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At least 775 records · Page 43

Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily

Enzyme catalysis is a complex process involving several steps along the reaction coordinates, including substrate recognition and binding, chemical transformation, and product release. Evidence continues to emerge linking the functional and evolutionary role of conformational exchange processes in optimal catalytic activity. Ligand binding changes the conformational landscape of enzymes, inducing long-range conformational rearrangements. Using functionally distinct members of the pancreatic ribonuclease superfamily as a model system, we characterized the structural and conformational changes associated with the binding of two mononucleotide ligands. By combining NMR chemical shift titration experiments with the chemical shift projection analysis (CHESPA) and relaxation dispersion experiments, we show that biologically distinct members of the RNase superfamily display discrete chemical shift perturbations upon ligand binding that are not conserved even in structurally related members. Amino acid networks exhibiting coordinated chemical shift displacements upon binding of the two ligands are unique to each of the RNases analyzed. Our results reveal the contribution of conformational rearrangements to the observed chemical shift perturbations. These observations provide important insights into the contribution of the different ligand binding specificities and effects of conformational exchange on the observed perturbations associated with ligand binding for functionally diverse members of the pancreatic RNase superfamily.

Biochemistry & Molecular Biology↗

Quantum optimal control of multiple weakly interacting molecular rotors in the time-dependent Hartree approximation

In this work we perform quantum optimal control simulations, based on the Time-Dependent Hartree (TDH) approximation, for systems of three to five dipole-dipole coupled OCS rotors. A control electric field is used to steer all of the individual rotors, arranged in chains and regular polygons in a plane, toward either identical or unique objectives. The goal is to explore the utility of the TDH approximation to model the field-induced dynamics of multiple interacting rotors in the weak dipole-dipole coupling regime. A stochastic hill climbing approach is employed to seek an optimal control field that achieves the desired objectives at a specified target time. We first show that multiple rotors in chain and polygon geometries can be identically oriented in the same direction; these cases do not significantly depend on the presence of the dipole-dipole interaction. Additionally, in particular geometrical arrangements, we demonstrate that individual rotors can be uniquely manipulated toward different objectives with the same field. Specifically, it is shown that for a three rotor chain, the two end rotors can be identically oriented in a specific direction while keeping the middle rotor in its ground state, and for an equilateral triangle, two rotors can be identically oriented in a specific direction while the third rotor is oriented in the opposite direction. These multirotor unique objective cases exploit the shape of the field in coordination with dipole-dipole coupling between the rotors. Comparisons to numerically exact calculations, utilizing the TDH-determined fields, are given for all optimal control studies involving systems of three rotors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Paravertebral Collateral Arteries in Patients with Carotid Stenosis: Is There a Safe Space for Transforaminal Cervical Nerve Root Injections?

Aim: Image-guided cervical nerve root injections can cause serious complications including spinal cord infarction. This risk may be increased in patients with carotid stenosis who develop collateral arteries. The aim of this study is to describe the prevalence, and anatomical location, of arterial collateral vessels in relation to the optimal needle tip position in cervical nerve root injections. Materials and Methods: This retrospective study included 25 patients who had > 70% stenosis on a carotid CT angiogram. For each foramen the position of collateral arteries and the most anterior point of the facet joint were recorded, as Cartesian coordinates, by two independent observers. Descriptive statistics were used to analyse and present the results. Results: 14 patients had unilateral and 11 had bilateral stenoses. A total of 85 collaterals were identified at all levels, the most common being C2/3. The median distance from collateral to optimal needle tip placement was 9.6 mm (95% CI median: 6.7–12.4, IQR: 5.6–15.6). The minimum distance was 2.9 mm. Inter-observer reliability was “substantial” (ICC 0.78, 95% CI 0.71–0.83). Conclusion: Collateral arteries were common in our cohort of patients with carotid artery stenosis and half lay within 10 mm of the optimal position for transforaminal cervical nerve root injection.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Kinematically redundant arm formulations for coordinated multiple arm implementations

Although control laws for kinematically redundant robotic arms were presented as early as 1969, redundant arms have only recently become recognized as viable solutions to limitations inherent to kinematically sufficient arms. The advantages of run-time control optimization and arm reconfiguration are becoming increasingly attractive as the complexity and criticality of robotic systems continues to progress. A generalized control law for a spatial arm with 7 or more degrees of freedom (DOF) based on Whitney's resolved rate formulation is given. Results from a simulation implementation utilizing this control law are presented. Furthermore, results from a two arm simulation are presented to demonstrate the coordinated control of multiple arms using this formulation.

Robert W Bailey↗

Aeroelastic tailoring of rotor blades for vibration reduction in forward flight

Modern structural optimization techniques are applied to vibration reduction of helicopter rotor blades in forward flight. The objective function minimized consists of the oscillatory vertical hub shears or the hub rolling moments at one particular advance ratio. The behavior constraints are the frequency placements of the blade and the requirement that aeroelastic stability margins, in hover, remain unaffected by the optimization process. The aeroelastic stability and response analysis is based on a fully coupled flap-lag-torsional analysis of the blade. The vertical hub shears and rolling moments used as the objective function are obtained by appropriate integration of the loads acting along the span of the blade combined with a transformation to a hub fixed coordinate system, and a summation over the total number of blades. Numerical results for both a stiff-in-plane and a soft-in-plane configuration are presented, indicating that structural optimization yields the highest benefits when applied to soft-in-plane blade configuration. The results indicate substantial (15-40 percent) reduction in vibration levels, as well as a blade which is 20 percent lighter than the initial design.

Friedmann, P. P.↗

Parallel Estimation and Control Architectures for Deep-Space Formation Flying Spacecraft

The formation flying of precisely controlled spacecraft in deep space can be used to implement optical instruments capable of imaging planets in other solar systems. The distance of the formation from Earth necessitates a significant level of autonomy and each spacecraft must base its actions on its estimates of the location and velocity of the other spacecraft. Precise coordination and control is the key requirement in such missions and the flow of information between spacecraft must be carefully designed. Doing this in an efficient and optimal manner requires novel techniques for the design of the on-board estimators. The use of standard Kalman filter-based designs can lead to unanticipated dynamics--which we refer to as disagreement dynamics--in the estimators' errors. We show how communication amongst the spacecraft can be designed in order to control all of the dynamics within the formation. We present several results relating the topology of the communication network to the resulting closed-loop control dynamics of the formation. The consequences for the design of the control, communication and coordination are discussed.

distributed control↗

Electronegativity-Guided Site Differentiation in High-Entropy Alloy for pH-universal Hydrogen Evolution Reactions

Enhancing the intrinsic activity of transition metal catalysts for the hydrogen evolution reaction (HER) remains a critical challenge in sustainable energy conversion. Herein, we report an electronegativity-guided site differentiation strategy in a single-phase CoNiCuMoW high-entropy alloy (HEA) via electrodeposition by incorporating high-electronegativity 4d/5d orbital transition metals (Mo, W) into the face-centered cubic (fcc) matrix (CoNiCu). The as-synthesized HEA demonstrates exceptional HER performance in all pH conditions, delivering an outstanding overpotential of 65 mV (alkaline), 28 mV (acidic), and 155 mV (neutral) at a current density of 100 mA cm−2, showing performance comparable to commercial Pt/C and has excellent long-term stability at high current density (1 A cm−2, 1000 h). X-Ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations reveal that the incorporation of Mo/W simultaneously alters the local coordination environment and induces element-dependent charge redistribution, accompanied by a system-level d-band center downshift, thereby optimizing the hydrogen binding strength across multimetallic sites. Meanwhile, oxophilic Mo/W sites lower the water dissociation energy barrier. These synergistic effects collectively enable efficient and durable pH-universal HER performance.

Wu, Yutong↗

Many Body Effects and Icosahedral Order in Superlattice Self-Assembly

Here, we elucidate how nanocrystals “bond” to form ordered structures. For that purpose we consider nanocrystal configurations consisting of regular polygons and polyhedra, which are the motifs that constitute single component and binary nanocrystal superlattices, and simulate them using united atom models. We compute the free energy and quantify many body effects, i.e., those that cannot be accounted for by pair potential (two-body) interactions, further showing that they arise from coalescing vortices of capping ligands. We find that such vortex textures exist for configurations with local coordination number ≤6. For higher coordination numbers, vortices are expelled and nanocrystals arrange in configurations with tetrahedral or icosahedral order. We provide explicit formulas for the optimal separations between nanocrystals, which correspond to the minima of the free energies. Our results quantitatively explain the structure of superlattice nanocrystals as reported in experiments and reveal how packing arguments, extended to include soft components, predict ordered nanocrystal aggregation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improving the reliability of automated non-destructive inspection

In automated NDE a region of an inspected component is often interrogated several times, be it within a single data channel, across multiple channels or over the course of repeated inspections. The systematic combination of these diverse readings is recognized to provide a means to improve the reliability of the inspection, for example by enabling noise suppression. Specifically, such data fusion makes it possible to declare regions of the component defect-free to a very high probability whilst readily identifying indications. Registration, aligning input datasets to a common coordinate system, is a critical pre-computation before meaningful data fusion takes place. A novel scheme based on a multiobjective optimization is described. The developed data fusion framework, that is able to identify and rate possible indications in the dataset probabilistically, based on local data statistics, is outlined. The process is demonstrated on large data sets from the industrial ultrasonic testing of aerospace turbine disks, with major improvements in the probability of detection and probability of false call being obtained.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improved initial guess for minimum energy path calculations

A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Model-Predictive Hierarchical-Control Framework for Aggregating Residential DERs to Provide Grid Regulation Services

This paper develops a hierarchical control frame-work to aggregate and to manage behind-the-meter distributed energy resources (DERs), which will be ubiquitous in future distribution systems. In the proposed framework, firstly, each controller in the hierarchy determines the flexibility of the DERs such that the obtained flexibility is feasible with respect to its operational purview. For example, the operational purview of a home energy management system may only consider consumer comfort preferences, while that for an aggregator or a grid controller may consider network voltage management as well. Based on the feasible flexibility, optimal setpoints for the DERs is then determined by the hierarchical controllers to help the distribution power network in voltage regulation, coordination issues with existing transmission-level conventional generators, etc. Therefore, the proposed strategy, which is based on model-predictive control, can be effectively utilized by the distribution network to coordinate several DERs to provide grid regulation services. Numerical simulations performed on the IEEE 37-bus test system demonstrate the efficacy of the proposed approach.

behind-the-meter↗

Architecture of a Residential Solid State Power Substation (SSPS) Node

High integration rates of new loads and distributed generation at the edge of the grid are posing new challenges. However, existing smart power electronic systems are not designed to coordinate and maximize grid support or provide multiple grid services simultaneously. This work presents the application of a solid-state power substation (SSPS) to residential systems to increase this coordination and reduce future challenges. The proposed residential SSPS is validated in simulation including power electronic converter models, feeder models, and optimization.

Krishna Moorthy, Radha↗

SU-F-T-65: AutomaticTreatment Planning for High-Dose Rate (HDR) Brachytherapy with a VaginalCylinder Applicator

Purpose: High dose rate (HDR) brachytherapy treatment planning is conventionally performed in a manual fashion. Yet it is highly desirable to perform computerized automated planning to improve treatment planning efficiency, eliminate human errors, and reduce plan quality variation. The goal of this research is to develop an automatic treatment planning tool for HDR brachytherapy with a cylinder applicator for vaginal cancer. Methods: After inserting the cylinder applicator into the patient, a CT scan was acquired and was loaded to an in-house developed treatment planning software. The cylinder applicator was automatically segmented using image-processing techniques. CTV was generated based on user-specified treatment depth and length. Locations of relevant points (apex point, prescription point, and vaginal surface point), central applicator channel coordinates, and dwell positions were determined according to their geometric relations with the applicator. Dwell time was computed through an inverse optimization process. The planning information was written into DICOM-RT plan and structure files to transfer the automatically generated plan to a commercial treatment planning system for plan verification and delivery. Results: We have tested the system retrospectively in nine patients treated with vaginal cylinder applicator. These cases were selected with different treatment prescriptions, lengths, depths, and cylinder diameters to represent a large patient population. Our system was able to generate treatment plans for these cases with clinically acceptable quality. Computation time varied from 3–6 min. Conclusion: We have developed a system to perform automated treatment planning for HDR brachytherapy with a cylinder applicator. Such a novel system has greatly improved treatment planning efficiency and reduced plan quality variation. It also served as a testbed to demonstrate the feasibility of automatic HDR treatment planning for more complicated cases.

60 APPLIED LIFE SCIENCES↗

HOMER Economic Models - US Navy

This LETTER REPORT has been prepared by Idaho National Laboratory for US Navy NAVFAC EXWC to support in testing pre-commercial SIREN (Simulated Integration of Renewable Energy Networks) computer software models. In the logistics mode SIREN software simulates the combination of renewable power sources (solar arrays, wind turbines, and energy storage systems) in supplying an electrical demand. NAVFAC EXWC will create SIREN software logistics models of existing or planned renewable energy projects at five Navy locations (San Nicolas Island, AUTEC, New London, & China Lake), and INL will deliver additional HOMER computer models for comparative analysis. In the transient mode SIREN simulates the short time-scale variation of electrical parameters when a power outage or other destabilizing event occurs. In the HOMER model, a variety of inputs are entered such as location coordinates, Generators, PV arrays, Wind Turbines, Batteries, Converters, Grid costs/usage, Solar resources, Wind resources, Temperatures, Fuels, and Electric Loads. HOMER's optimization and sensitivity analysis algorithms then evaluate the economic and technical feasibility of these technology options and account for variations in technology costs, electric load, and energy resource availability. The Navy can then use HOMER’s optimization and sensitivity results to compare to those of the SIREN model. The U.S. Department of Energy (DOE) Idaho National Laboratory (INL) possesses unique expertise and experience in the software, hardware, and systems design for the integration of renewable energy into the electrical grid. NAVFAC EXWC will draw upon this expertise to complete mission requirements.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Computing Properties of Hadrons, Nuclei and Nuclear Matter from Quantum Chromodynamics

This project was part of a coordinated software development effort which the nuclear physics lattice QCD community pursues in order to ensure that lattice calculations can make optimal use of present, and forthcoming leadership-class and dedicated hardware, including those of the national laboratories, and prepares for the exploitation of future computational resources in the exascale era. The UW team improved and extended software libraries used in lattice QCD calculations related to multi-nucleon systems, enhanced production running codes related to load balancing multi-nucleon production on large-scale computing platforms, and developed SQLite (addressable database) interfaces to efficiently archive and analyze multi-nucleon data and developed a Mathematica interface for the SQLite databases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Subcontract Report: Diffusion Mechanisms and Bond Dynamics in Solid Electrolyte Ion-Conductors

We employ first-principles molecular dynamics simulations and Maximally Localized Wannier Function (MLWF) analysis to explore how halide substitution and nano-phase microstructures affect diffusivity, through the activation energy barrier - E a and D 0 , in the solid electrolyte Li 3 InBr 6-x Cl x . We find that nano-phase microstructures with x=3 (50-50 Br-Cl) mixed composition have a higher diffusivity compared to x=2 and x=3 solid solutions. There is a positive linear relationship between ln(D 0 .) and E a , which suggests that for superionic conductivity optimizing both the activation energy and the D 0 is important. Bond frustration due to mismatch in crystal geometry and ideal coordination number leads to especially high diffusivity through a high D 0 in the x=3 composition.

25 ENERGY STORAGE↗

Computing the Properties of Hadrons, Nuclei, and Nuclear Matter from Quantum Chromodynamics, UNC-CH Final Report.

This is the final technical report for the UNC-CH component of a SciDAC3 project. This project served to coordinate the software development effort which the nuclear physics lattice QCD community is developing to ensure that lattice calculations can make optimal use of forthcoming leadership-class and dedicated hardware, including those of the national laboratories, and prepares for the exploitation of future computational resources in the exascale era. The project developed and optimized simulation software for lattice QCD calculations on leadership class computers and on GPUaccelerated heterogeneous architectures. The participating team at multiple instritutions improved and extended software libraries (Chroma, CPS, MILC, QLUA, QPhiX, QDP++, QDP-jit) by providing interfaces for heterogeneous computing environments and through the optimization of gauge field evolution algorithms and sparse matrix inverters. The former includes the development of new multi-time scale integrators and the latter focused on the development of new multi-grid and domain decomposition inverters for several QCD fermion discretization schemes. The sub-project at the University of North Carolina worked towards the development a domain specific language for lattice QCD computations with the express purpose of generating code with uncompromised performance.

97 MATHEMATICS AND COMPUTING↗

Self-calibration of robot-sensor system

The process of finding the coordinate transformation between a robot and an external sensor system has been addressed. This calibration is equivalent to solving a nonlinear optimization problem for the parameters that characterize the transformation. A two-step procedure is herein proposed for solving the problem. The first step involves finding a nominal solution that is a good approximation of the final solution. A varational problem is then generated to replace the original problem in the next step. With the assumption that the variational parameters are small compared to unity, the problem that can be more readily solved with relatively small computation effort.

Yeh, Pen-Shu↗