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Rotating view of a chromochloris zofingiensis cell dividing into 16 cells from cryo-soft X-ray tomography of a reconstructed cell with segmented nucleus (purple), chloroplast (green), mitochondria (red), lipids (yellow), and starch granules within the chloroplast (blue). Credit: Melissa Roth/HHMI and Andreas Walters/Berkeley Lab News story - https://newscenter.lbl.gov/2017/05/19/green-algae-genome/
This award supports one post-doctoral researcher for 1.5 years. Publications that acknowledge this grant: Refs. 1–14. Refs. 3,10,12 assess current methodology for the evaluation of magnetic exchange couplings in transition metal complexes. In particular, Ref. 10 validates the use of an approximate (non-iterative) Green’s function approach for the calculation of magnetic exchange couplings and will be the foundation for Thrust 2 in this proposal. Refs. 3 and 12 focus on widely used density functional approaches based on the standard energy differences methodology for the particular case of oxo-bridged Fe(III) complexes. Refs. 2,4–7,11 apply current methodologies to problems of practical interest in molecular magnetism. Ref. 13 presents a methodology to explicitly simulate the dynamics of open quantum systems within density functional theory (DFT) calculations based on the Liouville-von Neumann equation of motion for quantum systems driven out-of-equilibrium. Ref. 8 uses non-collinear spin DFT to explain the mechanical behavior of magnetic mono-atomic Pt wires produced in break-junction experiments in the presence of a magnetic field.
First- and second-order accurate numerical methods, implemented for CPUs, underpin the majority of industrial CFD solvers. Whilst this technology has proven very successful at solving steady-state problems via a Reynolds Averaged Navier–Stokes approach, its utility for undertaking scale-resolving simulations of unsteady flows is less clear. High-order methods for unstructured grids and GPU accelerators have been proposed as an enabling technology for unsteady scale-resolving simulations of flow over complex geometries. In this study we systematically compare accuracy and cost of the high-order Flux Reconstruction solver PyFR running on GPUs and the industry-standard solver STAR-CCM+ running on CPUs when applied to a range of unsteady flow problems. Specifically, we perform comparisons of accuracy and cost for isentropic vortex advection (EV), decay of the Taylor–Green vortex (TGV), turbulent flow over a circular cylinder, and turbulent flow over an SD7003 aerofoil. We consider two configurations of STAR-CCM+: a second-order configuration, and a third-order configuration, where the latter was recommended by CD-adapco for more effective computation of unsteady flow problems. Results from both PyFR and STAR-CCM+ demonstrate that third-order schemes can be more accurate than second-order schemes for a given cost e.g. going from second- to third-order, the PyFR simulations of the EV and TGV achieve 75× and 3× error reduction respectively for the same or reduced cost, and STAR-CCM+ simulations of the cylinder recovered wake statistics significantly more accurately for only twice the cost. Moreover, advancing to higher-order schemes on GPUs with PyFR was found to offer even further accuracy vs. cost benefits relative to industry-standard tools.
Experimental measurements and computer simulation of secondary electron emission coefficients for FEP-Teflon, for normal and oblique incidence in the presence of a normal electric field are reported. Knowledge of the electrostatic environment surrounding the specimen calculation of particle trajectories are considered. A simulation using a conformal mapping, a Green's integral, and a trajectory generator provides the necessary mathematical support for the measurements which have been made with normal fields of 1.5 and 2.7 kV/mm. When incidence is normal and energy exceeds the critical energy, the coefficient is given by V.58 and for oblique incidence this expression may be divided by the cosine of the angle. The parameter V sub 0 is a function of normal field. Measurements for values of V sub f are presented.
The structure of unstable planetary waves is computed by a quasi-geostrophic model extending from the surface up to 80 km by means of eigenvalue-eigenfunction techniques in spherical coordinates. Three kinds of unstable modes of distinct phase speeds and vertical structures are identified in the winter climate state: (1) the deep Green mode with its maximum amplitude in the stratosphere; (2) the deep Charney mode with its maximum amplitude in the troposphere: and (3) the shallow Charney mode which is largely confined to the troposphere. Both the Green mode and the deep Charney mode are characterized by very slow phase speeds. They are mainly supported by upward wave energy fluxes, but the local baroclinic energy conversion within the stratosphere also contributes in supporting these deep modes. The mesosphere and the troposphere are dynamically independent in the summer season decoupled by the deep stratospheric easterly. The summer mesosphere supports the easterly unstable waves 1-4. Waves 3 and 4 are identified with the observed mesospheric 2-day wave and 1.7-day wave, respectively.
Corotating energetic ion populations (CEIPs) associated with the forward and reverse shocks of corotating interaction regions (CIRs) are observed in CIRs at places where models say are magnetically unconnected to either shock. Such disconnections between CEIPs and shocks are common and have been documented with data from Pioneers 10 and 11 and confirmed with data from Ulysses. They pose a problem for models that account for these CEIPs in terms of ion energization at the shocks followed by ion propagation along field lines. Two possible resolutions to this problem have been suggested: diffusion of the ions across field lines and extension of the ion energization process to regions beyond the shock waves. Here we quantitatively examine the first of these possibilities. We give the Green's function solution to the convection-diffusion equation applied to idealized CIR geometry, with a source at the reverse shock -- the main producer of CEIPs. Two kinds of diffusion are considered: resonant diffusion and stochastic field line diffusion. We find that for resonant diffusion the computed ratio is many orders of magnitudes below the observed ratio. For stochastic field line diffusion, the computed ratio approximately equals the observed ratio if a diffusion coefficient appropriate to the free solar wind is used. It is several orders of magnitude below the observed ratio, however, if a diffusion coefficient appropriate to CIRs is used. We conclude that cross-field diffusion probably does not account for the presence of energetic ions in regions of CIRs that are magnetically unconnected to its shock waves. We suggest that the alternative possibility -- the energetic ions in regions magnetically unconnected to shocks result from an acceleration process that is independent of shocks -- be pursued to the point where quantitative tests can be performed.
Proteins interact to form protein complex to carry out biological functions such as catalytic chemical reaction. Therefore, it is important to develop computational methods to predict protein-protein interaction and the structures of protein complexes to study and enhance protein function. In this project, we successfully developed several deep learning methods to predict inter-protein contacts and the reinforcement learning and optimization methods to reconstruct protein complex structures from predicted inter-chain contacts. The methods were integrated with the MULTICOM protein complex structure prediction system and applied to predict the complex structures of biomass production-related proteins of green algae. During the two and a half years of research and development, all the specific milestones of the project were achieved successfully. 16 publications/manuscripts were produced. 10 software tools were developed. A patent application was submitted. Our MULTICOM predictors leveraging some tools developed in this project were ranked among the top predictors in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022.
Methods for downstream river flow prediction can be categorized into physics-based and empirical approaches. Although based on well-studied physical relationships, physics-based models rely on numerous hydrologic variables characteristic of the specific river system that can be costly to acquire. Moreover, simulation is often computationally intensive. Conversely, empirical models require less information about the system being modeled and can capture a system’s interactions based on a smaller set of observed data. This article introduces two empirical methods to predict downstream hydraulic variables based on observed stream data: a linear programming (LP) model, and a convolutional neural network (CNN). We apply both empirical models within the Colorado River system to a site located on the Green River, downstream of the Yampa River confluence and Flaming Gorge Dam, and compare it to the physics-based model Streamflow Synthesis and Reservoir Regulation (SSARR) currently used by federal agencies. Results show that both proposed models significantly outperform the SSARR model. Moreover, the CNN model outperforms the LP model for hourly predictions whereas both perform similarly for daily predictions. Although less accurate than the CNN model at finer temporal resolution, the LP model is ideal for linear water scheduling tools.
We derive equations of motion for higher order density response functions using the theory of thermodynamic Green’s functions. We also derive expressions for the higher order generalized dielectric functions and polarization functions. Moreover, we relate higher order response functions and higher order collision integrals within the Martin–Schwinger hierarchy. We expect our results to be highly relevant to the study of a variety of quantum many-body systems such as matter under extreme temperatures, densities, and pressures.
Here, we develop a method to construct a microscopic optical potential from chiral interactions for nucleon-nucleus scattering. The optical potential is constructed by combining the Green’s function approach with the coupled-cluster method. To deal with the poles of the Green’s function along the real energy axis we employ a Berggren basis in the complex energy plane combined with the Lanczos method. Using this approach, we perform a proof-of-principle calculation of the optical potential for the elastic neutron scattering on 16 O. For the computation of the ground-state of 16 O, we use the coupled-cluster method in the singles-and-doubles approximation, while for the A ±1 nuclei we use particle-attached/removed equation-of-motion method truncated at two-particle-one-hole and one-particle-two-hole excitations, respectively. We verify the convergence of the optical potential and scattering phase shifts with respect to the model-space size and the number of discretized complex continuum states. We also investigate the absorptive component of the optical potential (which reflects the opening of inelastic channels) by computing its imaginary volume integral and find an almost negligible absorptive component at low-energies. To shed light on this result, we computed excited states of 16 O using equation-of-motion coupled-cluster method with singles-and- doubles excitations and we found no low-lying excited states below 10 MeV. Furthermore, most excited states have a dominant two-particle-two-hole component, making higher-order particle-hole excitations necessary to achieve a precise description of these core-excited states. We conclude that the reduced absorption at low-energies can be attributed to the lack of correlations coming from the low-order cluster truncation in the employed coupled-cluster method.
Purpose: Head and neck (H&N) internal organ motion has previously been determined with low frequency and temporary nature based on population-based pre- and post-treatment studies. Using immobilization masks and adding a 4–6 mm planning-tumor-volume margin, geometric uncertainties of patients are routinely considered clinically inconsequential in H&N radiotherapy. Using the first commercially-available MR-IGRT system, we conducted the first quantitative study on inter-patient, intra- and inter-fractional H&N internal motion patterns to evaluate the necessity of individualized asymmetric internal margins. Methods: Ninety cine sagittal MR image sequences were acquired during the entire treatment course (6–7 weeks) of three H&N cancer patients using the ViewRay™ MR-IGRT system. The images were 5 mm thick and acquired at 4 frames/per second. One of the patients had a tracheostomy tube. The cross-sectional H&N airway (nasopharynx, oropharynx, and laryngopharynx portions) movement was analyzed comprehensively using in-house developed motion detection software. Results: Large inter-patient variations of swallowing frequency (0–1 times/per fraction), swallowing duration (1–3 seconds), and pharyngeal cross-sectional area (238–2516 mm2) were observed. Extensive pharyngeal motion occurred during swallowing, while nonzero and periodic change of airway geometry was observed in resting. For patient 1 with tracheostomy tube replacement, 30.3%, 30.0%, 48.7% and 0.3% of total frames showed ≥ 4 mm displacements in the anterior, posterior, inferior, and superior airway boundaries, respectively; similarly, (5.7%, 0.0%, 0.0%, 0.3%) and (23.3%, 0.0%, 35.7%, 1.7%) occurred for patients 2 and 3. Area overlapping coefficients with respect to the first frame were 76.3+/−6.4%, 90.3+/−0.6%, and 92.3+/−1.2% for the three patients, respectively. Conclusion: Both the resting and swallowing motions varied in frequency and amplitude among the patients and across fractions of a patient’s treatment. Patients receiving surgery that alters their respiratory and swallowing behavior can have significant intra-fractional internal motion. Patient-specific organ/tumor motion analysis may yield individualized asymmetric internal margins and improve the therapeutic ratio.
Bouguer gravity has been computed for the equatorial region of Mars by differencing free air gravity and the gravity predicted from topographic variations. The free air gravity was generated from an eighth-order set of spherical harmonic coefficients. The gravity from topographic variations was generated by integrating a two-dimensional Green's function over each contour level. The Bouguer gravity indicates crustal inhomogeneities on Mars that are postulated to be variations in crustal thickness. The Tharsis ridge is a region of thick continental type crust. The gravity data, structural patterns, topography, and surface geology of this region lead to the interpretation of the Tharsis topographic high as a broad crustal upwarp possibly associated with local formation of lower-density crustal material and subsequent rise of a thicker crust. The Amazonis region is one of several basins of relatively thin crust, analogous to terrestrial ocean basins. The Libya and Hellas basins, which are probable impact features, are also underlain by thin crust and are possible regions of mantle upwelling.
A Numerical Aerodynamic Simulation Facility (NASF) was designed for the simulation of fluid flow around three-dimensional bodies, both in wind tunnel environments and in free space. The application of numerical simulation to this field of endeavor promised to yield economies in aerodynamic and aircraft body designs. A model for a NASF/FMP (Flow Model Processor) ensemble using a possible approach to meeting NASF goals is presented. The computer hardware and software are presented, along with the entire design and performance analysis and evaluation.
A new code for the simulation of full (forebody and base region) flowfields about bluff bodies in the hypersonic regime of severe planetary entry is described. The present 'maximally conservative, maximally differenced' formulation of the unsteady compressible Navier-Stokes equations for 2-D axisymmetric 3-D flow is contrasted for stability with previous formulations of Viviand, Kutler, et al, and Thomas and Lombard. Discrete metric relations peculiar to the axisymmetric finite volume formulation are presented along with a general discussion of their relations to and consequences of failure to close computational cells. A computational mesh of curvilinear coordinate topology singular in the flow regime is presented that permits aligned capturing of the major physical features of the complex flowfield.
The factored-implicit, gas-dynamic algorithm has been adapted to the numerical simulation of equilibrium reactive flows. Changes required in the perfect gas version of the algorithm are developed, and the method of coupling gas-dynamic and chemistry variables is discussed. A flow-field solution that approximates a Jovian entry case was obtained by this method and compared with the same solution obtained by HYVIS, a computer program much used for the study of planetary entry. Comparison of surface pressure distribution and stagnation line shock-layer profiles indicates that the two solutions agree well.
Students Cloud Observations On-Line (S'COOL) is a hands-on educational project which supports NASA's Clouds and the Earth s Radiant Energy System (CERES) satellite instrument; part of the Earth Science Enterprise studying our planet. S'COOL meets science, math, technology and geography Standards of Learning (SOLs) as students observe clouds and related weather conditions, compute data and locate vital information while obtaining ground truth observations for the CERES instrument. These observations can then be used to help validate the CERES measurements; particularly detection of clear sky from space. Participants to date have been in 20 states and 5 countries and have reported great interest and learning among their students. Many have used this project as a stepping stone to further learning in other areas of Earth Science; and to do more with the Internet in the classroom. Satellite images and clues to their interpretation are used on the website ( http://asd-www.larc.nasa.gov/SCOOL/) . Background information is also given on Earth's Radiation Budget and it s importance in understanding our climate. Students can retrieve both their observations and the corresponding satellite data and participate in the validation efforts. A number of suggestions for studies to be done with the data, and related lesson plans, are available. Teachers can tailor this project to the appropriate level and subject matter needed for their students. The recommended grade level is 4th through 12th grade. The project is now open to new participants. We particularly seek schools in more remote areas, to obtain wider geographic coverage for ground truth data; so the project has been designed to use, but not require, computer technology. AGU participants attending the S'COOL presentation will be given a handout describing the project. Material for introducing the project in the classroom will be demonstrated in a participatory style.
Here, we present the open-source VOTCA-XTP software for the calculation of the excited-state electronic structure of molecules using many-body Green’s function theory in the GW approximation with the Bethe–Salpeter equation (BSE). This work provides a summary of the underlying theory and discusses the details of its implementation based on Gaussian orbitals, including resolution-of-identity techniques and different approaches to the frequency integration of the self-energy or acceleration by offloading compute-intensive matrix operations using graphics processing units in a hybrid OpenMP/Cuda scheme. A distinctive feature of VOTCA–XTP is the capability to couple the calculation of electronic excitations to a classical polarizable environment on an atomistic level in a coupled quantum- and molecular-mechanics (QM/MM) scheme, where a complex morphology can be imported from Molecular Dynamics simulations. The capabilities and limitations of the GW–BSE implementation are illustrated with two examples. First, we study the dependence of optically active electron–hole excitations in a series of diketopyrrolopyrrole-based oligomers on molecular-architecture modifications and the number of repeat units. Second, we use the GW–BSE/MM setup to investigate the effect of polarization on localized and intermolecular charge-transfer excited states in morphologies of low-donor content rubrene–fullerene mixtures. These showcases demonstrate that our implementation currently allows us to treat systems with up to 2500 basis functions on regular shared-memory workstations, providing accurate descriptions of quasiparticle and coupled electron–hole excited states of various characters on an equal footing.
In this work, we present algorithmic and implementation details for the fully self-consistent finite-temperature $GW$ method in Gaussian Bloch orbitals for solids. Our implementation is based on the finite-temperature Green's function formalism in which all equations are solved on the imaginary axis, without resorting to analytical continuation during the self-consistency. No quasiparticle approximation is employed and all matrix elements of the self-energy are explicitly evaluated. The method is tested by evaluating the band gaps of selected semiconductors and insulators. We show agreement with other, differently formulated, finite-temperature sc $GW$ implementations when finite-size corrections and basis-set errors are taken into account. By migrating computationally intensive calculations to graphics processing units, we obtain scalable results on large supercomputers with nearly optimal performance. Our work demonstrates the applicability of Gaussian orbital based sc $GW$ for ab initio correlated material simulations and provides a sound starting point for embedding methods built on top of $GW$.