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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Effects of anisotropic shale creep on the stress and permeability evolution of a geological nuclear waste repository

To ensure long-term safety and performance, geological nuclear waste repositories require low-permeability barriers such as bentonite buffers and/or shale host rock. Shale is not only known for its low permeability but also for its trend to undergo time-dependent deformation (i.e., creep), which could heal damage, but the effects of shale creep on the long-term performance of nuclear waste repositories have not been clearly understood. In particular, the anisotropic nature of shale (i.e., bedding) could have a significant effect on its creep behavior, and consequently, on the long-term performance of nuclear waste repositories. In this research, numerical simulations were carried out with the objective of showing the effects of anisotropic shale creep on the stress and permeability evolution of a generic geological nuclear waste repository in shale. The TOUGH-FLAC simulator, a thermo-hydromechanically (THM) coupled numerical code, was used for the simulations. To achieve the objective, comparisons were performed between the results of anisotropic shale creep simulations and those of different simulation cases, namely, no creep (i.e., elastic), isotropic creep, and long-term creep shale cases. Results of the comparisons show that the elastic and isotropic creep shale cases respectively led to the overestimation and underestimation of stress and permeability in the repository, whereas the long-term creep shale case, which accumulated greater creep in later periods than in earlier periods, helped to keep large shear and tensile stresses from developing while maintaining compressive spherical stress, resulting in consistently low permeability levels. These results indicate that performance assessments with elastic and isotropic creep formation models will provide the upper and lower bound estimates of stress and permeability, while more reasonable estimates will be given by an anisotropic creep formation model, and that shale with long-term creep characteristics will be beneficial in many aspects of the safety and performance of nuclear waste repositories.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Characterizing how size distribution and concentration affect echogenicity of ultrasound contrast agents

Here, we investigated the effects of UCA gas bubble size distribution and concentration on the generated ultrasound echogenicity signal. Gas bubble size characterization using Coulter Counter and cryogenic-SEM revealed the hollow structure and rare presence of microbubbles >10 µm in a commercial UCA product, Lumason™. Volume-weighed size and concentration were observed to be more sensitive to changes in UCA bubble stability than number-weighted size and concentration. Size distribution measurements showed that the force (e.g., shaking/agitation energy) used to redisperse the sample did not affect the size distribution, concentration, or echogenicity of the UCA sample. The ultrasound backscattering coefficient (BSC) of size fractionated and serial diluted microbubbles showed that the echogenicity signal correlates most with UCA bubble concentration, especially volume-weighted concentration. Findings from this study may be used to support demonstrating the equivalence of a generic UCA product to the reference listed drug.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions

Spontaneous reactions between metabolites are often neglected in favor of emphasizing enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be insignificant under physiological conditions. However, synthetic biology and engineering efforts can raise natural metabolites' levels or introduce unnatural ones, so that previously innocuous or nonexistent spontaneous reactions become an issue. Problems arise when spontaneous reaction rates exceed the capacity of a platform organism to dispose of toxic or chemically active reaction products. While various reliable sources list competing or toxic enzymatic pathways' side-reactions, no corresponding compilation of spontaneous side-reactions exists, nor is it possible to predict their occurrence. We addressed this deficiency by creating the Chemical Damage (CD)-MINE resource. First, we used literature data to construct a comprehensive database of metabolite reactions that occur spontaneously in physiological conditions. We then leveraged this data to construct 148 reaction rules describing the known spontaneous chemistry in a substrate-generic way. We applied these rules to all compounds in the ModelSEED database, predicting 180,891 spontaneous reactions. The resulting (CD)-MINE is available at https://minedatabase.mcs.anl. gov/cdmine/#/home and through developer tools. We also demonstrate how damage-prone intermediates and end products are widely distributed among metabolic pathways, and how predicting spontaneous chemical damage helps rationalize toxicity and carbon loss using examples from published pathways to commercial products. We explain how analyzing damage-prone areas in metabolism helps design effective engineering strategies. Finally, we use the CD-MINE toolset to predict the formation of the novel damage product N-carbamoyl proline, and present mass spectrometric evidence for its presence in Escherichia coli.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Impurity temperature screening in stellarators close to quasisymmetry

Impurity temperature screening is a favourable neoclassical phenomenon involving an outward radial flux of impurity ions from the core of fusion devices. Quasisymmetric magnetic fields lead to intrinsically ambipolar neoclassical fluxes that give rise to temperature screening for low enough $\unicode[STIX]{x1D702}^{-1}\equiv d\ln n/d\ln T$ . In contrast, neoclassical fluxes in generic stellarators will depend on the radial electric field, which is predicted to be inward for ion-root plasmas, potentially leading to impurity accumulation. Here, we examine the impurity particle flux in a number of approximately quasisymmetric stellarator configurations and parameter regimes while varying the amount of symmetry breaking in the magnetic field. For the majority of this work, neoclassical fluxes have been obtained using the SFINCS drift-kinetic equation solver with electrostatic potential $\unicode[STIX]{x1D6F7}=\unicode[STIX]{x1D6F7}(r)$ , where $r$ is a flux-surface label. Results indicate that achieving temperature screening is possible, but unlikely, at low-collisionality reactor-relevant conditions in the core. Thus, the small departures from symmetry in nominally quasisymmetric stellarators are large enough to significantly alter the neoclassical impurity transport. A further look at the magnitude of these fluxes when compared to a gyro-Bohm turbulence estimate suggests that neoclassical fluxes are small in configurations optimized for quasisymmetry when compared to turbulent fluxes.

Physics↗
DOE OSTI2020

A new frontier in laboratory physics: magnetized electron–positron plasmas

We describe here efforts to create and study magnetized electron–positron pair plasmas, the existence of which in astrophysical environments is well-established. Laboratory incarnations of such systems are becoming ever more possible due to novel approaches and techniques in plasma, beam and laser physics. Traditional magnetized plasmas studied to date, both in nature and in the laboratory, exhibit a host of different wave types, many of which are generically unstable and evolve into turbulence or violent instabilities. This complexity and the instability of these waves stem to a large degree from the difference in mass between the positively and the negatively charged species: the ions and the electrons. The mass symmetry of pair plasmas, on the other hand, results in unique behaviour, a topic that has been intensively studied theoretically and numerically for decades, but experimental studies are still in the early stages of development. A levitated dipole device is now under construction to study magnetized low-energy, short-Debye-length electron–positron plasmas; this experiment, as well as a stellarator device that is in the planning stage, will be fuelled by a reactor-based positron source and make use of state-of-the-art positron cooling and storage techniques. Relativistic pair plasmas with very different parameters will be created using pair production resulting from intense laser–matter interactions and will be confined in a high-field mirror configuration. We highlight the differences between and similarities among these approaches, and discuss the unique physics insights that can be gained by these studies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Finite orbit width effects in large aspect ratio stellarators

New orbit-averaged equations for low collisionality neoclassical fluxes in large aspect ratio stellarators with mirror ratios close to unity are derived. The equations retain finite orbit width effects by employing the second adiabatic invariant $J$ as a velocity-space coordinate and they have been implemented in the orbit-averaged neoclassical code KNOSOS (Velasco et al. , J. Comput. Phys. , vol. 418, 2020, 109512; Velasco et al. , Nucl. Fusion , vol. 61, 2021, 116013). The equations are used to study the $1/\nu$ regime and the lower collisionality regimes. For generic large aspect ratio stellarators with mirror ratios close to unity, as the collision frequency decreases, the $1/\nu$ regime transitions directly into the $\nu$ regime, without passing through a $\sqrt {\nu }$ regime. An explicit formula for the neoclassical fluxes in the $\nu$ regime is obtained. The formula includes the effect of particles that transition between different types of wells. While these transitions produce stochastic scattering independent of the value of the collision frequency in velocity space, the diffusion in real space remains proportional to the collision frequency. The $\sqrt {\nu }$ regime is only recovered in large aspect ratio stellarators close to omnigeneity: large aspect ratio stellarators with large mirror ratios and optimized large aspect ratio stellarators with mirror ratios close to unity. Neoclassical transport in large aspect ratio stellarators with large mirror ratios can be calculated with the orbit-averaged equations derived by Calvo et al. ( Plasma Phys. Control. Fusion , vol. 59, 2017, 055014). In these stellarators, the $\sqrt {\nu }$ regime exists in the collisionality interval $(a/R) \ln (R/a) \ll \nu _{ii} R a/\rho _i v_{ti} \ll R/a$ . In optimized large aspect ratio stellarators with mirror ratios close to unity, the $\sqrt {\nu }$ regime occurs in an interval of collisionality that depends on the deviation from omnigeneity $\delta$ : $\delta ^{2} |\ln \delta | \ll \nu _{ii} R a/\rho _i v_{ti} \ll 1$ . Here, $\nu _{ii}$ is the ion–ion collision frequency, $\rho _i$ and $v_{ti}$ are the ion gyroradius and thermal speed, and $a$ and $R$ are the minor and major radii.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Mean-field dynamo as a quantum-like modulational instability

Presented here is a novel formulation of the mean-field dynamo as a modulational instability of magnetohydrodynamic (MHD) turbulence. This formulation, termed mean-field wave kinetics (MFWK), is based on the Weyl symbol calculus and allows describing the interaction between the mean fields (magnetic field and fluid velocity) and turbulence without requiring scale separation that is commonly assumed in the literature. The turbulence is described by the Wigner–Moyal equation for the spectrum of the two-point correlation matrix (Wigner matrix) of magnetic-field and velocity fluctuations and depicts the turbulence as an effective plasma of quantum-like particles that interact via the mean fields. Eddy–eddy interactions, which serve as ‘collisions’ in this effective plasma, are modelled within the standard minimal tau approximation to aid comparison with existing theories. Using MFWK, the non-local electromotive force is calculated for generic turbulence from first principles, modulo the limitations of MFWK. This result is then used to study, both analytically and numerically, the modulational modes of MHD turbulence, which appear as linear instabilities of the said effective quantum-like plasma of fluctuations. The standard α 2 -dynamo and other known results are reproduced as special cases. A new dynamo effect is predicted that is driven by correlations between the turbulent flow velocity and the turbulent current.

astrophysical plasmas↗
DOE OSTI2026

Detecting shearless phase-space transport barriers in global gyrokinetic turbulence simulations with test particle map models

In magnetically confined fusion plasmas, the role played by zonal 𝐸 x 𝐵 flow shear layers in the suppression of turbulent transport is relatively well understood. However, less is understood about the role played by the weak shear regions that arise in the non-monotonic radial electric field profiles often associated with these shear layers. In electrostatic simulations from the global total-𝑓 gyrokinetic particle-in-cell code XGC, we demonstrate how shearless regions with non-zero flow curvature form zonal ‘jets’ that, in conjunction with neighbouring regions of shear, can act as robust barriers to particle transport and turbulence spreading. By isolating quasi-coherent fluctuations radially localised to the zonal jets, we construct a map model for the Lagrangian dynamics of gyrokinetic test particles in the presence of drift waves. We identify the presence of shearless invariant tori in this model and verify that these tori act as partial phase-space transport barriers in the simulations. We also demonstrate how avalanches impinging on these shearless tori cause eddy detachment events that form ‘cold/warm core ring’ structures analogous to those found in oceanic jets, facilitating transport across the barriers without destroying them completely. We discuss how shearless tori may generically arise from tertiary instabilities or other types of discrete eigenmodes, suggesting their potential relevance to broader classes of turbulent fluctuations.

fusion plasma↗
DOE OSTI2020

Numerical methods for nonlocal and fractional models

Partial differential equations (PDEs) are used with huge success to model phenomena across all scientific and engineering disciplines. However, across an equally wide swath, there exist situations in which PDEs fail to adequately model observed phenomena, or are not the best available model for that purpose. On the other hand, in many situations, nonlocal models that account for interaction occurring at a distance have been shown to more faithfully and effectively model observed phenomena that involve possible singularities and other anomalies. Here, we consider a generic nonlocal model, beginning with a short review of its definition, the properties of its solution, its mathematical analysis and of specific concrete examples. We then provide extensive discussions about numerical methods, including finite element, finite difference and spectral methods, for determining approximate solutions of the nonlocal models considered. In that discussion, we pay particular attention to a special class of nonlocal models that are the most widely studied in the literature, namely those involving fractional derivatives. The article ends with brief considerations of several modelling and algorithmic extensions, which serve to show the wide applicability of nonlocal modelling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Deep Learning-Enabled MS/MS Spectrum Prediction Facilitates Automated Identification Of Novel Psychoactive Substances

The market for illicit drugs has been reshaped by the emergence of more than 1100 new psychoactive substances (NPS) over the past decade, posing a major challenge to the forensic and toxicological laboratories tasked with detecting and identifying them. Tandem mass spectrometry (MS/MS) is the primary method used to screen for NPS within seized materials or biological samples. The most contemporary workflows necessitate labor-intensive and expensive MS/MS reference standards, which may not be available for recently emerged NPS on the illicit market. Here, we present NPS-MS, a deep learning method capable of accurately predicting the MS/MS spectra of known and hypothesized NPS from their chemical structures alone. NPS-MS is trained by transfer learning from a generic MS/MS prediction model on a large data set of MS/MS spectra. We show that this approach enables a more accurate identification of NPS from experimentally acquired MS/MS spectra than any existing method. We demonstrate the application of NPS-MS to identify a novel derivative of phencyclidine (PCP) within an unknown powder seized in Denmark without the use of any reference standards. We anticipate that NPS-MS will allow forensic laboratories to identify more rapidly both known and newly emerging NPS. NPS-MS is available as a web server at https://nps-ms.ca/, which provides MS/MS spectra prediction capabilities for given NPS compounds. Additionally, it offers MS/MS spectra identification against a vast database comprising approximately 8.7 million predicted NPS compounds from DarkNPS and 24.5 million predicted ESI-QToF-MS/MS spectra for these compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Predicting the Phase Stability of Multicomponent High-Entropy Compounds

A generic method to estimate the relative feasibility of formation of high-entropy compounds in a single phase, directly from first principles, is developed. As a first step, the relative formation abilities of 56 multicomponent, AO, oxides were evaluated. These were constructed from five cation combinations chosen from A = {Ca, Co, Cu, Fe, Mg, Mn, Ni, Zn}. Candidates for multicomponent oxides are predicted from descriptors related to the enthalpy and configurational entropy obtained from the mixing enthalpies of two-component oxides. The utility of this approach is evaluated by comparing the predicted combinations with the experimentally realized entropy-stabilized oxide, (MgCoCuNiZn)O. In the second step, Monte Carlo simulations are utilized to investigate the phase composition and local ionic segregation as a function of temperature. This approach allows for the evaluation of potential secondary phases, thereby making realistic predictions of novel multicomponent compounds that can be synthesized.

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

Optimal Design and Operation of Intensified Absorbers with 3D-Printed Packing for Solvent-Based CO 2 Capture

Many potential solvent-based carbon capture processes suffer from a high heat of absorption of CO 2 that adversely affects the thermodynamic driving force. While interstage coolers are often used for removing a portion of the generated heat by removing the solvent or a portion of the solvent from a stage and cooling and returning it back to the absorber, they can be placed only at discrete locations in the tower. This work investigates intensified absorbers with 3D-printed packing that includes an internal cooler and therefore can be potentially used for maximizing the operational efficiency of the absorbers for CO 2 capture. The intensified absorber is modeled by using a generic, first-principles, equation-oriented absorber column model. Since the placement of these intensified packings would cause a loss of area/volume used for mass transfer, optimization of the proposed intensified absorber is performed by optimally selecting the locations at which to place these devices and designing them such that the trade-off due to the addition of the heat removal area and the resulting loss in the mass transfer area is accounted for. Results show that optimally placed and designed intensified packings can lead to a significant increase in the capture efficiency of the process in comparison to a similar column with no internal cooling. It is also observed that by optimally placing and designing intensified packings, the lean solvent flow rate to the absorber can be decreased, and the CO 2 lean loading can be increased while still maintaining the same capture efficiency. These process changes can lead to a substantial reduction in the cost of capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Data-Driven Discovery of Linear Molecular Probes with Optimal Selective Affinity for PFAS in Water

Approaches to tackle the wide and growing variety of highly persistent per- and polyfluoroalkyl substances (PFAS) are of pressing global need because of their detrimental human health effects, such as cancer, birth defects, and hormone imbalance. Sensitive, selective, and easy-to-use real-time sensors to monitor and detect PFAS and sorbents to extract them are critical to meeting government-mandated environmental concentrations. In this work, we combine all-atom molecular dynamics simulations, enhanced sampling, deep representational learning, and Bayesian optimization to perform high-throughput virtual screening for highly sensitive and selective molecular probes. Our molecular design space consists of 3850 linear hydrocarbon chains with varying degrees of halogenation with and without amine- and phosphine-based headgroups. By employing a data-driven search process, we efficiently explore the molecular design space to optimize the sensitivity to perfluorooctanesulfonic acid (PFOS) as a prototypical PFAS analyte and selectivity relative to a sodium dodecyl sulfate (SDS) interferent. We calculate 504 Gibbs free energies of probe-analyte and probe-interferent interactions and identify probes with PFOS association free energies of up to (-ΔG PFOS ) = 9.8 ± 0.2 kJ/mol and selectivities relative to SDS of (-ΔΔG PFOS–SDS ) = 3.1 ± 1.5 kJ/mol. A C 11 Br 23 P(CH 3 ) 2 probe containing 11 backbone brominated carbons and a tertiary phosphine headgroup possesses the most sensitive binding constant to PFOS within the defined search space of K b PFOS = 177.4 ± 12.7, and a semibrominated probe C 5 H 11 C 7 Br 14 N(CH 3 ) 2 containing 12 backbone carbons and a tertiary amine headgroup possesses the highest selectivity relative to SDS of K b PFOS /K b SDS = 4.6 ± 1.7. A retrospective analysis of our data to extract interpretable design rules reveals that the sensitivity of linear hydrogenated probes increases by approximately 1 kJ/mol per C–C bond. The addition or removal of halogen atoms and amine or phosphine headgroups produces nonmonotonic changes in both sensitivity and selectivity with changes to the sensitivity of up to 2.5 kJ/mol. Finally, this work places empirical limitations on the performance of a wide range of linear probes for PFOS detection and offers a generic strategy for high-throughput computational screening to promote selective and sensitive binding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

LAN: A Materials Notation for Two-Dimensional Layered Assemblies

Two-dimensional (2D) layered materials offer intriguing possibilities for novel physics and applications. Before any attempt at exploring the materials space in a systematic fashion, or combining insights from theory, computation, and experiment, a formal description of information about an assembly of arbitrary composition is required. Here, we introduce a domain-generic notation that is used to describe the space of 2D layered materials from monolayers to twisted assemblies of arbitrary composition, existent or not yet fabricated. The notation corresponds to a theoretical materials concept of stepwise assembly of layered structures using a sequence of rotation, vertical stacking, and other operations on individual 2D layers. Its scope is demonstrated with several example structures using common single-layer materials as building blocks. This work overall aims to contribute to the systematic codification, capture, and transfer of materials knowledge in the area of 2D layered materials.

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

Autogenerating a Domain-Specific Question-Answering Data Set from a Thermoelectric Materials Database to Enable High-Performing BERT Models

We present a method for autogenerating a large domain-specific question-answering (QA) dataset from a thermoelectric materials database. We show that a small language model, BERT, once fine-tuned on this automatically generated dataset of 99,757 QA pairs about thermoelectric materials, affords better performance in the field of thermoelectric materials compared to a BERT model fine-tuned on the generic English-language QA data set, SQuAD-v2. We further show that mixing the two data sets (ours and SQuAD-v2), which have significantly different syntactic and semantic scopes, allows the BERT model to achieve even better performance. The best-performing BERT model fine-tuned on the mixed data set outperforms the models fine-tuned on the other two data sets by scoring an exact match of 67.93% and an F1 score of 72.29% when evaluated on our test data set. This has important implications as it demonstrates the ability to realize high-performing small language models, with modest computational resources, empowered by domain-specific materials data sets which can be generated according to our method.

biological databases↗
DOE OSTI2026

A Transferable Force Field for Simulating Adsorption in Metal–Organic Frameworks with Open Metal Sites Based on the 12–6–4 Lennard-Jones Potential

Metal−organic frameworks (MOFs) that contain coordinatively unsaturated open metal sites (OMSs) provide strong host− guest interactions, making them promising sorbents for low-concentration gas adsorption applications such as direct air capture and atmospheric water harvesting. However, accurately modeling host−guest interactions involving OMSs remains challenging for classical force fields (FFs) based on the 12−6 Lennard−Jones (LJ) potential, as the polarization effect of the guest molecule induced by the positively charged OMS is not considered. Here, we introduce an FF based on the 12−6−4 LJ potential, which incorporates charge−induced dipole interactions and is parametrized against a diverse set of host−guest potential energy surfaces (PESs) obtained from density functional theory (DFT). The resulting FF, trained on a generic trimetallic cluster, performs well in both host−guest binding energetics and gas adsorption isotherms across different OMS-containing MOFs, including MOF-74 series and Cu-BTC. These results highlight the excellent transferability of our approach and its potential to enhance the accuracy and robustness of high-throughput MOF discovery workflows, particularly for gas adsorption and separation in large and diverse MOF databases.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Fermi’s Golden Rule Rate Expression for Transitions Due to Nonadiabatic Derivative Couplings in the Adiabatic Basis

Starting from a general molecular Hamiltonian expressed in the basis of adiabatic electronic and nuclear position states, where a compact and complete expression for the nonadiabatic derivative coupling (NDC) Hamiltonian term is obtained, we provide a general analysis of the Fermi’s golden rule (FGR) rate expression for nonadiabatic transitions between adiabatic states. We then consider a quasi-adiabatic approximation that uses crude adiabatic states and NDC couplings, both evaluated at the minimum potential energy configuration of the initial adiabatic state, for the definition of the zeroth and first-order terms of the Hamiltonian. Although the application of this approximation is rather limited, it allows deriving a general FGR rate expression without further approximation while accounting for non-Condon contribution to the FGR rate arising from momentum operators of NDC terms and its coupling with vibronic displacements. For a generic and widely used model where all nuclear degrees of freedom and environmental effects are represented as linearly coupled harmonic oscillators, we derive a closed-form FGR rate expression that requires only Fourier transform. The resulting rate expression includes quadratic contributions of NDC terms and their couplings to Franck–Condon modes, which require evaluation of two additional bath spectral densities in addition to the conventional one that appears in a typical FGR rate theory based on the Condon approximation. Model calculations for the case where nuclear vibrations consist of both a sharp high-frequency mode and an Ohmic bath spectral density illustrate new features and implications of the rate expression. We then apply our theoretical expression to the nonradiative decay from the first excited singlet state of azulene, which illustrates the utility and implications of our theoretical results.

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