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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Modeling low cycle fatigue (LCF) of additively manufactured Hastelloy X using An accelerated crystal plasticity fatigue damage model

This paper presents a microstructure-based model for low cycle fatigue (LCF) behavior and life of Nickel-based alloy Hastelloy X manufactured using laser-powder bed fusion (L-PBF) additive manufacturing (AM). AM Hastelloy X, a solution-strengthened alloy, is tested at elevated temperature under fully reversed LCF conditions at different strain levels. A generalized plane strain finite element model is generated from electron backscatter diffraction (EBSD) characterization. The constitutive behavior of the material under fatigue is modeled using crystal plasticity and calibrated with both monotonic tensile and cyclic stress–strain data. The fatigue micro-crack initiation and propagation in the microstructure is modeled using a modified Chaboche fatigue damage model. An embedded boundary condition with a homogenous medium is used to apply the cyclic deformation and prevent numerically introduced over-constraints during fatigue simulation. A ‘cycle-jump’ method is used to accelerate the fatigue simulation and reduce the computational cost. The simulation results are compared to LCF experiments, showing satisfactory matches in cyclic stress behavior and number of cycles to macro-crack initiation for all applied strain ranges. In addition, the model illustrates the potential for quantifying microscale fatigue life impacting factors such as microstructure and surface roughness, which is needed to accurately quantify the reliability of AM components in service.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Assessment of Multi-Step CADIS Parameter Sensitivity to Neutron Flux Spectrum in Shutdown Dose Rate Calculations

Shutdown dose rate (SDDR) analysis requires (a) a neutron transport calculation to estimate neutron flux fields, (b) an activation calculation to compute radionuclide inventories and associated photon sources, and (c) a photon transport calculation to estimate final dose rate. In some applications, accurate full-scale Monte Carlo (MC) SDDR simulations are needed for very large systems with massive amounts of shielding materials. For example, SDDR assessments are required throughout the biological shield (bio-shield) of the ITER experimental facility to evaluate the required waiting period after the shutdown of ITER and to identify the locations where human accessibility should be prohibited. The bio-shield is a large cylindrical concrete structure (30 m tall and 34 m in diameter) surrounding the very complex tokamak machine. Determining the effects on SDDR of important factors, such as the cross talk (interactions) between the different ports of ITER, is possible only through full-scale simulations that involve all the complex inner details of the ITER tokamak machine. These simulations are impractical because calculation of space- and energy-dependent neutron fluxes throughout the structural materials is needed to estimate the distribution of radioisotopes causing the SDDR. Determining a good importance function that can be used in biasing a neutron MC calculation for SDDR is complicated because it is difficult to explicitly express the SDDR response function, which depends on subsequent computational steps. The Multi-Step Consistent Adjoint Driven Importance Sampling (MS-CADIS) hybrid MC/deterministic method was developed to speed up the SDDR MC neutron transport calculation using an importance function that represents the neutron importance to the final SDDR. The MS-CADIS method uses the CADIS method, which has been Notice: This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC0500OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for the United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). successfully used for more than a decade in radiation shielding applications to generate consistent source biasing and weight window (WW) variance reduction parameters to accelerate continuous-energy MC simulations. However, because MS-CADIS focuses on multi-step shielding calculations such as SDDR calculations, it develops an importance function for the initial radiation transport calculation (e.g., the neutron calculations in SDDR simulations) that represents the importance of particles to the final response of the overall simulation. To develop this importance function, the MS-CADIS method uses an adjoint calculation with a specific neutron adjoint source that represents the neutron's contribution to the final SDDR. Brute force calculation of the MS-CADIS neutron adjoint source requires a deterministic neutron transport calculation coupled with activation calculations in each element of the deterministic mesh. These calculations are needed to determine the MS-CADIS parameter for the neutron interactions that produce radioisotopes contributing to the SDDR. The MS-CADIS parameter is the microscopic cross section of the radioisotope-producing interaction, multiplied by the mass of this radioisotope existing at the end of the irradiation and decay scenario, and divided by the steady-state rate of the interaction. Because the activation calculations are performed for each radionuclide in each mesh element, implementation of the MS-CADIS method can be computationally expensive. However, these neutron transport and activation calculations are not needed if we assume that the radioisotopes are created due to single neutron interactions and their concentrations do not change as a result of burnup by neutron irradiation. The use of this approximation, which renders the MS-CADIS parameter independent of the neutron flux, seems reasonable in calculating the MS-CADIS importance function because this function is needed only to speed up the MC calculation, not to calculate the final SDDR. In this work, we investigate the validity of this approximation by investigating the behavior of the MS-CADIS parameter as a function of the neutron flux spectra in the Fusion Evaluated Nuclear Data Library (FENDL) Neutronics and Shielding Benchmark problem that contains representative isotopes and flux environments of fusion energy systems. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2019

A Global Hydrologic Framework to Accelerate Scientific Discovery

With the ability to simulate historical and future global water availability on a monthly time step at a spatial resolution of 0.5 geographic degree, the Python package Xanthos version 1 provided a solid foundation for continuing advancements in global water dynamics science. The goal of Xanthos version 2 was to build upon previous investments by creating a Python framework where core components of the model (potential evapotranspiration (PET), runoff generation, and river routing) could be interchanged or extended without having to start from scratch. Xanthos 2 utilizes a component-style architecture which enables researchers to quickly incorporate and test cutting-edge research in a stable modeling environment prebuilt with diagnostics. Major advancements for Xanthos 2 were also achieved by the creation of a robust default configuration with a calibration module, hydropower modules, and new PET modules, which are now available to the scientific community.

GCAM, Xanthos, global hydrology, modeling↗
DOE OSTI2017

Electron Pre-acceleration at Nonrelativistic High-Mach-number Perpendicular Shocks

We perform particle-in-cell simulations of perpendicular nonrelativistic collisionless shocks to study electron heating and pre-acceleration for parameters that permit the extrapolation to the conditions at young supernova remnants. Our high-resolution large-scale numerical experiments sample a representative portion of the shock surface and demonstrate that the efficiency of electron injection is strongly modulated with the phase of the shock reformation. For plasmas with low and moderate temperature (plasma beta β{sub p}=5⋅10{sup −4} and β{sub p}=0.5), we explore the nonlinear shock structure and electron pre-acceleration for various orientations of the large-scale magnetic field with respect to the simulation plane, while keeping it at 90° to the shock normal. Ion reflection off of the shock leads to the formation of magnetic filaments in the shock ramp, resulting from Weibel-type instabilities, and electrostatic Buneman modes in the shock foot. In all of the cases under study, the latter provides first-stage electron energization through the shock-surfing acceleration mechanism. The subsequent energization strongly depends on the field orientation and proceeds through adiabatic or second-order Fermi acceleration processes for configurations with the out-of-plane and in-plane field components, respectively. For strictly out-of-plane field, the fraction of suprathermal electrons is much higher than for other configurations, because only in this case are the Buneman modes fully captured by the 2D simulation grid. Shocks in plasma with moderate β{sub p} provide more efficient pre-acceleration. The relevance of our results to the physics of fully 3D systems is discussed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals

Massively parallel computer architectures create new opportunities for the performance of long-time scale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics method that takes advantage of distributed computing to reduce the wall-clock time of MD simulation via parallelization with respect to stochastic MD time steps. The marginal distribution for the time evolution of a system is expressed in terms of a path integral, enabling the use of path sampling techniques to numerically integrate MD trajectories. By parallelizing the evaluation of the path action with respect to time and by initializing the path configurations from a nonequilibrium distribution, the algorithm enables significant speedups in terms of the length of MD trajectories that can be integrated in a given amount of wall-clock time. The method is demonstrated for Brownian dynamics, although it is generalizable to other stochastic equations of motion including open systems. We apply the method to two simple systems, a harmonic oscillator and a Lennard-Jones liquid, and we show that in comparison to the conventional Euler integration scheme for Brownian dynamics, the new method can reduce the wall-clock time for integrating trajectories of a given length by more than three orders of magnitude in the former system and more than two in the latter. This new method for parallelizing MD in the dimension of time can be trivially combined with algorithms for parallelizing the MD force evaluation to achieve further speedup.

Rosa-Raíces, Jorge L.↗
DOE OSTI2012

Design and Start-to-End Simulation of an X-Band RF Driven Hard X-Ray FEL with LCLS Injector

In this note, it is briefly discussed the accelerator design and start-to-end 3D macro particles simulation (using ELEGANT and GENESIS) of an X-band RF driven hard X-ray FEL with LCLS injector. A preliminary design and LiTrack 1D simulation studies were presented before in an older publication. In numerical simulations this X-band RF driven hard X-ray FEL achieves/exceeds LCLS-like performance in a much shorter overall length of 350 m, compared with 1200 m in the LCLS case. One key feature of this design is that it may achieve a higher final beam current of 5 kA plus a uniform energy profile, mainly due to the employment of stronger longitudinal wake fields in the last X-band RF linac.

43 PARTICLE ACCELERATORS↗
NASA NTRS2000

Electric Plasma Arc-Lamp Combustor Liner Durability Test System Developed

Silicon carbide matrix composites are candidate materials for high-temperature combustor liners. Because through-the-thickness thermal gradients are the primary cause of stress on combustor liners, a unique test facility was developed at the NASA Glenn Research Center at Lewis Field to simulate in-service pure thermal stress distributions in fiber reinforced silicon carbide cylinders. It was developed initially under Phase II of the High- Speed Research Program. This test stand can accommodate 8-in.-long test cylinders that have outer diameters of 4 in. and a wall thickness of about 0.08 to 0.12 in. One cylinder at a time is loaded vertically into the test stand. Water-cooled plates enclose the open ends of the cylinder and provide cooling. Load plates on the exterior side of the water-cooled plates provide support and compression loads. To evaluate a combustor liner material s potential performance, researchers induce thermal gradients with an axisymmetric, direct-current, electric arc within the cylinder while refrigerated air at a rate of 1.5 lb/sec impinges on the outside surface of the cylinder. The achievable through-the-thickness thermal gradient is predicted to be in excess of 200 C. The 8-in. long, 0.5-in.-diameter plasma arc emits full spectrum visible light; radiant intensity exceeds 300 Watts per square centimeters to produce temperatures in excess of 1500 C on materials with emissivity near unity. Because the system does not rely upon the combustion of fuels to achieve the related thermal conditions, ancillary environmental reactions with the sample are eliminated. The system incorporates a standard mechanical test frame, which can impose constant as well cyclical axial stresses up to 2200 lb upon the test piece. Silicon-carbide-fiber reinforced silicon carbide matrix composite cylinders were instrumented with thin-film thermocouples to obtain through-the-thickness thermal flux measurements. Inside wall temperatures reached 1200 C with only 250 A of current. One of the special features of this configuration is the creation of hoop stress states within the cylinder, which up this point have not been obtainable in planar coupon tests. This facility will allow various operational modes, including accelerated tests of thermal transients simulating the effects of repeated engine ignition as well as prescribed thermal and mechanical histories to simulate various duty cycle profiles. Tests can now be performed on thermal-barrier-coated metallic liners and ceramic composite liners that require a combination of high heat flux and controlled mechanical stresses.

Goldsby, Jon C.↗
NASA NTRS2011

First Lunar Wake Passage of ARTEMIS: Discrimination of Wake Effects and Solar Wind Fluctuations by 3D Hybrid Simulations

The spacecraft P1 of the new ARTEMIS (Acceleration, Reconnection, Turbulence, and Electrodynamics of the Moon's Interaction with the Sun) mission passed the lunar wake for the first time on February 13, 2010. We present magnetic field and plasma data of this event and results of 3D hybrid simulations. As the solar wind magnetic field was highly dynamic during the passage, a simulation with stationary solar wind input cannot distinguish whether distortions were caused by these solar wind variations or by the lunar wake; therefore, a dynamic real-time simulation of the flyby has been performed. The input values of this simulation are taken from NASA OMNI data and adapted to the P1 data, resulting in a good agreement between simulation and measurements. Combined with the stationary simulation showing non-transient lunar wake structures, a separation of solar wind and wake effects is achieved. An anisotropy in the magnitude of the plasma bulk flow velocity caused by a non-vanishing magnetic field component parallel to the solar wind flow and perturbations created by counterstreaming ions in the lunar wake are observed in data and simulations. The simulations help to interpret the data granting us the opportunity to examine the entire lunar plasma environment and, thus, extending the possibilities of measurements alone: A comparison of a simulation cross section to theoretical predictions of MHD wave propagation shows that all three basic MHD modes are present in the lunar wake and that their expansion governs the lunar wake refilling process.

Wiehle, S.↗
DOE OSTI2024

Benchmarking of hydrodynamic plasma waveguides for multi-GeV laser-driven electron acceleration

Hydrodynamic plasma waveguides initiated by optical field ionization have recently become a key component of multi-GeV laser wakefield accelerators. Here, we present the most complete and accurate experimental and simulation-based characterization to date, applicable to current multi-GeV experiments and future 100 GeV-scale laser plasma accelerators. Crucial to the simulations is the correct modeling of intense Bessel beam interaction with meter-scale gas targets, the results of which are used as initial conditions for hydrodynamic simulations. The simulations are in good agreement with our experiments measuring evolving plasma and neutral hydrogen density profiles using two-color short pulse interferometry, enabling realistic determination of the guided mode structure for application to laser-driven plasma accelerator design. Published by the American Physical Society 2024

Physics↗
DOE OSTI2019

Unveiling Carbon Ring Structure Formation Mechanisms in Polyacrylonitrile-Derived Carbon Fibers

As the demand for electric vehicles (EVs) and autonomous vehicles (AVs) rapidly grows, lower-cost, lighter, and stronger carbon fibers (CFs) are urgently needed to respond to consumers’ call for greater EV traveling range and stronger safety structures for AVs. Converting polymeric precursors to CFs requires a complex set of thermochemical processes; a systematic understanding of each parameter in fiber conversion is still, to a large extent, lacking. Here, we demonstrate the effect of carbonization temperature on carbon ring structure formation by combining atomistic/microscale simulations and experimental validation. Experimental testing, as predicted by simulations, exhibited that the strength and ductility of PAN CFs decreased, whereas the Young’s modulus increased with increasing carbonization temperature. Our simulations unveiled that high carbonization temperature accelerated the kinetics of graphitic phase nucleation and growth, leading to the decrease in strength and ductility but increase in modulus. The methodology presented herein using combined atomistic/microscale simulations and experimental validation lays a firm foundation for further innovation in CF manufacturing and low-cost alternative precursor development.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Accelerated Aging Humidity Chamber for Nuclear Grade HEPA Filter Media

A unique accelerated aging humidity chamber for simulating the natural aging process of nuclear grade high efficiency particulate air (HEPA) filter media is being designed, implemented, and tested. The nuclear industry currently lacks information regarding the shelf life and service life of HEPA filter media. The Department of Energy recommends disposing of HEPA filters 10 years after the manufacture date for filters operated under dry conditions. Studies have shown the tensile strength and water repellency of HEPA filter media diminish with age. The chamber's principal function is to sustain an elevated relative humidity condition for an extended duration specified by the Arrhenius aging model. To accomplish this, various design parameters were established: (1) consistently achieve uniform humidity conditions within the chamber to equally expose media sheets, (2) ensure the chamber is sufficiently sealed to mitigate the uncontrolled infiltration of air, (3) confidently secure the media sheets to avert the introduction of unnecessary stressing/creasing, (4) fabricate the chamber from clear polycarbonate material to allow inspection of the media sheets, (5) provide a safe and ergonomic design for personnel, (6) ensure the chamber design is replicable and relatively easy to fabricate/assemble. A humidity source, fan, PID controller, humidity and temperature transmitters, and data loggers are required for proper operation and control of the chamber. The humidity source must accommodate target values up to 95% relative humidity throughout the chamber. The three humidity and temperature transmitters are strategically spaced throughout the chamber to ensure uniform conditions. The 10 cubic feet per minute (CFM) fan selected intends to accomplish the desired air change rate inside the chamber of approximately 20 air changes per hour (ACH). The 2 plenums on the upper and lower portions of the chamber utilize a perforated design to uniformly distribute air, promote air mixing, and control the air velocity entering the chamber. Industrial blueprint hanging clamps are being retrofitted to be seated within the chamber drawers and firmly secure the nuclear grade filter media. The aged media will be evaluated using autopsy methodology, and the results obtained intend to help clarify the useful life of nuclear grade HEPA filters. Nuclear grade high efficiency particulate air (HEPA) filters are defined as disposable, extended-media, dry-type filters with a rigid casing enclosing the full depth of the pleats and have a minimum particle removal efficiency of 99.97%. [1] - HEPA filters are constantly exposed to stressors and subsequently have been shown to degrade as the filter ages. Properties such as tensile strength and water repellency, along with others, are negatively impacted. [2] - Due to the scarcity of naturally aged HEPA filters available, it is crucial to develop accelerated aging methods which effectively mimic the natural degradation effects. - After accelerated aging, the filters are subject to testing in the Axial Flow Large Scale Test Stand (ALSTS) and other analysis techniques such as the same qualification tests performed directly after being manufactured. - Quality data is necessary for future decisions regarding the lifetime of nuclear grade HEPA filters. - The objective is to develop a prototype accelerated aging humidity chamber for nuclear grade HEPA filter media. The chamber should expose the media to commonly occurring stressors to expedite the degradation process caused by aging. PID yields reliable and reproducible results: - CFD model correlates well with actual performance; - Further analysis is needed to complete characterization; - Future work for the chamber is still to be completed. The data shown in Figure 5 and Table 1 indicate the system is functioning as designed. As can be determined from the system response evaluation in Table 1, the PID controller is yielding reliable and reproducible results at each set point. As the set point increases, the time constant and 20% settling time increase accordingly. From the results in Table 1, it stands to reason that the CFD model correlates well with the actual performance of the system. Each system response parameter for the 90%RH* CFD model is slightly lower than the parameters collected from the physical model tested at an equivalent set point. This is to be expected considering the inlet in the CFD model is a constant supply of water vapor, whereas the physical model uses a PID controller to monitor the amount of water vapor needed and reacts accordingly. More analysis is still to be done on the prototype chamber. A pressure test will be conducted in order to determine the hourly leak rate of the chamber. This test will involve constant air flow into the chamber until the desired pressure is reached. A uniformity test will also be conducted in order to ensure each filter medium is being exposed to equivalent relative humidity levels. This test will involve an array of humidity meters strategically oriented inside the chamber to record any possible gradients. Future work for the chamber includes dehumidification abilities, tests while fully loaded with filters, and temperature control. Once completed, the autopsy team at Institute of Clean Energy Technology will conduct necessary accelerated aging studies as needed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2012

Electron acceleration by Z-mode waves associated with cyclotron maser instability

We demonstrate by a particle simulation that Z-mode waves generated by the cyclotron maser instability can lead to a significant acceleration of energetic electrons. In the particle simulation, the initial electron ring distribution leads to the growth of Z-mode waves, which then accelerate and decelerate the energetic ring electrons. The initial ring distribution evolves into an X-like pattern in momentum space, which can be related to the electron diffusion curves. The peak kinetic energy of accelerated electrons can reach 3 to 6 times the initial kinetic energy. We further show that the acceleration process is related to the 'nonlinear resonant trapping' in phase space, and the test-particle calculations indicate that the maximum electron energy gain {Delta}{epsilon}{sub max} is proportional to B{sub w}{sup 0.57}, where B{sub w} is the wave magnetic field.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2005

Particle acceleration magnetic field generation, and emission in Relativistic pair jets

Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) are responsible for particle acceleration in relativistic pair jets. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic pair jet propagating through a pair plasma. Simulations show that the Weibel instability created in the collisionless shock accelerates particles perpendicular and parallel to the jet propagation direction. Simulation results show that this instability generates and amplifies highly nonuniform, small-scale magnetic fields, which contribute to the electron's transverse deflection behind the jet head. The "jitter' I radiation from deflected electrons can have different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants. The growth rate of the Weibel instability and the resulting particle acceleration depend on the magnetic field strength and orientation, and on the initial particle distribution function. In this presentation we explore some of the dependencies of the Weibel instability and resulting particle acceleration on the magnetic field strength and orientation, and the particle distribution function.

Nishikawa, K.-I.↗
DOE OSTI2014

Ion shock acceleration by large amplitude slow ion acoustic double layers in laser-produced plasmas

A kinetic model for the shock acceleration of ions in laser-produced plasmas is developed. A fraction of the warm ions are accelerated by the large amplitude monotonic potential of the shock created due the plasma compression and electron heating by the laser. The kinetic model for the monotonic shock is based on the slow ion acoustic double layer (SIADL). It is found that the amplitude of the large amplitude SIADL is almost uniquely defined by the electron temperature. Therefore, a balance between electron heating and plasma compression is needed for optimal ion acceleration by this scheme. Typical Mach numbers of the monotonic shocks are close to 1.5. The scheme could potentially produce monoenergetic ions with a relative energy spread of less than 1%. The model is compared with recent simulations and experiments, where efficient shocks acceleration and production of monoenergetic protons have been observed. Similarities and differences with other shock models are pointed out and discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1981

Vibration of a liquid with a free surface in a spinning spherical tank

The problem of forced fluid vibrations in a partially filled spinning spherical tank is solved numerically by using the finite element method. The governing equations include Coriolis acceleration and spatially homogeneous vorticity. An exponential instability is detected in the present simulation for fill ratios below 0.5 and centrifugal acceleration to thrust ratios less than 1.7. This fictitious instability appears in the model as a result of the homogeneous vortex assumption since the free slosh equations are neutrally stable in the Liapunov sense.

El-Raheb, M.↗
DOE OSTI2015

FPGA-based Klystron linearization implementations in scope of ILC

We report the development and implementation of four FPGA-based predistortion-type klystron linearization algorithms. Klystron linearization is essential for the realization of ILC, since it is required to operate the klystrons 7% in power below their saturation. The work presented was performed in international collaborations at the Fermi National Accelerator Laboratory (FNAL), USA and the Deutsches Elektronen Synchrotron (DESY), Germany. With the newly developed algorithms, the generation of correction factors on the FPGA was improved compared to past algorithms, avoiding quantization and decreasing memory requirements. At FNAL, three algorithms were tested at the Advanced Superconducting Test Accelerator (ASTA), demonstrating a successful implementation for one algorithm and a proof of principle for two algorithms. Furthermore, the functionality of the algorithm implemented at DESY was demonstrated successfully in a simulation.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Strong Coupling of Hydrodynamics and Reactions in Nuclear Statistical Equilibrium for Modeling Convection in Massive Stars

We build on the simplified spectral deferred corrections (SDC) coupling of hydrodynamics and reactions to handle the case of nuclear statistical equilibrium (NSE) and electron/positron captures/decays in the cores of massive stars. Our approach blends a traditional reaction network on the grid with a tabulated NSE state from a very large, ${\mathcal O }(100)$ nuclei network. We demonstrate how to achieve second-order accuracy in the simplified-SDC framework when coupling NSE to hydrodynamics, with the ability to evolve the star on the hydrodynamics time step. We discuss the application of this method to convection in massive stars leading up to core collapse. We also show how to initialize the initial convective state from a 1D model in a self-consistent fashion. All of these developments are done in the publicly available Castro simulation code and the entire simulation methodology is fully GPU-accelerated.

Explosive nucleosynthesis↗
DOE OSTI2025

Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ~21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether β-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. Furthermore, the approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.

Wu, Jiangbo [University of Chicago, IL (United Sta↗