MCP agents in PanDA
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97 MATHEMATICS AND COMPUTING↗
Engineering topics
Yang, Wei
Publications and source records attributed to Yang, Wei.
Diffusing protein binders to intrinsically disordered proteins
Not provided.
Science & Technology - Other Topics↗
AI Surrogate Model for Distributed Computing Workloads
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97 MATHEMATICS AND COMPUTING↗
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
Not provided.
Biochemistry & Molecular Biology↗
Overview of the distributed image processing infrastructure to produce the Legacy Survey of Space and Time
The Vera C. Rubin Observatory is preparing to execute the most ambitious astronomical survey ever attempted, the Legacy Survey of Space and Time (LSST). Currently the final phase of construction is under way in the Chilean Andes, with the Observatory’s ten-year science mission scheduled to begin in 2025. Rubin’s 8.4-meter telescope will nightly scan the southern hemisphere collecting imagery in the wavelength range 320–1050 nm covering the entire observable sky every 4 nights using a 3.2 gigapixel camera, the largest imaging device ever built for astronomy. Automated detection and classification of celestial objects will be performed by sophisticated algorithms on high-resolution images to progressively produce an astronomical catalog eventually composed of 20 billion galaxies and 17 billion stars and their associated physical properties. In this article we present an overview of the system currently being constructed to perform data distribution as well as the annual campaigns which reprocess the entire image dataset collected since the beginning of the survey. These processing campaigns will utilize computing and storage resources provided by three Rubin data facilities (one in the US and two in Europe). Each year a Data Release will be produced and disseminated to science collaborations for use in studies comprising four main science pillars: probing dark matter and dark energy, taking inventory of solar system objects, exploring the transient optical sky and mapping the Milky Way. Also presented is the method by which we leverage some of the common tools and best practices used for management of large-scale distributed data processing projects in the high energy physics and astronomy communities. We also demonstrate how these tools and practices are utilized within the Rubin project in order to overcome the specific challenges faced by the Observatory.
79 ASTRONOMY AND ASTROPHYSICS↗
Integrating the PanDA Workload Management System with the Vera C. Rubin Observatory
The Vera C. Rubin Observatory will produce an unprecedented astronomical data set for studies of the deep and dynamic universe. Its Legacy Survey of Space and Time (LSST) will image the entire southern sky every three to four days and produce tens of petabytes of raw image data and associated calibration data over the course of the experiment’s run. More than 20 terabytes of data must be stored every night, and annual campaigns to reprocess the entire dataset since the beginning of the survey will be conducted over ten years. The Production and Distributed Analysis (PanDA) system was evaluated by the Rubin Observatory Data Management team and selected to serve the Observatory’s needs due to its demonstrated scalability and flexibility over the years, for its Directed Acyclic Graph (DAG) support, its support for multi-site processing, and its highly scalable complex workflows via the intelligent Data Delivery Service (iDDS). PanDA is also being evaluated for prompt processing where data must be processed within 60 seconds after image capture. This paper will briefly describe the Rubin Data Management system and its Data Facilities (DFs). Finally, it will describe in depth the work performed in order to integrate the PanDA system with the Rubin Observatory to be able to run the Rubin Science Pipelines using PanDA.
79 ASTRONOMY AND ASTROPHYSICS↗
Anomaly detection in PV systems using constrained low-rank and sparse decomposition
PV (photovoltaic) systems, also known as solar panel systems, play an essential role in the mitigation of greenhouse gas emissions and the promotion of renewable energy. Through the conversion of sunlight into usable energy, electricity is generated without emitting greenhouse gases and producing pollutants. Notwithstanding the evolutionary significance of PV systems, the occurrence of defects and anomalies in PV systems may result in diminished power output, consequently impeding the efficiency of the systems and potentially resulting in hazards in certain circumstances. Therefore, early detection of faults and anomalies in PV systems is imperative to guarantee the reliability, efficiency, and safety of the systems. In this article, we develop a signal decomposition for the purpose of anomaly detection in PV systems. The proposed methodology is grounded on the concept of low-rank and sparse decomposition, with consideration given to the signs of the decomposed low-rank and sparse components, as well as the smooth variations within and between periods in the mean signals. Through the implementation of Monte Carlo simulations, we showcase the efficacy of our proposed methodology in identifying anomalies of varying durations and magnitudes in PV systems. A case study is employed to validate the proposed methodology in detecting anomalies in real PV systems.
14 SOLAR ENERGY↗
Accurate computational design of three-dimensional protein crystals
Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here, in this study, we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.
59 BASIC BIOLOGICAL SCIENCES↗
An uncertainty-aware strategy for plasma mechanism reduction with directed weighted graphs
In this work, we present a framework for the analysis and reduction of plasma mechanisms by means of weighted directed graphs, in which reactions and species are both treated as nodes. The methodology consists of two distinct analyses. The first, which is qualitative, relies on graph spatializations via force-directed algorithms to discover the predominant global patterns in the chemical model. The second ranks the reactions based on their shortest paths' lengths from/to the species of interest and their relative contributions to the power balance. Further, this quantitative investigation enables a strategy for mechanism reduction that is fully automatized, as it does not require any expert knowledge, highly effective, as it generates reduced mechanisms that are highly accurate while relying on a small number of processes, and easily interpretable, as the algorithm justifies the importance of the retained reactions by outputting their related chemical pathways. Additionally, the work proposes a methodology extension that employs ensembles of graphs to improve the robustness of the reduced mechanism to reaction parameter uncertainties. The approach, here tested for steady-state predictions of a plasma system characterizing negative hydrogen ion sources, is general and can be used in a wide variety of applications outside the particular nuclear fusion context demonstrated in this work.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins
A challenge for design of protein–small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.
59 BASIC BIOLOGICAL SCIENCES↗
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field
With the continual development of lanthanides (Ln) in current technological devices, an efficient separation process is needed that can recover greater amounts of these rare elements. Dicyclohexano-18-crown-6(DCH18C6) is a crown ether that may be a promising candidate for Ln separation, but additional research is required. As such, molecular dynamics(MD) simulations have been performed on four divalent lanthanide halide salts(Sm 2+ , Eu 2+ , Dy 2+ , and Yb 2+ ) and one divalent actinide halide salt (Cf 2+ ) bound to three diastereoisomers of DCH18C6. Dy 2+ , Yb 2+ , Cf 2+ , DCH18C6, and tetrahydrofuran (THF) solvent were parameterized for the AMOEBA polarizable force field for the first time, whereas existing parameters for Sm 2+ and Eu 2+ were utilized from our previous efforts. A coordination number (CN) of six for Ln 2+ /An 2+ –O solvated in THF indicated that the cations interacted almost entirely with the oxygens of the polyether ring. A CN of one for Ln 2+ /An 2+ -N solvated in acetonitrile for systems containing iodide suggested that theN atom of acetonitrile was competitive with I – for cation interactions. Fluctuation between five and six CNs for Dy 2+ and Yb 2+ suggested that although the cations remained in the polyether ring, the size of the ring may not be an ideal fit as these cations possess comparatively smaller ionic radii. Gibbs binding free energies of Sm 2+ in all DCH18C6 diastereoisomers solvated in THF were calculated. The binding free energy of the cis-syn-cis diastereoisomer was the most favorable, followed by cis-anti-cis, and then trans-anti-trans. Lastly, two major types of conformation were observed for each diastereoisomer that were related to the electrostatic interactions and charge density of the cations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A charged diatomic triple-bonded U≡N species trapped in C 82 fullerene cages
Actinide diatomic molecules are ideal models to study elusive actinide multiple bonds, but most of these diatomic molecules have so far only been studied in solid inert gas matrices. Herein, we report a charged U≡N diatomic species captured in fullerene cages and stabilized by the U-fullerene coordination interaction. Two diatomic clusterfullerenes, viz. UN@C s (6)-C 82 and UN@C 2 (5)-C 82 , were successfully synthesized and characterized. Crystallographic analysis reveals U-N bond lengths of 1.760(7) and 1.760(20) Å in UN@C s (6)-C 82 and UN@C 2 (5)-C 82 . Moreover, U≡N was found to be immobilized and coordinated to the fullerene cages at 100 K but it rotates inside the cage at 273 K. Quantum-chemical calculations show a (UN) 2+ @(C 82 ) 2- electronic structure with formal +5 oxidation state (f 1 ) of U and unambiguously demonstrate the presence of a U≡N bond in the clusterfullerenes. This study constitutes an approach to stabilize fundamentally important actinide multiply bonded species.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Relaxation dynamics of deformed polymer nanocomposites as revealed by small-angle scattering and rheology
Here, the relaxation dynamics of polystyrene (PS)/silica nanocomposites after a large step deformation are studied by a combination of small-angle scattering techniques and rheology. Small-angle X-ray scattering measurements and rheology show clear signatures of nanoparticle aggregation that enhances the mechanical properties of the polymer nanocomposites (PNCs) in the linear viscoelastic regime and during the initial phase of stress relaxation along with accelerated relaxation dynamics. Small-angle neutron scattering experiments under the zero-average-contrast condition reveal, however, smaller structural anisotropy in the PNCs than that in the neat polymer matrix, as well as accelerated anisotropy relaxation. In addition, the degrees of anisotropy reduction and relaxation dynamics acceleration increase with increasing nanoparticle loading. These results are in sharp contrast to the prevailing viewpoint of enhanced molecular deformation as the main mechanism for the mechanical enhancement in PNCs. Furthermore, the observed acceleration of stress relaxation and reduction in structural anisotropy point to two types of nonlinear effects in the relaxation dynamics of PNCs at large deformation.
36 MATERIALS SCIENCE↗
A Sparse and Low Rank Penalized Signal Decomposition Model with Constraints: Anomaly Detection in PV Systems
Recently, robust PCA has seen its wide application in various industries for its ability to perform the task of anomaly detection. The essence of robust PCA approach is to break down the signal into a low rank component and sparse component. In many applications, a simple breakdown of the signal without accounting for the signs of low rank components and sparse components would violate the physical constraints of the decomposed signal. In addition, often times, the signals in the real world collected for a long duration has smooth changes within a day and between days. As an example, the power signals collected in a photovoltaic (PV) system are cyclostationary, exhibiting these characteristics. Neglecting the smoothness of signals would result in miss detection of anomalous signals which are smooth within a day but non-smooth between days and vice versa. In this paper, we developed a signal decomposition approach for the purpose of anomaly detection based on the idea of low rank and sparse decomposition taking into consideration the signs of the decomposed low rank and sparse components and the within-day and between-day smooth changes in the original signals. The proposed unsupervised approach for fault detection eliminates the need for faulty samples required by other machine learning methods. It does not require the full I-V characteristics to work. Furthermore, there is no need for complex modelling of PV systems as in the case of power loss analysis. Using Monte Carlo simulations, we demonstrate the ability of our proposed approach for detecting anomalies of different duration and severity in PV systems.
14 SOLAR ENERGY↗
Hydration of divalent lanthanides, Sm 2+ and Eu 2+ : A molecular dynamics study with polarizable AMOEBA force field
The chemistry of divalent lanthanides, Ln 2+ , is a growing sub-field of heavy element chemistry owing to new synthetic approaches. However, some theoretical aspects of these unusual cations are currently underdeveloped, especially as they relate to their dynamic properties in solution. In this study, we address the hydration of two of the classical Ln 2+ cations, Sm 2+ and Eu 2+ , using atomic multipole optimized energetic for biomolecular applications (AMOEBA) force fields. These cations have not been parameterized to date with AMOEBA, and few studies are available because of their instability with respect to oxidation in aqueous media. Coordination numbers (CN's) of 8.2 and 8.1 respectively for Sm 2+ and Eu 2+ , and 8.8 for both Sm 3+ and Eu 3+ have been obtained and are in good agreement with the few available AIMD and X-ray absorption fine structures studies. The decreased CN of Ln 2+ compared with Ln 3+ arises from progressive water exchange events that indicates the gradual stabilization of 8-coordinate structures with respect to 9-coordinate geometries. Moreover, the effects of the chloride counter anions on the coordination of Ln 2+ cations have been studied at different chloride concentrations in this work. Lastly, water exchange times of Ln 2+ cations have been calculated to provide a comprehensive understanding of the behavior of Eu 2+ and Sm 2+ in aqueous chloride media.
AMOEBA force field parameterization↗
Analysis Facilities for HL-LHC
The HL-LHC presents significant challenges for the HEP analysis community. The number of events in each analysis is expected to increase by an order of magnitude and new techniques are expected to be required; both challenges necessitate new services and approaches for analysis facilities. These services are expected to provide new capabilities, a larger scale, and different access modalities (complementing -- but distinct from -- traditional batch-oriented approaches). To facilitate this transition, the US-LHC community is actively investing in analysis facilities to provide a testbed for those developing new analysis systems and to demonstrate new techniques for service delivery. This whitepaper outlines the existing activities within the US LHC community in this R&D area, the short- to medium-term goals, and the outline of common goals and milestones.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗