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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Air-coupled tsunamis generated from impacts and airbursts: Our understanding before Hunga-Tonga Hunga-Ha'apai

The effort to prevent or mitigate the effects of an impact on Earth is known as planetary defense. A significant component of planetary defense research involves risk assessment. Much of our understanding of the risk from near-Earth objects comes from the geologic record in the form of impact craters, but not all asteroid impacts are crater-forming events. Small asteroids explode before reaching the surface, generating an airburst, and most impacts into the ocean do not penetrate the water to form a crater in the sea floor. The risk from these non-crater-forming ocean impacts and airbursts is difficult to quantify and represents a significant uncertainty in our assessment of the overall threat. We are currently working to better understand impact scenarios that can generate dangerous tsunamis. One of the suggested mechanisms for the production of asteroid–generated tsunamis is by direct coupling of the pressure wave to the water, analogous to the means by which a moving weather front can generate a meteotsunami. To test this hypothesis, we ran a series of airburst simulations and provided time-resolved pressure and wind profiles to use as source functions for tsunami models. We used the CTH hydrocode to model the various airburst scenarios to compare to the results of other simulations and provide time dependent boundary conditions as input to shallow-water wave propagation codes. The strongest and most destructive meteotsunamis are generated by atmospheric pressure oscillations with amplitudes of only a few hPa1 (mbar), corresponding to changes in sea level of a few cm. The resulting wave is strongest when there is a resonance between the ocean and the atmospheric forcing. A Proudman resonance takes place when the atmospheric disturbance’s translational speed (U) equals the longwave phase speed $\sqrt{gh}$ of shallow water wave. Coupling is strongest when the Froude number (Fr=U/c) is unity. A weather front propagates much slower than the speed of sound, so meteotsunamis are most common and dangerous in shallow bodies of water such as the Mediterranean Sea or Lake Michigan. By contrast, the blast wave from an airburst or crater-forming impact propagates at a speed faster than a tsunami in the deepest ocean, and a Proudman resonance cannot be achieved even though the overpressures are orders of magnitude greater. However, blast wave profiles are N-waves in which a sharp shock wave leading to overpressure is followed by a more gradual rarefaction to a much longer-duration underpressure phase. Even though the blast outruns the water wave it is forcing, the tsunami should continue to be driven by the out-of-resonance gradient associated with the suction phase, which may depend strongly on the details of the airburst or impact scenario. The open question is whether there are any conditions under which such an airburst-driven tsunami can be dangerous enough to contribute to the overall impact risk. We have also identified other potential mechanisms for airburst-generated tsunamis: 1) reaction force at the surface from the plume ejected into space, which carries significant momentum, 2) expanding toroidal vortices at the surface, which travel more slowly than the shock wave and can generate a Proudman resonance in relatively shallow ocean (such as continental shelf), and 3) steam explosion from seawater ablation by a “Type II” (Libyan Desert Glass-type) airburst in which the hot vapor jet descends to the surface. On January 15, 2022, the Hunga-Tonga Hunga-Ha’apai volcano, located approximately 60 km north of Tongatapu, the main island of Tonga, violently erupted with a powerful explosion, culminating the period of volcanic activity that started in December of 2021. This event and resulting tsunamis provided an existence proof for the air pressure wave coupling mechanism we proposed. It also suggests that it can be stronger and more significant over much greater distances than we contemplated, leading to global tsunamis associated with impact events on land as well as in the water. Large atmospheric explosions generate global Lamb waves with larger amplitudes, longer periods, and slower speeds than the local and regional blast waves we modeled prior to that event. This paper reviews our analysis and modeling of airburst-driven tsunamis prior to the 2022 Hunga-Tonga Hunga-Ha’apai tsunami, which was the subject of two presentations at the 2023 Planetary Defense Conference and is the subject of another paper currently in preparation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Phase transformation path in Aluminum under ramp compression; simulation and experimental study

Abstract We present a framework based on non-equilibrium molecular dynamics (NEMD) to reproduce the phase transformation event of Aluminum under ramp compression loading. The simulated stress-density response, virtual x-ray diffraction patterns, and structure analysis are compared against the previously observed experimental laser-driven ramp compression in-situ x-ray diffraction data. The NEMD simulations show the solid–solid phase transitions are consistent to experimental observations with a close-packed face-centered cubic (fcc) (111), hexagonal close-packed (hcp) structure (002), and body-centered cubic bcc (110) planes remaining parallel. The atomic-level analysis of NEMD simulations identifiy the exact phase transformation pathway happening via Bain transformation while the previous in situ x-ray diffraction data did not provide sufficient information for deducing the exact phase transformation path.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Magnetic tunnel junction random number generators applied to dynamically tuned probability trees driven by spin orbit torque

Abstract Perpendicular magnetic tunnel junction (pMTJ)-based true-random number generators (RNGs) can consume orders of magnitude less energy per bit than CMOS pseudo-RNGs. Here, we numerically investigate with a macrospin Landau–Lifshitz-Gilbert equation solver the use of pMTJs driven by spin–orbit torque to directly sample numbers from arbitrary probability distributions with the help of a tunable probability tree. The tree operates by dynamically biasing sequences of pMTJ relaxation events, called ‘coinflips’, via an additional applied spin-transfer-torque current. Specifically, using a single, ideal pMTJ device we successfully draw integer samples on the interval [0, 255] from an exponential distribution based on p -value distribution analysis. In order to investigate device-to-device variations, the thermal stability of the pMTJs are varied based on manufactured device data. It is found that while repeatedly using a varied device inhibits ability to recover the probability distribution, the device variations average out when considering the entire set of devices as a ‘bucket’ to agnostically draw random numbers from. Further, it is noted that the device variations most significantly impact the highest level of the probability tree, with diminishing errors at lower levels. The devices are then used to draw both uniformly and exponentially distributed numbers for the Monte Carlo computation of a problem from particle transport, showing excellent data fit with the analytical solution. Finally, the devices are benchmarked against CMOS and memristor RNGs, showing faster bit generation and significantly lower energy use.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Feedback and Oscillations: Constructing Feedback Systems for Root Cause Analysis of Oscillations in Power Grids

Dynamic phenomena linked to inverter-based resources (IBRs) have gained global attention. Several IBR-induced dynamics have caused bulk power system-connected wind or solar power plants to trip, and some have even led to widespread outages. In addition, many oscillations have been observed involving IBR power plants. In 2023, the IEEE Power & Energy Society (PES) IBR Subsynchronous Oscillations (SSO) task force published a journal article, “Real-World Subsynchronous Oscillation Events in Power Grids With High Penetrations of Inverter-Based Resources,” in which 19 IBR oscillation events were examined for their causation. Earlier in 2020, another PES task force article, “Definition and Classification of Power System Stability-Revisited & Extended,” authored by prominent academics, introduced converter-driven stability as a new category of stability. The international power grid industry community also took action by publishing the CIGRE Green Book, Power System Dynamic Modelling and Analysis in Evolving Networks (led by Babak Badrzadeh and Zia Emin) in 2024. In August 2024, the Energy Systems Integration Group (ESIG) released a practical guide led by Nick Miller, “Diagnosis and Mitigation of Observed Oscillations in IBR-Dominant Power System: A Practical Guide.” The goal of the guide is to assist practicing engineers in making initial judgments and conducting detailed analyses about oscillations. Finally, when addressing the classification of stability and oscillations, the guide emphasizes a causality-based taxonomy for grouping, such as voltage control-induced oscillations, synchronization-induced oscillations, and frequency or active power control-induced oscillations.

Fan, Lingling [Univ. of South Florida, Tampa, FL (↗
DOE OSTI2022

A Data Quality-Aware Framework to Reliably Forecast Photovoltaic Generation and Consumer Load for an Improved Resilience of Microgrids

Photovoltaic (PV) power and consumer load forecasting plays a critical role to ensure operational resilience of the electric grid. Most data-driven forecasting algorithms rely heavily on the continuous availability of good quality data for periodic training and validation. When deployed at the grid’s edge, prolonged disruptions to communications during extreme events degrade data quality. Factors such as missing observations, epistemic uncertainties, data drift, and concept drift are manifestations of data quality that impact the generalization of such field-deployed forecasting models. Currently, there exists no mechanism in the literature to dynamically switch between models under varying degrees of data quality as quantified by certain metrics for each factor highlighted above. This paper addresses this shortcoming by conceptually introducing a data qualityaware framework for reliable PV generation and consumer load forecasting. The framework’s design incorporates components of missing values, divergence tests, and continuous monitoring of generalization performance to detect changes in data quality caused by communications disruptions and trigger specific classes of forecasting models grouped under three use cases (UC1- UC3). As a first step towards validating this framework, real data collected from an actual field microgrid system is used to demonstrate the viability of the three use cases. Results show that the performance is the best in UC1 with an unadjusted R-square value of 0.954, followed by 0.939 for UC2 and 0.757 for UC3.

Sundararajan, Aditya↗
DOE OSTI2021

Supernova neutrino signals based on long-term axisymmetric simulations

ABSTRACT We study theoretical neutrino signals from core-collapse supernova (CCSN) computed using axisymmetric CCSN simulations that cover the post-bounce phase up to ∼4 s. We provide basic quantities of the neutrino signals such as event rates, energy spectra, and cumulative number of events at some terrestrial neutrino detectors, and then discuss some new features in the late phase that emerge in our models. Contrary to popular belief, neutrino emissions in the late phase are not always steady, but rather have temporal fluctuations, the vigour of which hinges on the CCSN model and neutrino flavour. We find that such temporal variations are not primarily driven by proto-neutron star convection, but by fallback accretion in exploding models. We assess the detectability of these temporal variations, and find that IceCube is the most promising detector with which to resolve them. We also update fitting formulae first proposed in our previous paper for which the total neutrino energy emitted at the CCSN source is estimated from the cumulative number of events in each detector. This will be a powerful technique with which to analyse real observations, particularly for low-statistics data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Enhanced Component Performance Study: Turbine-Driven Pumps 1998–2018

This report presents an enhanced performance evaluation of turbine-driven pumps (TDPs) at U.S. commercial nuclear power plants. The data used in this study are based on the operating experience failure reports from calendar year 1998 through 2018 as reported in the Institute of Nuclear Power Operations (INPO) Consolidated Events Database (ICES). The TDP failure modes considered are failure to start (FTS), failure to run less than or equal to one hour (FTR≤1H), failure to run more than one hour (FTR>1H), and normally running systems FTS and failure to run (FTR). The component reliability estimates and the reliability data are trended for the most recent 10-year period while yearly estimates for reliability are provided for the entire study period. A highly statistically significant decreasing trend was identified in the standby TDP unavailability estimates.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Core-collapse supernova neutrino emission and detection informed by state-of-the-art three-dimensional numerical models

ABSTRACT Based on our recent three-dimensional core-collapse supernova (CCSN) simulations including both exploding and non-exploding models, we study the detailed neutrino signals in representative terrestrial neutrino observatories, namely Super-Kamiokande (Hyper-Kamiokande), DUNE, JUNO, and IceCube. We find that the physical origin of difference in the neutrino signals between 1D and 3D is mainly proto-neutron-star convection. We study the temporal and angular variations of the neutrino signals and discuss the detectability of the time variations driven by the spiral standing accretion shock instability (spiral SASI) when it emerges for non-exploding models. In addition, we determine that there can be a large angular asymmetry in the event rate (${\gtrsim} 50 {{\ \rm per\ cent}}$), but the time-integrated signal has a relatively modest asymmetry (${\lesssim} 20 {{\ \rm per\ cent}}$). Both features are associated with the lepton-number emission self-sustained asymmetry and the spiral SASI. Moreover, our analysis suggests that there is an interesting correlation between the total neutrino energy (TONE) and the cumulative number of neutrino events in each detector, a correlation that can facilitate data analyses of real observations. We demonstrate the retrieval of neutrino energy spectra for all flavours of neutrino by applying a novel spectrum reconstruction technique to the data from multiple detectors. We find that this new method is capable of estimating the TONE within the error of ∼20 per cent if the distance to the CCSN is ≲6 kpc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Identifying neutron sources using recoil and time-of-flight spectroscopy

Identification of neutron sources is central to nuclear physics and its applications, from planetary science to nuclear security, yet direct source discrimination from measured neutron spectra remains fundamentally elusive. Here, we introduce a Bayesian protocol that directly infers source ensembles from measured neutron spectra by combining full-spectrum template matching with probabilistic evidence evaluation. Applying this protocol to recoil and time-of-flight spectroscopy, we recover single- and two-source configurations with strong statistical significance (beyond 4⁢𝜎) at event counts as low as ∼10 3 . These results demonstrate that neutron spectral signatures can be leveraged for robust source identification, opening a new observational window for both fundamental research and operationally driven applications.

neutron physics↗
DOE OSTI2021

Multiple Indicators of Extreme Changes in Snow-Dominated Streamflow Regimes, Yakima River Basin Region, USA

Snow plays a major role in the hydrological cycle. Variations in snow duration and timing can have a negative impact on water resources. Excluding predicted changes in snowmelt rates and amounts could result in deleterious infrastructure, military mission, and asset impacts at military bases across the US. A change in snowpack can also lead to water shortages, which in turn can affect the availability of irrigation water. We performed trend analyses of air temperature, snow water equivalent (SWE) at 22 SNOTEL stations, and streamflow extremes for selected rivers in the snow-dependent and heavily irrigated Yakima River Basin (YRB) located in the Pacific Northwest US. There was a clear trend of increasing air temperature in this study area over a 30 year period (water years 1991–2020). All stations indicated an increase in average air temperatures for December (0.97 °C/decade) and January (1.12 °C/decade). There was also an upward trend at most stations in February (0.28 °C/decade). In December–February, the average air temperatures were 0.82 °C/decade. From these trends, we estimate that, by 2060, the average air temperatures for December–February at most (82%) stations will be above freezing. Furthermore, analysis of SWE from selected SNOTEL stations indicated a decreasing trend in historical SWE, and a shift to an earlier peak SWE was also assumed to be occurring due of the shorter snow duration. Decreasing trends in snow duration, rain-on-snow, and snowmelt runoff also resulted from snow modeling simulations of the YRB and the nearby area. We also observed a shift in the timing of snowmelt-driven peak streamflow, as well as a statistically significant increase in winter maximum streamflow and decrease in summer maximum and minimum streamflow trends by 2099. From the streamflow trends and complementary GEV analysis, we show that the YRB basin is a system in transition with earlier peak flows, lower snow-driven maximum streamflow, and higher rainfall-driven summer streamflow. This study highlights the importance of looking at changes in snow across multiple indicators to develop future infrastructure and planning tools to better adapt and mitigate changes in extreme events.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Design of a High-Pressure Fuel System for Use with Dimethyl Ether

The paper documents the modeling and experimental work on a common rail fuel injection system for Dimethyl Ether, a potential diesel substitute with a low carbon intensity signature. The DME fuel system is deployed on a light duty 2.2L compression ignition engine. The paper describes the injector optimization to shift to higher flows to account for the lower heating value and density of the DME when compared to diesel. The type of the injection system used for the DME application is an advanced rendering of the Common rail noted for a one-piece piston-needle injector construction and a solenoid driven spill valve featuring a pressure balanced poppet. A dedicated high-pressure fuel pump designed to pressurize DME is used. The design results in a fast acting open and close injection event, reduced leakage, with reduced cavitation in the fuel injector volume. Design parameters for system optimization included fill and spill orifices, needle lift, bias spring, and injector hole size. The design model provides good correlation of the instantaneous rates of injection with experiments across a wide range of pressure and injection timings. Proposed performance milestones for the design included similar DME injection duration to the diesel counterpart for same fuel energy injected into the cylinder to retain high engine cycle efficiency. Here, the dedicated DME design provided reduced hydraulic delays of 50%. Tests demonstrated sustained operation at pressures of 1000 bar, with capability to reach 1500bar. Durability tests showed no cavitation-deterioration over a 200-hour test cycle by means of spray imaging and hardware inspection.

De Ojeda, William [WM International Engineering, L↗
DOE OSTI2026

A Data-Driven Method for Synthetic Extreme Weather Generation and Solar Impact Assessment: Preprint

High-resolution, high-fidelity weather datasets are essential for testing and evaluating the resilience of power systems, particularly under extreme weather conditions. However, existing extreme weather datasets are typically derived from historical events that are localized and may lack the spatial and temporal resolution or scenario diversity needed to test largescale power systems. In this work, we propose a synthetic extreme weather simulation approach capable of generating targeted extreme events, such as hurricanes, using publicly available data sources. Preliminary results demonstrate the impact of a simulated Category 1 hurricane on renewable generation and critical infrastructure in California. The work aims to provide a flexible approach for creating multiple types of extreme weather scenarios across different regions, enabling comprehensive system stress testing, training, and resilience assessment.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

The 2024 July 16 solar event: a challenge to the coronal mass ejection origin of long-duration gamma-ray flares

We present a multi-spacecraft analysis of the 2024 July 16 long-duration gamma-ray flare (LDGRF) detected by the Large Area Telescope on the Fermi satellite. The measured > 100 MeV γ-ray emission persisted for over seven hours after the flare impulsive phase, and was characterized by photon energies exceeding 1 GeV and a remarkably hard parent-proton spectrum. In contrast, the phenomena related to the coronal mass ejection (CME)-driven shock linked to this eruption were modest, suggesting an inefficient proton acceleration unlikely to achieve energies well above the 300 MeV pion-production threshold to account for the observed γ-ray emission. Specifically, the CME was relatively slow (∼600 km/s) and the accompanying interplanetary type-II/III radio bursts were faint and short-lived, unlike those typically detected during large events. In particular, the type-II emission did not extend to kilohertz frequencies and disappeared ∼5.5 hours prior to the LDGRF end time. Furthermore, the associated solar energetic particle (SEP) event was very weak, short-duration, and limited to a few tens of MeV, even at magnetically well-connected spacecraft. These findings demonstrate that a very fast CME resulting in a high-energy SEP event is not a necessary condition for the occurrence of LDGRFs, challenging the idea that the high-energy γ-ray emission is produced by the back-precipitation of shock-accelerated ions into the solar surface. The alternative origin scenario based on local particle trapping and acceleration in large-scale coronal loops is instead favored by the observation of giant arch-like structures of hot plasma over the source region that persisted for the entire duration of this LDGRF.

Sun: UV radiation↗
DOE OSTI2023

Northern Hemisphere Snow Drought in Earth System Model Simulations and ERA5‐Land Data in 1980–2014

Abstract Low snow levels over the past few decades and predictions of a low‐to‐no snow future have spurred research into snow droughts, which pose a threat to water security and management. Systematic data‐model comparisons of snow drought have been lacking, hindering our understanding of the drivers of snow drought in the past. To address this gap, we analyzed snow drought events using standardized snow water equivalent index derived from monthly results of four numerical experiments using the E3SM Land Model (ELM) and ERA5‐Land data during the period of 1980–2014. Additionally, we compared snow drought duration calculated from models with those from the ERA5‐Land data during selected El Niño‐Southern Oscillation (ENSO) years. The numerical experiments were conducted with ELM driven by two prescribed atmospheric forcings, and with the coupled land‐atmosphere configuration of E3SM with and without plant hydraulics scheme feedback. Analysis reveals that 20%–30% of snow droughts occur due to factors other than above‐normal temperature and low snowfall, such as low soil moisture, warm soil temperature, and low relative humidity, etc., especially in high latitudes (50° North). Furthermore, our study highlights the exacerbating effect of ENSO events on snow drought conditions in various regions, despite some discrepancies between model and ERA5‐Land results. We also identified limitations of the coupled land‐atmosphere models in our current configuration in capturing the spatial patterns of snow droughts. This study underscores the challenge of predicting and mitigating snow drought and the need for a comprehensive understanding of the factors contributing to snow drought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Grain boundary softening from stress assisted helium cavity coalescence in ultrafine-grained tungsten

The formation of helium cavities in coarse-grained materials produces hardening proportional to the number density and size of the cavities and due to the interaction of dislocations with intragranular helium defects. In nanostructured metals containing a high density of interfacial sinks, preferential cavity formation in the grain boundaries instead produces softening that is often attributed to enhanced interfacial plasticity. Here, employing two grades of ultrafine-grained tungsten, we explore this effect using targeted implantation studies to map cavity evolution as a function of the irradiation conditions and quantify its impact on the mechanical response through nanoindentation. Softening is reported at implantation temperatures above the threshold for preferential grain boundary cavity formation but at a sufficiently low fluence prior to the growth of intragranular cavities. Collective changes in the mean cavity size, density, and morphology beneath a residual impression on an implanted surface indicate that cavity coalescence accompanied the reduction in hardness. Complementary atomistic simulations demonstrate that, in tungsten grain structures exhibiting softening, grain boundary bubble coalescence is driven by stress concentrations that further act to localize strain in the grain boundaries through cooperative deformation processes involving local atomic shuffling and sliding, dislocation emission, and even the nucleation of unstable twinning events.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Insights into Methodologies and Operational Details of Resource Adequacy Assessment: A Case Study with Application to a Broader Flexibility Framework

Assessing and maintaining resource adequacy (RA) is a core pillar of power systems. However, recent changes in the physical makeup of these systems and the conditions under which these systems must operate have yielded a renewed interest in the methods, metrics, and assumptions that underpin RA assessments. In this paper, we systematically explore a wide range of RA modeling dimensions, including: the objective function and level of operational detail in the underlying model formulation; the quantity (look-ahead) and quality (accuracy) of data that is available for making operational decisions within those models; and the physical configuration of solar photovoltaics (PV) with battery storage hybrid resources. We apply a set of probabilistic RA tools and production cost modeling tools to a realistic test system based loosely on a future Electric Reliability Council of Texas power system dominated by solar PV resources. Under the assumptions of our system and models, we find that multi-stage probabilistic assessments may provide a more robust evaluation of RA by capturing a wider range of operational and system interactions, but this comes at a computational cost of 1-2 orders of magnitude longer run time depending on the specific configuration. In addition, the information on thermal generator availability impacts RA performance by an order of magnitude more than solar resource forecasts, which is driven by the comparatively larger magnitude of thermal outages than solar forecast errors within our test system. Lastly, the flexibility provided by hybrid and other resources can help reduce system load-shedding event frequencies and enable the system to be more robust to inaccurate forecast information, and alternative hybrid inverter sizes can impact RA levels by 1-2 orders of magnitude. Our results point to the importance of a broader flexibility framework to describe the interaction between (1) flexibility "supply" from both physical resource capabilities and operational constraints considered in the modeling, and (2) flexibility "demand" from forecast errors, thermal generator outages, and other sources of uncertainty, as well as their RA impacts. Results are likely sensitive to the system buildout explored; future work could consider additional system configurations and conditions.

ENERGY PLANNING, POLICY, AND ECONOMY,POWER TRANSMI↗
DOE OSTI2024

CO–induced roughening of Cu(111): formation and detection of reactive nanoclusters on metal surfaces

The formation of nanoclusters on metal surfaces in the presence of reactive environments is a phenomenon with important implications for catalysis. These nanoclusters are composed of atoms ejected from undercoordinated sites such as step edges, and their presence alters the catalytic properties of solid materials. We perform density functional theory (DFT) and kinetic Monte Carlo (KMC) simulations to investigate the formation and reactivity of copper clusters on Cu(111). Our results indicate a considerably higher reactivity of small copper nanoclusters, with up to seven atoms in size on roughened copper surfaces than on pristine Cu(111) and Cu(211). Regarding the restructuring events that give rise to nanoclusters under CO atmospheres, we determine that the ejection of Cu atoms from step edges and their migration therefrom to adjacent Cu(111) terraces are, by and large, driven by CO coverage effects. By means of KMC simulations, which account for CO–CO lateral interactions and CO–induced surface restructuring, we show that temperature programmed desorption (TPD) holds promise for the detection of highly reactive nanoclusters. Furthermore, our approach showcases how surface restructuring and surface–adsorbate bond breaking can be combined when modeling surface reactions and contributes to the development of an advanced understanding of the nature of active site under reaction conditions.

catalyst dynamic restructuring↗
DOE OSTI2024

A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop

The folding and unfolding of RNA stem-loops are critical biological processes; however, their computational studies are often hampered by the ruggedness of their folding landscape, necessitating long simulation times at the atomistic scale. Here, we adapted DeepDriveMD (DDMD), an advanced deep learning-driven sampling technique originally developed for protein folding, to address the challenges of RNA stem-loop folding. Although tempering- and order parameter-based techniques are commonly used for similar rare-event problems, the computational costs or the need for a priori knowledge about the system often present a challenge in their effective use. DDMD overcomes these challenges by adaptively learning from an ensemble of running MD simulations using generic contact maps as the raw input. DeepDriveMD enables on-the-fly learning of a low-dimensional latent representation and guides the simulation toward the undersampled regions while optimizing the resources to explore the relevant parts of the phase space. We showed that DDMD estimates the free energy landscape of the RNA stem-loop reasonably well at room temperature. Our simulation framework runs at a constant temperature without external biasing potential, hence preserving the information on transition rates, with a computational cost much lower than that of the simulations performed with external biasing potentials. Here, we also introduced a reweighting strategy for obtaining unbiased free energy surfaces and presented a qualitative analysis of the latent space. This analysis showed that the latent space captures the relevant slow degrees of freedom for the RNA folding problem of interest. Finally, throughout the manuscript, we outlined how different parameters are selected and optimized to adapt DDMD for this system. We believe this compendium of decision-making processes will help new users adapt this technique for the rare-event sampling problems of their interest.

Gupta, Ayush↗