTI2023

Measuring scale-dependent shape anisotropy by coarse-graining: Application to inhomogeneous Rayleigh-Taylor turbulence

Here, we generalize the “filtering spectrum” to probe scales along different directions by spatial coarse-graining. This multidimensional filtering spectrum quantifies the spectral content of flows that are not necessarily homogeneous. From multidimensional spectral information, we propose a simple metric for shape anisotropy at various scales. The method is applied to simulations of two-dimensional (2D) and 3D Rayleigh-Taylor (RT) turbulence, which is inhomogeneous and anisotropic. We show that 3D RT has clear shape anisotropy at large scales with approximately 4:3 vertical to horizontal aspect ratio but tends toward isotropy at small scales as expected. In sharp contrast, we find that RT in 2D simulations, which are still the main modeling framework for many applications, is isotropic at large scales and its shape anisotropy increases at smaller scales where structures tend to be horizontally elongated. While this may be surprising, it is consistent with recent results that large-scale isotropy in 2D RT is due to the generation of a large-scale overturning circulation via an upscale cascade, while small-scale anisotropy is due to the stable stratification resultant from such overturning and the inefficient mixing in 2D.

42 ENGINEERING↗
DOE OSTI2026

Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics

In this work, we evaluate the biomolecular dynamics behaviors when conventionally iterating between all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations over multiple cycles. We implemented the workflow to iterate between AA and CG in OpenMM, namely the iterative multiscale MD (iMMD) simulation workflow. In particular, we aim to identify practical applications for iterating between AA and CG simulations in a conventional manner without any constraints or model modifications. We evaluate the iMMD workflow on four representative systems, spanning folding of two soluble proteins and protein-protein as well as protein-lipid interactions of two membrane proteins. We observe that iteration between AA and CG representations could help the soluble proteins exit undesirable metastable states to fold, resulting from random protein structural distortions due to cycling. Consequently, the most reliable use of iterative AA and CG simulations appears to be to accelerating complex lipid mixing for membrane-bound protein systems rather than sampling protein conformational space. Our work explores the practical usages and limitations for iterative AA and CG simulations using readily available AA and CG force fields. The evaluated iMMD workflow in OpenMM is made available at https://github.com/lanl/iMMD.

59 BASIC BIOLOGICAL SCIENCES↗