Engineering topics

Haas, Roland

Publications and source records attributed to Haas, Roland.

5 records

DOE OSTI2024

APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics

The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Theoretical and experimental constraints for the equation of state of dense and hot matter

Abstract This review aims at providing an extensive discussion of modern constraints relevant for dense and hot strongly interacting matter. It includes theoretical first-principle results from lattice and perturbative QCD, as well as chiral effective field theory results. From the experimental side, it includes heavy-ion collision and low-energy nuclear physics results, as well as observations from neutron stars and their mergers. The validity of different constraints, concerning specific conditions and ranges of applicability, is also provided.

Kumar, Rajesh (ORCID:0000000327463956)↗

DOE OSTI2023

General relativistic simulations of collapsing binary neutron star mergers with Monte Carlo neutrino transport

Recent gravitational wave observations of neutron-star-neutron-star and neutron-star-black-hole binaries appear to indicate that massive neutron stars may not be too uncommon in merging systems. These discoveries have led to an increased interest in the simulation of merging compact binaries involving massive stars. In this paper, we present a first set of evolution of massive neutron star binaries using Monte Carlo radiation transport for the evolution of neutrinos. Here, we study a range of systems, from nearly symmetric binaries that collapse to a black hole before forming a disk or ejecting material, to more asymmetric binaries in which tidal disruption of the lower mass star leads to the production of more interesting postmerger remnants. For the latter type of systems, we additionally study the impact of viscosity on the properties of the outflows, and compare our results to two recent simulations of identical binaries performed with the whiskyTHC code. We find agreement on the black hole properties, disk mass, and mass and velocity of the outflows within expected numerical uncertainties, and some minor but noticeable differences in the evolution of the electron fraction when using a subgrid viscosity model, with viscosity playing a more minor role in our simulations. The method used to account for r-process heating in the determination of the outflow properties appears to have a larger impact on our result than those differences between numerical codes. We also use the simulation with the most ejected material to verify that our newly implemented Lagrangian tracers provide a reasonable sampling of the matter outflows as they leave the computational grid. We note that, given the lack of production of hot outflows in these mergers, the main role of neutrinos in these systems is to set the composition of the postmerger remnant. One of the main potential uses of our simulations is, thus, as improved initial conditions for longer evolutions of such remnants.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Numerical relativity higher order gravitational waveforms of eccentric, spinning, nonprecessing binary black hole mergers

We use the open source, community-driven, numerical relativity software, the EINSTEIN TOOLKIT to study the physics of eccentric, spinning, nonprecessing binary black hole mergers with mass-ratios q = {2; 4; 6}, individual dimensionless spin parameters chi 1z = +/- 0.6, chi 2z = +/- 0.3, that include higher order gravitational wave modes l <= 4, except for memory modes. Assuming stellar mass binary black hole mergers that may be detectable by the advanced LIGO detectors, we find that including modes up to l = 4 increases the signal-to-noise of compact binaries between 3.5% to 35%, compared to signals that only include the l = ImI = 2 mode. We use two waveform models, TEOBResumS and SEOBNRE, which incorporate spin and eccentricity corrections in the waveform dynamics, to quantify the orbital eccentricity of our numerical relativity catalog in a gauge-invariant manner through fitting factor calculations. Our findings indicate that the inclusion of higher order wave modes has a measurable effect in the recovery of moderately and highly eccentric black hole mergers, and thus it is essential to develop waveform models and signal processing tools that accurately describe the physics of these astrophysical sources.

Joshi, Abhishek V.↗

DOE OSTI2023

Addition of tabulated equation of state and neutrino leakage support to illinoisgrmhd

Here we have added support for realistic, microphysical, finite-temperature equations of state (EOS) and neutrino physics via a leakage scheme to illinoisgrmhd, an open-source GRMHD code for dynamical spacetimes in the einstein toolkit. These new features are provided by two new, nrpy+-based codes: nrpyeos, which performs highly efficient EOS table lookups and interpolations, and nrpyleakage, which implements a new, adaptive mesh refinement (AMR)-capable neutrino leakage scheme in the einstein toolkit. We have performed a series of strenuous validation tests that demonstrate the robustness of these new codes, particularly on the Cartesian AMR grids provided by carpet. Furthermore, we show results from fully dynamical GRMHD simulations of single unmagnetized neutron stars, and magnetized binary neutron star mergers. This new version of illinoisgrmhd, as well as nrpyeos and nrpyleakage, is pedagogically documented in jupyter notebooks and fully open source. The codes will be proposed for inclusion in an upcoming version of the einstein toolkit.

79 ASTRONOMY AND ASTROPHYSICS↗