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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
NASA NTRS2012

An Efficient Deterministic Approach to Model-based Prediction Uncertainty Estimation

Prognostics deals with the prediction of the end of life (EOL) of a system. EOL is a random variable, due to the presence of process noise and uncertainty in the future inputs to the system. Prognostics algorithm must account for this inherent uncertainty. In addition, these algorithms never know exactly the state of the system at the desired time of prediction, or the exact model describing the future evolution of the system, accumulating additional uncertainty into the predicted EOL. Prediction algorithms that do not account for these sources of uncertainty are misrepresenting the EOL and can lead to poor decisions based on their results. In this paper, we explore the impact of uncertainty in the prediction problem. We develop a general model-based prediction algorithm that incorporates these sources of uncertainty, and propose a novel approach to efficiently handle uncertainty in the future input trajectories of a system by using the unscented transformation. Using this approach, we are not only able to reduce the computational load but also estimate the bounds of uncertainty in a deterministic manner, which can be useful to consider during decision-making. Using a lithium-ion battery as a case study, we perform several simulation-based experiments to explore these issues, and validate the overall approach using experimental data from a battery testbed.

Daigle, Matthew J.↗
DOE OSTI2025

Enhancing 2D hydrodynamic flood models through machine learning and urban drainage integration

Two-dimensional hydrodynamic flood models are commonly employed for simulating flood extent and inundation depth. However, the influence of urban drainage network (UDN) is frequently overlooked in these models, potentially compromising their accuracy. Furthermore, the expensive computational costs and longer processing times make them challenging for large-scale hydrodynamic simulation. To address these challenges, this paper develops a machine learning (ML)-driven emulator for an open-source flood model, the Two-dimensional Runoff Inundation Toolkit for Operational Needs (TRITON). A TRITON-ML Emulator (TR-Emulator) that utilizes Convolutional Long Short-Term Memory is developed to capture the spatiotemporal features of flood events based on the outputs from TRITON. We further enhance the emulator by integrating UDN parameters (TR-UDN), such as the flow capacity of drainage pipes, pipe size, and pipe length, via an ML stacking technique to improve the water surface elevation (WSE) simulation. Hurricane Harvey 2017 in Houston, TX is used as the case study. We compare WSE results from TRITON, TR-Emulator, TR-UDN, and the United States Geological Survey (USGS) observations to evaluate the performance of these models. The results indicate that the TR-Emulator effectively replicates the WSE simulated by TRITON. Additionally, TR-UDN performs well in capturing WSE patterns and peak flows, aligning more closely with USGS observations, except in areas with milder slopes where conveyance discrepancies are observed. We further test the generalizability of our ML-based models using another smaller event. This paper shows that the TR-Emulator is effective for users and engineers to emulate a 2D hydrodynamic model, and the enhanced version of the TR-Emulator, TR-UDN, can be an efficient tool for predicting WSEs during urban flooding.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Computational modeling of graphite degradation in molten salt reactors: Role of infiltration

Molten salt reactors (MSRs) often employ graphite as a moderator and reflector. An important challenge for deploying graphite in these reactors is that, due to limited experimental data, our understanding of graphite’s structural integrity in molten salt environments remains incomplete. Here, this study addresses heat generation from fuel-bearing salt that has infiltrated open pores in the graphite, driven primarily by pressure differentials. This is one of multiple identified physical and chemical mechanisms through which molten salt could potentially degrade graphite. Thermally driven stresses are quantified using the Molten-Salt Reactor Experiment (MSRE) graphite moderator elements as a case study. Finite element simulations predict stress distributions at varying infiltration levels, indicating that thermal stresses increase with higher infiltration. Rare-event simulations using the parallel subset simulation framework identify the combinations and corresponding ranges of input parameters that lead to stresses above a specified threshold. In particular, combinations involving high infiltration amounts, high power density, and low thermal conductivity tend to induce the highest stresses. Under the inputs and assumptions considered in this work, the magnitudes of the thermally driven stresses are quite low, with a very low likelihood of causing failure due to exceeding the graphite’s tensile strength. Additionally, rare-event simulations were performed for two more scenarios: a scaled-up moderator geometry and a localized hotspot in the original geometry. Both cases resulted in increased susceptibility to failure, though not to a detrimental extent. Furthermore, the combined effects of irradiation and infiltration-induced thermal stresses were evaluated. The results showed that thermal stresses from infiltration were negligible compared to those caused by irradiation. The findings of such a study are inherently component-specific, but the methodology presented here could be used for similar assessments of salt-infiltration effects in other graphite components.

36 - MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Lunar Search & Rescue Applications of Lunar GNSS

Accurate lunar navigation and timing knowledge provides for the development of safety-critical services in the cislunar and lunar surface domain. Currently under development, the Goddard Space Flight Center’s (GSFC) Search and Rescue Mission Office is investigating and integrating search and rescue (SAR) capability into planned and future lunar communication and navigation interfaces. Lunar Search and Rescue (LunaSAR) development has a stated end-goal for assured, reliable, and timely indication of distress events for a wide variety of lunar surface users, including government-sponsored, commercial, and international users. LunaSAR performance requirements are modelled after the current terrestrial Cospas-Sarsat distress notification system, leveraging an internationally robust global navigation satellite system (GNSS) ecosystem as a core element of survivor locating capability. This presentation will discuss NASA’s work to develop user-focused distress messaging capabilities including infusion of example sensor data for triggering of automated distress alerts coupled with location-tagging. Additionally, the presentation will examine overall message structures, rotating fields for use in bi-directional distress messaging, and specific use cases based on NASA’s lunar exploration and lunar communication relay architectures. Modelling and simulation of LunaSAR use by individual lunar explorers will be discussed, based on notional industry and government design reference missions and mission considerations. Results from GSFC-funded Internal Research and Development (IRAD) efforts will be detailed, including successful distress message formulation simulating the ingestion of example legacy space suit telemetry fields. Hardware-in-the-loop testing using high-reliability software defined radio (SDR) modules serve as an example of IRAD successes and the framework for technical requirements. Architectural development and technical evolution from 2020 to 2021 included alignment of LunaSAR distress waveforms with ongoing NASA LunaNet interoperability development, as well as engagement with NASA Lunar Spectrum authorities for allocation of UHF-band distress frequencies on the lunar surface. S-Band and UHF-band transmission characteristics will be detailed, along with band-specific applications of each emission type. Additionally, examples of ingestion and formatting of GNSS signals (using historical terrestrial National Marine Electronics Association-formatted GNSS data) will be detailed, underscoring lunar user needs for a common lunar GNSS receiver output message framework. Maturity and ability to support evolving lunar exploration goals has been demonstrated and will be detailed, with maturity gaps such as position, navigation, and timing (PNT) and lunar reference frames identified within the context of distress message generation. Provision of LunaSAR services for lunar surface users represents a new era of ensured safety for lunar explorers and builds off of forty years of the Cospas-Sarsat program, underscoring the importance of lunar GNSS for safety-critical applications and growing interest in safe, reliable lunar surface operations. Enabled by new GNSS systems being developed by government and industry partners, NASA will continue to evolve and integrate lunar GNSS types into distress message generation, with a focus on compact and efficient message transmission over various lunar communication links. When fielded, LunaSAR will be the first dedicated search and rescue notification system employed on another celestial body. Robust lunar navigation and timing services form the core of LunaSAR capabilities, allowing for system syncing with time-dominant sensors, and high-accuracy location of those in distress while engaged in lunar surface activities.

Search and Rescue↗
DOE OSTI2026

Implementation of a Three-Dimensional Planetary Boundary Layer Parameterization in a Coupled Modeling System and Evaluation of "Gray Zone" Simulations of a Wind-Wave Event Off the US California Coast Using Observations

A three-dimensional (3D) planetary boundary layer (PBL) parameterization was added to the Coupled Ocean Atmosphere Wave Sediment Transport (COAWST) model and the first coupled atmosphere/wave "gray zone" simulations were carried out using the 3D PBL parameterization. A case study of a significant wind-wave event from 4-8 November 2020 off the US west coast was examined, with a focus on the impacts of the event within an approximate 280x280 km central California coastal region covering the Bureau of Ocean Energy Management Morro Bay wind energy lease area. Simulations with both one-dimensional (1D; Yonsei University) and 3D PBL parameterizations were examined in this nest with ..delta..x=400 m. Two-way coupling was active, with near-surface winds feeding back to the wave model and bulk wave statistics feeding back to the atmospheric model. Both simulations compared favorably with buoy observations in capturing the timing and magnitude of wind speed, temperature, dewpoint, and significant wave height, as the front associated with the maritime weather system moved southward across coastal California. However, wind speed errors over land were larger. Time series of the vertical profile of winds below z=250 m from the simulations compared favorably with observations from the US Dept. of Energy Morro Bay Doppler lidar buoy. Differences between the coupled 1D and 3D PBL simulations were minor. The most notable difference was that the simulation using the 3D PBL parameterization had approximately 10 % weaker winds at the peak of the event causing 10 % lower significant wave heights. This difference was shown to be mostly due to differences in the vertical mixing treatment between the parameterizations, in particular the nonlocal downward mixing of higher momentum air in the 1D Yonsei University parameterization in convective conditions. Overall, this work demonstrates that the 3D PBL parameterization can be used in a coupled atmosphere/wave modeling framework with similar behaviors as traditional PBL parameterizations that do not provide horizontal turbulent variances and fluxes.

16 TIDAL AND WAVE POWER↗
NASA NTRS2010

Attempts to Simulate Anisotropies of Solar Wind Fluctuations Using MHD with a Turning Magnetic Field

We examine a "two-component" model of the solar wind to see if any of the observed anisotropies of the fields can be explained in light of the need for various quantities, such as the magnetic minimum variance direction, to turn along with the Parker spiral. Previous results used a 3-D MHD spectral code to show that neither Q2D nor slab-wave components will turn their wave vectors in a turning Parker-like field, and that nonlinear interactions between the components are required to reproduce observations. In these new simulations we use higher resolution in both decaying and driven cases, and with and without a turning background field, to see what, if any, conditions lead to variance anisotropies similar to observations. We focus especially on the middle spectral range, and not the energy-containing scales, of the simulation for comparison with the solar wind. Preliminary results have shown that it is very difficult to produce the required variances with a turbulent cascade.

Ghosh, Sanjoy↗
NASA NTRS1994

Numerical simulation of three-dimensional self-gravitating flow

The three-dimensional flow of a self-gravitating fluid is numerically simulated using a Fourier pseudospectral method with a logarithmic variable formulation. Two cases with zero total angular momentum are studied in detail, a 32(exp 3) simulation (Run A) and a 64(exp 3) simulation (Run B). Other than the grid size, the primary differences between the two cases are that Run A modeled atomic hydrogen and had considerably more compressible motion initially than Run B, which modeled molecular hydrogen. ('Compressible motion' is that part of the velocity which has zero curl, but non-zero divergence). The numerical results indicate that gravitational collapse can proceed in a variety of ways. In Run A, collapse led to an elongated tube-like structure, while in Run B, collapse led to a flatter, disk-like structure.

Shebalin, J. V.↗
DOE OSTI2026

Direct Ab Initio Simulation of the Synthesis of BaZrO 3 and the Microstructure Impacts on Proton Transport

Controlling and predicting the processing-structure-performance relationship in functional materials is a grand challenge in materials science, with important implications for a wide range of emerging applications; a high fidelity understanding of the performance impact of microstructures formed under synthesis conditions is required to develop advanced materials, such as solid-state fuel cells and electrolyzers. Using the ceramic BaZrO 3 as a case study, we directly simulate the synthesis and investigate how proton transport is dictated by microstructures. We develop a framework that couples density functional theory (DFT), machine-learning interatomic potential (MLIP) driven molecular dynamics, and grand canonical Monte Carlo to perform large-scale, microstructure-resolved, atomistic simulations of proton transport in experimentally representative polycrystalline structures. Our fully ab initio approach, using a MLIP as a proxy for DFT, allows us to quantify the competition between two distinct diffusion mechanisms: one associated with grain-boundary regions and another within grains. When the impacts of grain boundaries are taken into account, proton transport exhibits substantial deviation from the bulk oxide limit. This addresses long-standing discrepancies between theory and experiments. Our integrated approach provides atomistic insight into microstructure-dependent proton pathways in BaZrO 3 and establishes a general protocol for predicting processing-structure-performance relationships.

organic↗
NASA NTRS2002

The NASA Low-Pressure Turbine Flow Physics Program: A Review

An overview of the NASA Glenn Low-Pressure Turbine (LPT) Flow Physics Program will be presented. The flow in the LPT is unique for the gas turbine. It is characterized by low Reynolds number and high freestream turbulence intensity and is dominated by interplay of three basic mechanisms: transition, separation and wake interaction. The flow of most interest is on the suction surface, where large losses are generated due to separation. The LPT is a large, multistage, heavy, jet engine component that suffers efficiency degradation between takeoff and cruise conditions due to decrease in Reynolds number with altitude. The performance penalty is around 2 points for large commercial bypass engines and as much as 7 points for small, high cruise altitude, military engines. The gas-turbine industry is very interested in improving the performance of the LPT and in reducing its weight, part count and cost. Many improvements can be accomplished by improved airfoil design, mainly by increasing the airfoil loading that can yield reduction of airfoils and improved performance. In addition, there is a strong interest in reducing the design cycle time and cost. Key enablers of the needed improvements are computational tools that can accurately predict LPT flows. Current CFD tools in use cannot yet satisfactorily predict the unsteady, transitional and separated flow in the LPT. The main reasons are inadequate transition & turbulence models and incomplete understanding of the LPT flow physics. NASA Glenn has established its LPT program to answer these needs. The main goal of the program is to develop and assess models for unsteady CFD of LPT flows. An approach that consists of complementing and augmenting experimental and computational work elements has been adopted. The work is performed in-house and by several academic institutions, in cooperation and interaction with industry. The program was reviewed at the Minnowbrook II meeting in 1997. This review will summarize the progress that was made since and will introduce newly started projects. The LPT program is focused on three areas: acquisition of experimental and numerical databases and on modeling and computation. Priority was initially given to experiments. There are three classes of experiments: simulated LPT passages, linear cascade, both with and without wakes, and low-speed rotating rig. They are being conducted as follows: At NASA GRC on a flat surface with blade pressure distribution, at the US Naval Academy on a curved surface. The addition of wakes is studied at the University of Minnesota in a curved passage with a retractable wake generator, and at Texas A&M University in a linear cascade with continuously running wake generator. The pressure distribution of the Pratt & Whitney blade 'Pak B' is used in all these experiments. Experiments have been performed also in the GEAE Low-Speed Rotating Turbine (LSRT) rig with GE-designed airfoils. Work on numerically generated database is in progress at the University of Kentucky, using the DNS/LES code LESTool developed there. Turbulence/transition model assessment and development is performed also at the University of Kentucky, where a new intermittency transport model was developed and many experimental test cases have been numerically computed. Assessments of models using simulations of multistage LPT experiments were performed at Virginia Commonwealth University using the Corsair code. Work on suction surface separation delay, using passive and active flow-control, has also been initiated. Following the overview, Principal Investigators attending the workshop will present in detail several of the projects supported by NASA.

Ashpis, David E.↗
NASA NTRS2003

A Study of Fan Stage/Casing Interaction Models

The purpose of the present study is to investigate the performance of several existing and new, blade-case interactions modeling capabilities that are compatible with the large system simulations used to capture structural response during blade-out events. Three contact models are examined for simulating the interactions between a rotor bladed disk and a case: a radial and linear gap element and a new element based on a hydrodynamic formulation. The first two models are currently available in commercial finite element codes such as NASTRAN and have been showed to perform adequately for simulating rotor-case interactions. The hydrodynamic model, although not readily available in commercial codes, may prove to be better able to characterize rotor-case interactions.

Lawrence, Charles↗
NASA NTRS1988

A new algorithm for modeling friction in dynamic mechanical systems

A method of modeling friction forces that impede the motion of parts of dynamic mechanical systems is described. Conventional methods in which the friction effect is assumed a constant force, or torque, in a direction opposite to the relative motion, are applicable only to those cases where applied forces are large in comparison to the friction, and where there is little interest in system behavior close to the times of transitions through zero velocity. An algorithm is described that provides accurate determination of friction forces over a wide range of applied force and velocity conditions. The method avoids the simulation errors resulting from a finite integration interval used in connection with a conventional friction model, as is the case in many digital computer-based simulations. The algorithm incorporates a predictive calculation based on initial conditions of motion, externally applied forces, inertia, and integration step size. The predictive calculation in connection with an external integration process provides an accurate determination of both static and Coulomb friction forces and resulting motions in dynamic simulations. Accuracy of the results is improved over that obtained with conventional methods and a relatively large integration step size is permitted. A function block for incorporation in a specific simulation program is described. The general form of the algorithm facilitates implementation with various programming languages such as FORTRAN or C, as well as with other simulation programs.

Hill, R. E.↗
NASA NTRS1991

Simulating Dynamics Of The Gamma-Ray Observatory Satellite

GRODY developed alongside GROSS computer program (GSC-13147), a FORTRAN dynamics-simulator program performing same functions. GRODY conceived for use in case study to assess feasibility and effectiveness of Ada programming language for development of flight-dynamics software. Designed for those familiar with analysis of attitudes of spacecraft. Supports planning of maneuvers as well as analytical testing and evaluation of attitude-determination and -control system used on board Gamma-Ray Observatory (GRO) satellite. Simulates computer and control processor electronics aboard GRO satellite. Enables analyst to check and update commands sent from ground and values of parameters, obtain displays of status of simulation, interrupt simulation, analyze previous runs, and obtain printed output of simulation runs. Written mainly in Ada (99 percent) with remainder in FORTRAN.

Stark, M.↗
DOE OSTI2026

Scattering Processes from Quantum Simulation Algorithms for Scalar Field Theories

We provide practical simulation methods for scalar field theories on a quantum computer that yield improved asymptotics as well as concrete gate estimates for the simulation and physical qubit estimates using the surface code. We achieve these improvements through two optimizations. First, we consider a finite volume approach for estimating the elements of the S-matrix. This approach is appropriate in general for 1+1D and for certain low-energy elastic collisions in higher dimensions. Second, we implement our approach using a series of different fault-tolerant simulation algorithms for Hamiltonians formulated both in the field occupation basis and field amplitude basis. Our algorithms are based on either second-order Trotterization or qubitization. The cost of Trotterization in occupation basis scales as O ( λ N 7 | Ω | 3 / ( M 5 / 2 ϵ 3 / 2 ) ) where λ is the coupling strength, N is the occupation cutoff, | Ω | is the volume of the spatial lattice, M is the mass of the particles and ϵ is the uncertainty in the energy calculation used for the S -matrix determination. Qubitization in the field basis scales as O ( | Ω | 2 ( k 2 Λ + k M 2 ) / ϵ ) , where k is the cutoff in the field and Λ is a scaled coupling constant. We find in both cases that the bounds suggest physically meaningful simulations can be performed using on the order of 4 × 10 6 physical qubits and 10 12 T -gates which corresponds to roughly one day on a superconducting quantum computer with surface code and a cycle time of 100 ns. This places the simulation of scalar field theory within striking distance of the gate counts for the best available chemistry simulation results.

Hardy, Andrew [Toronto U.] (ORCID:0000000235817382↗
NASA NTRSDate not supplied

Fast-Time Simulation of Airport Surface Movement

Fast-time simulation of airport surface operations allows forthe thorough testing and analysis of modeling concepts andalgorithms for managing aircraft movement. However, air-port surface movement operations present a difficult, large-scale logistics problem. This paper summarizes the resultsof a multi-year effort to build a fast-time simulator of largeairport surface movement, using San Francisco IntrnationalAirport as a case study.

Simulation↗
NASA NTRS1992

Numerical simulations of the electrodynamic interactions between the Tethered-Satellite-System and space plasma

The first Tethered-Satellite-System (TSS-1), scheduled for a flight in late 1992, is expected to provide relevant information related to the concept of generating an emf in a 20-km-long (or longer) conducting wire. This paper presents numerical simulations of the electrodynamic interactions between the TSS system and space plasma, using a 2D and 3D models of the system. The 2D case code simulates the motion of a long cylinder past a plasma, which is composed of electrons and H(+) ions. The system is solved by allowing the plasma to flow past the cylinder with an imposed magnetic field. The more complex 3D case is considered to study the dynamics in great detail. Results of 2D simulation show that the interaction of a satellite with plasma flowing perpendicularly to the magnetic field results in an enhancement in the current collection.

Vashi, Bharat I.↗
DOE OSTI2025

Warm-phase microphysical evolution in large-eddy simulations of tropical cumulus congestus: evaluating drop size distribution evolution using polarimetry retrievals, in situ measurements, and a thermal-based framework

Owing to uncertainties in convective microphysics processes, improving parameterizations in Earth system models (ESMs) can benefit from observationally constrained cases suitable for scaling between cloud-resolving models and ESMs. We propose a benchmark large-eddy simulation (LES) cumulus congestus case study from the NASA Cloud, Aerosol, and Monsoon Processes Philippines Experiment (CAMP 2 Ex) for evaluating and improving ESMs in single-column model (SCM) mode. We seek observational constraints using novel polarimetric retrievals and in situ cloud microphysics measurements. Simulations using bulk and bin microphysics initialized with observed aerosol profiles are compared to cloud-top retrievals of cloud droplet effective radius (R eff ), effective variance (ν eff ), and number concentration (N d ) from the airborne Research Scanning Polarimeter (RSP). Both schemes reproduce characteristics of cloud-top N d and R eff that increase and decrease with altitude, respectively. Cloud-top N d is low-biased relative to RSP retrievals in both schemes, potentially due to limitations in both simulations and retrieval assumptions. Cloud-top R eff is low-biased in the bulk scheme but reasonably reproduced by the bin scheme. Profiles of N d and R eff are sensitive to the collision–coalescence process and the vertical variation in aerosol size distribution. Comparison of simulated and in situ droplet size distributions (DSDs) shows that, to first order, integrated moments are always sensitive to sizes < ~ 30 µm and can also be sensitive to larger sizes if the DSDs are sufficiently broad, with implications for the assumed maximum observed size retrieved by the RSP. The bin scheme captures the observed extended tail of the DSD, while the bulk scheme is unable to due to parametric constraints. Differences in expected relationships between in situ measurements of cloud cores and cloud-top retrievals by RSP demonstrate difficulty in constraining well the case presented herein. Finally, a thermal-tracking framework demonstrates that the dilution of N d throughout a thermal's lifetime is heavily determined by collision–coalescence and the height-varying aerosol distribution and that, in the absence of these, the impact of entrainment on diluting N d is largely offset by secondary activation. Implications for evaluating warm-phase convective microphysics schemes in ESMs and translating results for use on global, space-based polarimetry platforms are discussed.

Stanford, McKenna Wallace [Columbia Univ., New Yor↗
DOE OSTI2025

Does provable absence of barren plateaus imply classical simulability?

A large amount of effort has recently been put into understanding the barren plateau phenomenon. In this perspective article, we face the increasingly loud elephant in the room and ask a question that has been hinted at by many but not explicitly addressed: Can the structure that allows one to avoid barren plateaus also be leveraged to efficiently simulate the loss classically? We collect evidence-on a case-by-case basis-that many commonly used models whose loss landscapes avoid barren plateaus can also admit classical simulation, provided that one can collect some classical data from quantum devices during an initial data acquisition phase. This follows from the observation that barren plateaus result from a curse of dimensionality, and that current approaches for solving them end up encoding the problem into some small, classically simulable, subspaces. Thus, while stressing that quantum computers can be essential for collecting data, our analysis sheds doubt on the information processing capabilities of many parametrized quantum circuits with provably barren plateau-free landscapes. We end by discussing the (many) caveats in our arguments including the limitations of average case arguments, the role of smart initializations, models that fall outside our assumptions, the potential for provably superpolynomial advantages and the possibility that, once larger devices become available, parametrized quantum circuits could heuristically outperform our analytic expectations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗