Simulating Spatial Architectures With The Structural Simulation Toolkit
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Hughes, Clayton [Sandia National Laboratories (SNL↗
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Multiscale simulation of spatially correlated microstructure via a latent space representation
When deformation gradients act on the scale of the microstructure of a part due to geometry and loading, spatial correlations and finite-size effects in simulation cells cannot be neglected. We propose a multiscale method that accounts for these effects using a variational autoencoder to encode the structure–property map of the stochastic volume elements making up the statistical description of the part. In this paradigm the autoencoder can be used to directly encode the microstructure or, alternatively, its latent space can be sampled to provide likely realizations. Furthermore, we demonstrate the method on three examples using the common additively manufactured material AlSi10Mg in: (a) a comparison with direct numerical simulation of the part microstructure, (b) a push forward of microstructural uncertainty to performance quantities of interest, and (c) a simulation of functional gradation of a part with stochastic microstructure.
Elastoplasticity↗
Adaptive Tau-Leaping Strategies for Efficient Kinetic Monte Carlo Simulations in Spatially Non-Uniform Systems
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Han, Xiaoying↗
Realistic Precipitation Diurnal Cycle in Global Convection-Permitting Models by Resolving Mesoscale Convective Systems
Accurately representing the precipitation diurnal cycle has long been a challenge for global climate models (GCMs). Here we evaluate the precipitation diurnal cycle in the DYAMOND global convection-permitting models (CPMs) and CMIP6 HighResMIP models. Comparison of the high- (25–50 km) and low-resolution (100–250 km) models with parameterized convection in HighResMIP shows that simply increasing model resolution does not noticeably improve the precipitation diurnal cycle. In contrast, CPMs can better capture the observed amplitude and timing of precipitation diurnal cycle. However, the simulated spatial variation of timing in CPMs is smaller than observed, leading to an exaggeration of the spatially averaged diurnal amplitude. The better-simulated precipitation diurnal cycle in the CPMs is tied to mesoscale convective systems (MCSs), which contribute about half of the total precipitation. The observed life cycle of MCSs, including initiation and mature stages, is well captured in the CPMs, leading to a more realistic precipitation diurnal cycle.
54 ENVIRONMENTAL SCIENCES↗
Assessing Cloud and Precipitation Properties on Temporal and Spatial Scales Using LASSO Simulations over ENA
Low clouds and precipitation representation remain a major source of uncertainty in Earth System Models (ESMs), particularly due to challenges in representing their sub-grid variability and scale-dependent sampling. This study evaluates the performance of preliminary simulations from the Large-Eddy Simulation (LES) ARM Symbiotic Simulation and Observation (LASSO) project over the Eastern North Atlantic (ENA), with a focus on liquid water path (LWP), ice water path (IWP), cloud fraction (CF), and surface precipitation simulated across closed-cell, open-cell, and transitional cloud regimes. Using LES (100 m horizontal grid spacing) driven by ERA5 and MERRA-2 reanalyses, we assess the representativeness of ground-based point observations by analyzing their correspondence to model-resolved spatial and temporal means. Results suggest that observational sampling of at least 6 hours is required to achieve consistency with domain-scale averages, in particular for observations that exhibit pronounced sub-grid heterogeneity, such as precipitation. ERA5-forced simulations exhibit improved spatial coherence and agreement with domain-averaged quantities when compared to MERRA-2 runs, with performance discrepancies largest for convective cloud conditions due to differences in forcing fidelity and temporal resolution. These findings highlight the importance of regime-aware model evaluation strategies and potentially demonstrate how LES can inform observation-model comparison practices and the development of cloud and precipitation parameterizations in ESMs.
Liang, Jiakun [University of Hawai'i at Manoa] (OR↗
Myna: Connecting powder bed fusion build data to simulation tools for digital twin applications
Additive manufacturing (AM), as a digital process, can generate a detailed digital thread linking a part’s design and manufacturing to its operational performance. As AM systems advance, an increasing amount of process data is stored in manufacturing databases. In principle, this data can be utilized by simulation-based digital twin approaches, such as real-time process control and asynchronous post-processing guidance. However, few tools currently exist for systematically integrating digital thread data with computational tools. Here, in this study, we propose a software package, called Myna, for connecting data from powder bed fusion processes to simulation tools. The utility of such a platform is demonstrated using build data from the Oak Ridge National Laboratory Manufacturing Demonstration Facility “Peregrine v2023-10” public dataset to automatically configure and run 54 semi-analytical 3DThesis melt pool simulations, 78 numerical Additive FOAM melt pool simulations, and 3 ExaCA microstructure simulations. The simulated, spatially registered microstructures are then compared directly with electron backscatter diffraction characterization of the corresponding as-built part locations. The resulting simulated microstructure showed variation as a function of process parameters, particularly stripe width; however, the experimental data had little variation between the microstructure texture and grain size resulting from different processing conditions. Analysis of the discrepancies suggest that it is possible a two-phase ferritic-austenitic solidification model is needed to accurately predict grain size and texture for certain stainless steel 316L feedstock compositions under powder bed fusion conditions, providing direction for future research. As illustrated here, due to the number and complexity of the simulations involved in AM process-structure–property predictions, automated methods to connect process data and simulations will remain necessary tools for testing hypotheses and implementing digital twin applications.
Knapp, Gerald L. [Oak Ridge National Laboratory (O↗
Quantitative Nonlinear Optical Polarimetry with High Spatial Resolution
Nonlinear optical microscopy such as in the optical second-harmonic generation (SHG) modality has become a popular tool today for probing materials in the physical and biological sciences. While imaging and spectroscopy are widely used in the microscopy mode, nonlinear polarimetry, which can shed light on materials’ symmetry and microstructure, is relatively underdeveloped. This is partly because quantitative analytical modeling of the optical SHG response for anisotropic crystals and films largely assumes low-numerical aperture (NA) focusing of light, where the plane-wave approximation is sufficient. Tight focusing provides unique benefits in revealing out-of-plane polarization responses, which cannot be detected by near-plane-wave illumination at normal incidence. Here, we outline a method for quantitatively analyzing SHG polarimetry measurements obtained under high-NA focusing within a microscope geometry. Experiments and simulations of a variety of standard samples, from single crystals to thin films, are in good agreement, including measured and simulated spatial SHG maps of ferroelectric domains. A solution to the inverse problem is demonstrated, where the spatial distribution of an SHG tensor with unknown tensor coefficient magnitudes is determined by experimentally measured polarimetry. The ability to extract the out-of-plane component of the nonlinear polarization in normal incidence is demonstrated, which can be valuable for high-resolution polarimetry of 2D materials, thin films, heterostructures, and uniaxial crystals with a strong out-of-plane response.
36 MATERIALS SCIENCE↗
Observationally constrained analysis on the distribution of fine- and coarse-mode nitrate in global models
Nitrate plays an important role in the Earth system and air quality. A key challenge in simulating the life cycle of nitrate aerosol in global models is to accurately represent mass size distribution of nitrate aerosol. In this study, we evaluate the performance of the Energy Exascale Earth System Model version 2 (E3SMv2) and the Community Earth System Model version 2 (CESM2), along with Aerosol Comparisons between Observations and Models (AeroCom) phase III models, in simulating spatial distribution of fine-mode nitrate, the mass size distribution of fine- and coarse-mode nitrate, and the gas–aerosol partitioning between nitric acid gas and nitrate, using long-term ground-based observations and measurements from multiple aircraft campaigns. We find that most models underestimate the annual mean PM 2.5 (particulate matter with diameter less than 2.5 µm) nitrate surface concentration averaged over all sites. The observed nitrate PM 2.5 / PM 10 and PM 1 / PM 4 ratios are influenced by the relative contribution of fine sulfate or organic particles and coarse dust or sea salt particles. Overall, the ground-based observations give an annual mean surface nitrate PM 2.5 / PM 10 ratio of 0.7. Most models underestimate the annual mean PM 2.5 / PM 10 ratio in all regions. There are large spreads in the modeled nitrate PM 1 / PM 4 ratios, which span the full range from 0 to 1. Most models underestimate the surface molar ratio of nitrate to total inorganic nitrate averaged across all sites. Our study indicates the importance of gas–aerosol partition parameterization and the simulation of dust and sea salt in correctly simulating the mass size distribution of nitrate.
Nitrate↗
A lumped particle direct simulation Monte-Carlo method combined with the collisional-radiative model for simulations of non-equilibrium laser-induced plasma plumes
Collisional plasma plumes induced by laser irradiation of material targets exhibit large variations in local density as well as ionization and excitation states, making purely hydrodynamic or kinetic simulations inaccurate or infeasible. To address this challenge and capture non-equilibrium effects in laser-induced plasma plumes at arbitrary degrees of ionization, we develop a hybrid computational approach that combines the kinetic direct simulation Monte Carlo (DSMC) method with a collisional-radiative model (CRM). This ℓDSMC-CRM approach utilizes a lumped particle method to represent minor fractions of excited ions in particle-based simulations and a special coarse-graining technique for atomic spectra and photoionization rates, ensuring numerical convergence at reduced computational cost. The hybrid approach is applied to simulate spatially homogeneous relaxation as well as one- and two-dimensional expansions of plasma plumes induced by irradiation of a copper target by a nanosecond laser pulse in a vacuum or background gas. The comparison with an equilibrium model, where local Saha-Boltzmann equilibrium is enforced, shows that the non-equilibrium effects play a dominant role. The equilibrium model can fail to predict the flow structure and strongly underestimate the degree of absorption of laser radiation by the plume. The ℓDSMC-CRM approach is validated against experimental data demonstrating reasonable agreement with the experimental electron density and temperature, while the equilibrium model is found to dramatically underestimate electron density and temperature. The flexibility of the ℓDSMC-CRM approach allows for its seamless integration into existing DSMC frameworks, making it a valuable tool for high-fidelity plasma modeling in laser-material interactions, laser-based manufacturing, and beyond.
97 MATHEMATICS AND COMPUTING↗
Global Simulations of Phase State and Equilibration Time Scales of Secondary Organic Aerosols with GEOS-Chem
The phase state of secondary organic aerosols (SOA) can range from liquid through amorphous semisolid to glassy solid, which is important to consider as it influences various multiphase processes including SOA formation and partitioning, multiphase chemistry, and cloud activation. In this study, we simulate the glass transition temperature and viscosity of SOA over the globe using the global chemical transport model, GEOS-Chem. The simulated spatial distributions show that SOA at the surface exist as liquid over equatorial regions and oceans, semisolid in the midlatitude continental regions, and glassy solid over lands with low relative humidity. The predicted SOA viscosities are mostly consistent with the available measurements. In the free troposphere, SOA particles are mostly predicted to be semisolid at 850 hPa and glassy solid at 500 hPa, except over tropical regions including Amazonia, where SOA are predicted to be low viscous. Phase state also exhibits seasonal variation with a higher frequency of semisolid and solid particles in winter compared to warmer seasons. We calculate equilibration time scales of SOA partitioning (τ eq ) and effective mass accommodation coefficient (α eff ), indicating that τ eq is shorter than the chemical time step of GEOS-Chem of 20 min and αeff is close to unity for most locations at the surface level, supporting the application of equilibrium SOA partitioning. However, τ eq is prolonged and α eff is lowered over drylands and most regions in the upper troposphere, suggesting that kinetically limited growth would need to be considered for these regions in future large-scale model studies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Stable Simulation of the Community Atmosphere Model Using Machine‐Learning Physical Parameterization Trained With Experience Replay
In recent years, machine learning (ML) models have been used to improve physical parameterizations of general circulation models (GCMs). A significant challenge of integrating ML models into GCMs is the online instability when they are coupled for long‐term simulation. We present a new strategy that demonstrates robust online stability when the physical parameterization package of an atmospheric GCM is replaced by a deep ML model. The method uses experience replay with a multistep training scheme of the ML model in which the model's own output at the previous time step is used in the training. Predicted physics tendencies in the replay buffer with the most recent errors in the training iterations are reused, making the ML model learn from its own errors. The training method reduces the gap between the offline and online environments of the ML model. The method is used to train the ML model as the physical parameterization of the Community Atmosphere Model (CAM5) with training data from the Multi‐scale Modeling Framework high resolution simulations. Three 6‐year online simulations of the CAM5 are carried out by using the ML physics package. The simulated spatial distributions of precipitation, surface temperature and zonally averaged atmospheric fields demonstrate overall better accuracy than that of the standard CAM5 and benchmark model even without the use of additional physical constraints or tuning. This work is the first to demonstrate a solution to address the online instability problem in climate modeling with ML physics by using experience replay.
54 ENVIRONMENTAL SCIENCES↗
Poleward Migration of the Latitude of Maximum Tropical Cyclone Intensity—Forced or Natural?
Abstract Past studies have shown a significant observed poleward trend in the latitude at which tropical cyclones reach their lifetime maximum intensity (LMI), especially in the northwest Pacific basin. Given the brevity of the historical record, it remains difficult to separate the forced trend from internal variability of the climate system. A recently developed tropical cyclone downscaling model is used to downscale the Community Earth System Model, version 2 (CESM2), preindustrial control simulation. It is found that the observed trend in the latitude at which tropical cyclones reach their LMI in the northwest Pacific is very unlikely to be caused by internal variability. The same downscaling model is then used to downscale CESM2 simulations under historical forcing. The resulting trend distribution shows a significant poleward migration of tropical cyclone LMI even after regressing out both natural variability and the part of the forced warming pattern that projects onto natural variability. The results indicate that the observed poleward migration of the latitude at which tropical cyclones reach their LMI in the northwest Pacific basin is likely to be, at least in part, forced. However, the magnitude of the projected poleward trend in climate models can be significantly modulated by the simulated spatial pattern of ocean warming. This highlights how discrepancies between models and observations, with regard to projected changes to the equatorial zonal sea surface temperature gradient under anthropogenic forcing, can lead to large uncertainties in projected changes to the LMI latitude of tropical cyclones. Significance Statement Observations in the northwest Pacific basin show that the latitude at which tropical cyclones are at their most intense has been trending northward in the recent half century. These changes are important since tropical cyclones could bring hazardous weather to coastal areas that are poorly equipped to handle them. Here, we show that natural variations in Earth’s climate are very unlikely to explain the observed poleward trend in the latitude that tropical cyclone reach their maximum intensity. We find that it is much more likely that the observed trend is forced by human-related emissions, though the spatial pattern of warming in response to greenhouse emissions can have significant impacts on the magnitude of the trend.
Lin, Jonathan↗
Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape: Modeling Archive
This modeling archive is in support of the Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) publication "Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape", by Murphy et al. (2025). This archive contains model input files and outputs from landscape-scale simulations conducted using ELM, the land model component of the Department of Energy’s Energy Exascale Earth System Model (E3SM), at the Council NGEE Arctic field site (Council Road mile marker 71) on Alaska’s Seward Peninsula. Input data and model output from two sets of ELM simulations are provided. The first set of simulations were conducted with the two default ELM Arctic plant functional types (PFTs; broadleaf deciduous boreal shrub and a C3 grass) and the second set of simulations were conducted with a set of nine Arctic-specific PFTs including nonvascular mosses and lichens, graminoids, forbs, evergreen dwarf shrubs, three height classes of deciduous shrubs (dwarf, low, and low to tall), and deciduous alder shrubs (Sulman et al., 2021). Parameter names and major parameter changes in the Arctic-specific PFT configuration are described in Sulman et al. (2021) and archived in the Sulman et al. (2021) dataset (see below). Simulations were spatially explicit, covering an approximately 6.4X3.3 km domain at the Council site with a spatial resolution of 100 m for a total of 2,112 simulated grid cells under each ELM PFT configuration. The modeling archive contains meteorological forcing (seven *.nc files and one *.txt file), a domain definition file (one *.nc files), land surface configuration files (two *.nc files), parameter files (two *.nc files), annual ELM output files spanning 1980-2014 (68 *.nc files), and a User’s Guide (*pdf file). Additional information on the provided files is in the “Modeling Archive Contents” section of the User’s Guide. Model outputs are aggregated to the column scale (i.e. PFT-specific outputs are not provided here).
Murphy, Bailey [ORNL] (ORCID:0000000203995221)↗
Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra: Modeling Archive
This dataset is a model archive of the paper Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra (in prep) to support a modeling study investigating how projected increases in Arctic temperature and precipitation will jointly influence hydrologic conditions in ice-rich tundra landscapes. With this dataset, this study is to address the research question: Will Arctic tundra landscapes become wetter or drier with increasing precipitation and temperature in the future when thaw-induced ground subsidence and associated microtopographic evolution are represented? The simulations focus on ice-wedge polygon tundra, a widespread form of ice-rich permafrost terrain that is highly sensitive to thaw-driven landscape change. This dataset contains model input and output data for four study watersheds in Alaska: Anaktuvuk, Utqiagvik (formerly Barrow), Brooks Foothills, and Prudhoe Bay. Simulations were performed using the Advanced Terrestrial Simulator (ATS, v1.5), a physics-rich integrated surface–subsurface hydrologic model. For each watershed, ten modeling cases were performed representing two landscape evolution conditions (with subsidence and without subsidence) combined with five climate forcing scenarios derived from Shared Socioeconomic Pathways (SSP5, SSP5 with precipitation trend, SSP2, SSP2 with precipitation trend, and SSP2 with double precipitation trend). Particularly, for each watershed under the forcing SSP2 with precipitation trend, there are two additional simulations considering spatially heterogeneous subsidence distributions: one assumes randomly distributed scaling and the other includes elevation dependent distribution scaling. These simulations span 1980–2099 and include spin-up runs (1980–2009) followed by transient projections (2010–2099). To facilitate reproducibility of simulations, all datasets are organized by watershed. For each study watershed, the dataset contains: (1) Pre-partitioned mesh files for 32-core modeling (.par.32.XX), located in EACH_WATERSHED/mesh/basin; and also a non-partitioned mesh file (.exo) located in EACH_WATERSHED/mesh; (2) Climate forcings corresponding to the five SSP scenarios (.h5), located in EACH_WATERSHED/data; (3) Final states (.h5) from column spin-up modeling used to initialize historical watershed-scale spin-up runs from 1980 to 2009, located in EACH_WATERSHED/PreSpinupHistorical; (4) Final states (.h5) of historical watershed-scale spin-up runs from 1980 to 2009 used to initialize projection runs, located in EACH_WATERSHED/Spinup_daymetERA5; (5) ATS modeling input files (.xml), located in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/inputfiles; (6) ATS modeling output files (.dat), located in in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/combined_obs; (7) For the Brooks Foothills watershed, additional spatial model outputs are provided (.h5) for selected years (2033 and 2093) used to generate spatial figures in this study, located in Brooksfoothills/EACH_SIMULATION_SCENARIO/results-WITH/WITHOUT_SUBSIDENCE-year2033/2093. All data files with suffix .h5 can be accessible through Python h5py, and all data files with suffix of .dat can be imported by Python pandas. Mesh file with .exo can be visualized through Paraview or read by Python netCDF. The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research. Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.
EARTH SCIENCE > ATMOSPHERE > PRECIPITATION↗
Simulations of divertor designs that spatially separate power and particle exhaust using mid-leg divertor particle pumping
Predictive design modeling of a Dissipation-Focused Divertor for future operation in DIII-D reveals that increasing the poloidal distance of the pump duct entrance from the target surface along the low-field side divertor baffle increases neutral compression and modifies the spatial distribution of power dissipation. With a divertor pump located mid-leg between the target and the X-point, SOLPS-ITER boundary plasma simulations without drifts predict the formation of a dense neutral cloud near the target with > 30x higher neutral compression in detachment, a more stable detachment front located further from the target, and ~25% lower outer midplane separatrix density required for detachment onset, compared to a pump located in the scrape-off layer at the target surface. Up to 19 MW of power flowing into the divertors is modeled using the following two numerical implementations for particle pumping: a specified fraction of particles incident on variable wall sections of the plasma grid is removed from the computational domain (so-called albedo pumping), and a pump duct is modeled which includes dynamics of kinetic neutrals in the duct. The simulations show that the detachment front is located between the divertor target and the X-point and is relatively stable near the pump entrance, without a strong dependence on gas puff rate or injected power. The mid-leg pump design spatially separates the two primary functions of a divertor (power handling and particle exhaust), with the majority of power dissipation occurring near the target plate and particle exhaust taking place further upstream. The benefit of enhanced dissipation using mid-leg pumping comes at the cost of a higher outer midplane separatrix density for a given amount of particle injection.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Convergence in simulating global soil organic carbon by structurally different models after data assimilation
Abstract Current biogeochemical models produce carbon–climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first‐order or Michaelis–Menten kinetics at the global scale. Nevertheless, a wider range of data with high‐quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics‐function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.
54 ENVIRONMENTAL SCIENCES↗
Comparison of spatial dynamics and point kinetics approaches in multiphysics modeling of the molten salt reactor experiment
In this work, we present validation test results of fully coupled neutronics and thermal-hydraulics models of the Molten Salt Reactor Experiment (MSRE) against experimental data of the zero power pump transients and the natural circulation tests at low power. To capture the strong coupling between neutronics and thermal-hydraulics due to fuel circulation, and to account for the delayed neutron precursor (DNP) distribution, the porous media thermal-hydraulics solver Pronghorn was fully coupled to the spatial neutron dynamics code Griffin, which solves the neutron diffusion equation, and to the 0-D point kinetics solver Squirrel, using a 2-D homogenized representation of the MSRE. The validation test results show very good agreement with experimental data for both point kinetics and spatial dynamics simulations, capturing the strong feedback effect and DNP losses in the MSRE. The 0-D code Squirrel accurately predicted the time-dependent behavior in the MSRE given the steady-state spatial dynamics solution of Griffin.
42 - ENGINEERING↗
Generating Protein Structures for Pathway Discovery Using Deep Learning
Resolving the intricate details of biological phenomena at the molecular level is fundamentally limited by both length- and time scales that can be probed experimentally. Molecular dynamics (MD) simulations at various scales are powerful tools frequently employed to offer valuable biological insights beyond experimental resolution. However, while it is relatively simple to observe long-lived, stable configurations of, for example, proteins, at the required spatial resolution, simulating the more interesting rare transitions between such states often takes orders of magnitude longer than what is feasible even on the largest supercomputers available today. One common aspect of this challenge is pathway discovery, where the start and end states of a scientific phenomenon are known or can be approximated, but the mechanistic details in between are unknown. Here, we propose a representation-learning-based solution that uses interpolation and extrapolation in an abstract representation space to synthesize potential transition states, which are automatically validated using MD simulations. The new simulations of the synthesized transition states are subsequently incorporated into the representation learning, leading to an iterative framework for targeted path sampling. Our approach is demonstrated by recovering the transition of a RAS-RAF protein domain (CRD) from membrane-free to interacting with the membrane using coarse-grain MD simulations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗