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At least 235 records · Page 13

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform ( RPX ) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

59 BASIC BIOLOGICAL SCIENCES↗

Development and Evaluation of Distributed Energy Resource Device Models: Electric Vehicles, Electric Water Heaters, and Commercial Refrigeration Systems

In order to validate distributed energy resource (DER) models operated with grid services in the GMLC 1.4.2 team’s February (GMLC 2019a) and July (GMLC 2019b) reports, a test and measurement program using actual DER devices was conducted by national laboratories for three devices: (1) electric vehicles (EVs), (2) water heaters, and (3) commercial refrigeration. Test procedures were developed and carried out to identify the mathematical models and their parameters that describe the operational function, characterize the physics, and obey transient response of the devices. This report focuses on the experimental results obtained to develop and verify simulations of three specific EV models. This section summarizes elements of the mathematical model and shows the necessity data collected from the EVs while charging and discharging (driving). In the course of the study, we found it necessary to make some modifications to the model to deal with observed transient behavior. Section 1.2 details the model assumptions and equations, Section 1.3 provides details of the EVs tested, Section 1.4 outlines the test procedures developed for the projects, and Section 1.5 presents the experimental results obtained for the three different EVs tested and how these results compare to the models running the same test profiles.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Experience of Migrating a Parallel Graph Coloring Program from CUDA to SYCL

We describe the experience of converting a CUDA implementation of a parallel graph coloring algorithm to SYCL. The goals are for our work to be useful to application and compiler developers by providing a detailed description of migration paths between CUDA and SYCL. We will describe how CUDA functions are mapped to SYCL functions. Evaluating the CUDA and SYCL implementations of the algorithm shows that the performance of SYCL and CUDA kernels are comparable over the test graph set on NVIDIA P100 and V100 GPUs. The SYCL program also allows for performance evaluation with the OpenCL and Level Zero interfaces and power profiling on an Intel GPU computing platform.

97 MATHEMATICS AND COMPUTING↗

3013 Surveillance Program Interim Summary Report (FY16-FY21)

The K-Area Documented Safety Analysis (DSA) requires the facility participate in the SRS Site Surveillance Program as a part of Shipping Package Qualification and Storage Surveillance Program. The Site Surveillance Program outlines activities for field surveillance and laboratory tests that demonstrate the 3013 containers meet the functional performance requirements described in the DSA. The SRS Surveillance Program also supports the complex-wide Integrated Surveillance Program (ISP) for 3013 containers in accordance with DOESTD-3013. The purpose of this report is to provide a summary of the SRS portion of the surveillance program activities from FY16 through FY21 and formally communicate the interpretation of these results by the Surveillance Program Authority (SPA).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Advanced Closures for Nonlinear Fluid Simulations of Plasmas (Final Report)

Advanced Closures for Nonlinear Fluid Simulations of Plasmas E. Held, Utah State University (Principal Investigator) J.-Y. Ji, Utah State University (Co-Investigator) Utah State University (USU) continued to develop and apply closures for hybrid fluid/kinetic simulations of magnetized fusion plasmas. The closures developed by USU's fusion theory and computation group use the drift ordering and are referred to as "continuum" and "general moment" approaches. They differ in their representation for the distribution functions which probabilistically describe the density of particles in 5 dimensional phase space. The two chosen velocity variables, needed in studies of kinetic physics for magnetized plasmas, are the speed and the component of a particle's velocity along the magnetic field. In magnetized plasmas, the charged particle trajectories are tied closely to the magnetic field lines. Both approaches account for binary interactions between particles using the Coulomb collision operator. Theoretical and computational development along both lines provided avenues for verification between the two approaches. This funding allowed USU to further develop physically accurate and numerically efficient models that advance our understanding of kinetic physics in experiments like the International Thermonuclear Experimental Reactor (ITER). The ITER device will likely prove the physical practicality of thermonuclear fusion by producing 500 megawatts of clean, abundant fusion power. This work helped to realize this goal by advancing our simulation capability using hybrid fluid/kinetic models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil ® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the Is PETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as Is PETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.

59 BASIC BIOLOGICAL SCIENCES↗

The Evolution and Mass Dependence of Galaxy Cluster Pressure Profiles at 0.05 ≤ z ≤ 0.60 and 4 × 10 14 M ⊙ ≤ M 500 ≤ 30 × 10 14 M ⊙

Abstract We have combined X-ray observations from Chandra with Sunyaev–Zel’dovich effect data from Planck and Bolocam to measure intracluster medium pressure profiles from 0.03 R 500 ≤ R ≤ 5 R 500 for a sample of 21 low- z galaxy clusters with a median redshift of 〈 z 〉 = 0.08 and a median mass of 〈 M 500 〉 = 6.1 × 10 14 M ⊙ and a sample of 19 mid- z galaxy clusters with 〈 z 〉 = 0.50 and 〈 M 500 〉 = 10.6 × 10 14 M ⊙ . The mean scaled pressure in the low- z sample is lower at small radii and higher at large radii, a trend that is accurately reproduced in similarly selected samples from The Three Hundred simulations. This difference appears to be primarily due to dynamical state at small radii, evolution at intermediate radii, and a combination of evolution and mass dependence at large radii. Furthermore, the overall flattening of the mean scaled pressure profile in the low- z sample compared to the mid- z sample is consistent with expectations due to differences in the mass accretion rate and the fractional impact of feedback mechanisms. In agreement with previous studies, the fractional scatter about the mean scaled pressure profile reaches a minimum of ≃20% near 0.5 R 500 . This scatter is consistent between the low- z and mid- z samples at all radii, suggesting it is not strongly impacted by sample selection, and this general behavior is reproduced in The Three Hundred simulations. Finally, analytic functions that approximately describe the mass and redshift trends in mean pressure profile shape are provided.

79 ASTRONOMY AND ASTROPHYSICS↗

Galactic Bar Resonances with Diffusion: An Analytic Model with Implications for Bar–Dark Matter Halo Dynamical Friction

Abstract The secular evolution of disk galaxies is largely driven by resonances between the orbits of “particles” (stars or dark matter) and the rotation of non-axisymmetric features (spiral arms or a bar). Such resonances may also explain kinematic and photometric features observed in the Milky Way and external galaxies. In simplified cases, these resonant interactions are well understood: for instance, the dynamics of a test particle trapped near a resonance of a steadily rotating bar is easily analyzed using the angle-action tools pioneered by Binney, Monari, and others. However, such treatments do not address the stochasticity and messiness inherent to real galaxies—effects that have, with few exceptions, been previously explored only with complex N -body simulations. In this paper, we propose a simple kinetic equation describing the distribution function of particles near an orbital resonance with a rigidly rotating bar, allowing for diffusion of the particles’ slow actions. We solve this equation for various values of the dimensionless diffusion strength Δ, and then apply our theory to the calculation of bar–halo dynamical friction. For Δ = 0, we recover the classic result of Tremaine and Weinberg that friction ultimately vanishes, owing to the phase mixing of resonant orbits. However, for Δ > 0, we find that diffusion suppresses phase mixing, leading to a finite torque. Our results suggest that stochasticity—be it physical or numerical—tends to increase bar–halo friction, and that bars in cosmological simulations might experience significant artificial slowdown, even if the numerical two-body relaxation time is much longer than a Hubble time.

79 ASTRONOMY AND ASTROPHYSICS↗

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

Solid composites containing polymeric matrix with carbon fibers embedded therein

A functionalized carbon fiber having covalently bound on its surface a partially cured epoxy or amine-containing sizing agent, wherein at least a portion of epoxide or amine groups in the sizing agent are available as uncrosslinked epoxide or amine groups, which corresponds to a curing degree of epoxide or amine groups of no more than about 0.6. Composites comprised of these functionalized carbon fibers embedded in a polymeric matrix are also described. Methods for producing the functionalized carbon fibers and composites thereof are also described.

36 MATERIALS SCIENCE↗

Tagged DVCS on neutron with the CLAS12 Experiment and the detector BONuS12 at Jefferson Lab (USA)

Hadronic physics studies the properties of the proton and neutron. The theory of Quantum Chromodynamics (QCD) governs the structure of hadrons. Non-perturbative structure functions are used to describe the hadrons? structure. Generalized Parton Distributions (GPDs) are a set of structure functions providing access to a 3D view of the nucleon. GPDs contain information about the longitudinal momentum and transverse position of quarks and their correlation. They are related to the spin structure and play a role in solving the proton spin puzzle. They provide access to the quarks? orbital angular momentum, a crucial puzzle piece. For this, measurements on the proton, already present, and neutron are necessary. This thesis aims to explore Compton scattering on the neutron with a deuterium target by measuring the spectator proton with the CLAS12 detector and the BONuS12 RTPC at Jefferson Lab. This work first describes the implementation, which I carried out, of a Kalman filter to reconstruct spectator protons in the BONuS12 detector. The second part of the manuscript is dedicated to the work on the analysis of DVCS on the neutron with the subtraction of background noises. Two different methods for the subtraction of ?0 will be detailed. Finally, the obtained results are presented and discussed

Ouillon, Mathieu↗

Functional equations and separation of variables for exact g -function

The g-function is a measure of degrees of freedom associated to a boundary of two-dimensional quantum field theories. In integrable theories, it can be computed exactly in a form of the Fredholm determinant, but it is often hard to evaluate numerically. In this paper, we derive functional equations — or equivalently integral equations of the thermodynamic Bethe ansatz (TBA) type — which directly compute the g-function in the simplest integrable theory; the sinh-Gordon theory at the self-dual point. The derivation is based on the classic result by Tracy and Widom on the relation between Fredholm determinants and TBA, which was used also in the context of topological string. We demonstrate the efficiency of our formulation through the numerical computation and compare the results in the UV limit with the Liouville CFT. As a side result, we present multiple integrals of Q-functions which we conjecture to describe a universal part of the g-function, and discuss its implication to integrable spin chains.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Challenges for density functional theory: calculation of CO adsorption on electrocatalytically relevant metals

Density Functional Theory (DFT) is currently the most tractable choice of theoretical model used to understand the mechanistic pathways for electrocatalytic processes such as CO 2 or CO reduction. In this work, we assess the performance of two DFT functionals designed specifically to describe surface interactions, RTPSS and RPBE, as well as two popular meta-GGA functionals, SCAN and B97M-rV, that have not been a priori optimized for better interfacial properties. We assess all four functionals against available experimental data for prediction of bulk and bare surface properties on four electrocatalytically relevant metals, Au, Ag, Cu, and Pt, and for binding CO to surfaces of these metals. To partially mitigate issues such as thermal and anharmonic corrections associated with comparing computations with experiments, molecular benchmarks against high level quantum chemistry are reported for CO complexes with Au, Ag, Cu and Pt atoms, as well as the CO–water complex and the water dimer. Overall, we find that the surface modified RPBE functional performs reliably for many of the benchmarks examined here, and the meta-GGA functionals also show promising results. Specifically B97M-rV predicts the correct site preference for CO binding on Ag and Au (the only functional tested here to do so), while RTPSS performs well for surface relaxations and binding of CO on Pt and Cu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TurboRVB: A many-body toolkit for ab initio electronic simulations by quantum Monte Carlo

TurboRVB is a computational package for ab initio Quantum Monte Carlo (QMC) simulations of both molecular and bulk electronic systems. The code implements two types of well established QMC algorithms: Variational Monte Carlo (VMC) and diffusion Monte Carlo in its robust and efficient lattice regularized variant. A key feature of the code is the possibility of using strongly correlated many-body wave functions (WFs), capable of describing several materials with very high accuracy, even when standard mean-field approaches [e.g., density functional theory (DFT)] fail. The electronic WF is obtained by applying a Jastrow factor, which takes into account dynamical correlations, to the most general mean-field ground state, written either as an antisymmetrized geminal power with spin-singlet pairing or as a Pfaffian, including both singlet and triplet correlations. This WF can be viewed as an efficient implementation of the so-called resonating valence bond (RVB) Ansatz, first proposed by Pauling and Anderson in quantum chemistry [L. Pauling, The Nature of the Chemical Bond (Cornell University Press, 1960)] and condensed matter physics [P.W. Anderson, Mat. Res. Bull 8, 153 (1973)], respectively. The RVB Ansatz implemented in TurboRVB has a large variational freedom, including the Jastrow correlated Slater determinant as its simplest, but nontrivial case. Moreover, it has the remarkable advantage of remaining with an affordable computational cost, proportional to the one spent for the evaluation of a single Slater determinant. Therefore, its application to large systems is computationally feasible. The WF is expanded in a localized basis set. Several basis set functions are implemented, such as Gaussian, Slater, and mixed types, with no restriction on the choice of their contraction. The code implements the adjoint algorithmic differentiation that enables a very efficient evaluation of energy derivatives, comprising the ionic forces. Thus, one can perform structural optimizations and molecular dynamics in the canonical NVT ensemble at the VMC level. For the electronic part, a full WF optimization (Jastrow and antisymmetric parts together) is made possible, thanks to state-of-the-art stochastic algorithms for energy minimization. In the optimization procedure, the first guess can be obtained at the mean-field level by a built-in DFT driver. The code was efficiently parallelized by using a hybrid MPI-OpenMP protocol, which is also an ideal environment for exploiting the computational power of modern Graphics Processing Unit accelerators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single-Determinant Ground State in Ce 4+ Imidophosphorane Complexes

X-ray spectroscopy techniques are critical in the electronic structure analysis of high-valent lanthanides. The interpretation of multipeaked features at the lanthanide L 3 -edge has remained a challenging question, as it is observed across a range of material classes. A series of structurally related Ce 4+ complexes were prepared to probe the potential ligand field perturbation of the ground state within the series. The tuning of relative 4f and ligand orbital energies in homoleptic and heteroleptic tetravalent Ce imidophosphorane complexes is achieved through ligand derivatization and is clearly demonstrated by UV−vis spectroscopy and electrochemically measured redox potentials. However, Ce L 3 - edge high-energy resolution fluorescence-detected (HERFD) X-ray absorption near-edge structure (XANES) spectra present features at consistent numbers and energies across the range of complexes. Resonant inelastic X-ray scattering (RIXS) is employed to visualize the observed features in the HERFD-XANES spectra. Large complete active space configuration interaction singles and doubles (CASCISD) calculations demonstrate that the ground-state wave function of all complexes can be described employing a single determinant. As a result, the multielectron feature at the L 3 -edge observed in this study for the Ce 4+ imidophosphorane complexes is described as excited-state multiconfigurational behavior that is independent of ligand variation, in systems where the ground state is described using the simple single determinant wave function.

Lanthanides↗