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At least 973 records · Page 54

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Functional determinants of radial operators in AdS 2

We study the zeta-function regularization of functional determinants of Laplace and Dirac-type operators in two-dimensional Euclidean AdS 2 space. More specifically, we consider the ratio of determinants between an operator in the presence of background fields with circular symmetry and the free operator in which the background fields are absent. By Fourier-transforming the angular dependence, one obtains an infinite number of one-dimensional radial operators, the determinants of which are easy to compute. The summation over modes is then treated with care so as to guarantee that the result coincides with the two-dimensional zeta-function formalism. The method relies on some well-known techniques to compute functional determinants using contour integrals and the construction of the Jost function from scattering theory. Here, our work generalizes some known results in flat space. The extension to conformal AdS 2 geometries is also considered. We provide two examples, one bosonic and one fermionic, borrowed from the spectrum of fluctuations of the holographic 1/4-BPS latitude Wilson loop.

Wilson↗

Extending Rucio with modern cloud storage support

Rucio is a software framework designed to facilitate scientific collaborations in efficiently organising, managing, and accessing extensive volumes of data through customizable policies. The framework enables data distribution across globally distributed locations and heterogeneous data centres, integrating various storage and network technologies into a unified federated entity. Rucio offers advanced features like distributed data recovery and adaptive replication, and it exhibits high scalability, modularity, and extensibility. Originally developed to meet the requirements of the high-energy physics experiment ATLAS, Rucio has been continuously expanded to support LHC experiments and diverse scientific communities. Recent R&D projects within these communities have evaluated the integration of both private and commercially-provided cloud storage systems, leading to the development of additional functionalities for seamless integration within Rucio. Furthermore, the underlying systems, FTS and GFAL/Davix, have been extended to cater to specific use cases. This contribution focuses on the technical aspects of this work, particularly the challenges encountered in building a generic interface for self-hosted cloud storage, such as MinIO or CEPH S3 Gateway, and established providers like Google Cloud Storage and Amazon Simple Storage Service. Additionally, the integration of decentralised clouds like SEAL is explored. Key aspects, including authentication and authorisation, direct and remote access, throughput and cost estimation, are highlighted, along with shared experiences in daily operations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Cumulants and correlation functions versus the QCD phase diagram

Here, we discuss the relation of particle number cumulants and correlation functions. It is argued that measuring couplings of the genuine multiparticle correlation functions could provide cleaner information on possible nontrivial dynamics in heavy-ion collisions. We also extract integrated multiproton correlation functions from the presently available experimental data on proton cumulants. We find that the STAR data contain significant four-proton correlations, at least at the lower energies, with indication of changing dynamics in central collisions. We also find that these correlations are rather long ranged in rapidity. Finally, using the Ising model, we demonstrate how the signs of the multiproton correlation functions may be used to exclude certain regions of the phase diagram close to the critical point.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Adaptive control system for line-commutated inverters

A control system for a permanent magnet motor driven by a multiphase line commutated inverter is provided with integration for integrating the back EMF of each phase of the motor. This is used in generating system control signals for an inverter gate logic using a sync and firing angle (alpha) control generator connected to the outputs of the integrators. A precision full wave rectifier provides a speed control feedback signal to a phase delay rectifier via a gain and loop compensation circuit and to the integrators for adaptive control of the attenuation of low frequencies by the integrators as a function of motor speed. As the motor speed increases, the attenuation of low frequency components by the integrators is increased to offset the gain of the integrators to spurious low frequencies.

Dolland, C. R.↗

Semiclassical Green’s functions and an instanton formulation of electron-transfer rates in the nonadiabatic limit

We present semiclassical approximations to Green’s functions of multidimensional systems, extending Gutzwiller’s work to the classically forbidden region. Based on steepest-descent integrals over these functions, we derive an instanton method for computing the rate of nonadiabatic reactions, such as electron transfer, in the weak-coupling limit, where Fermi’s golden-rule can be employed. This generalizes Marcus theory to systems for which the environment free-energy curves are not harmonic and where nuclear tunnelling plays a role. The derivation avoids using the Im F method or short-time approximations to real-time correlation functions. A clear physical interpretation of the nuclear tunnelling processes involved in an electron-transfer reaction is thus provided. In Paper II [J. O. Richardson, J. Chem. Phys. 143, 134116 (2015)], we discuss numerical evaluation of the formulae.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NREL/SCE High-Penetration PV Integration Project: Report on Field Demonstration of Advanced Inverter Functionality in Fontana, CA

The National Renewable Energy Laboratory/Southern California Edison High-Penetration PV Integration Project is (1) researching the distribution system level impacts of high-penetration photovoltaic (PV) integration, (2) determining mitigation methods to reduce or eliminate those impacts, and (3) seeking to demonstrate these mitigation methods on actual high-penetration PV distribution circuits. This report describes a field demonstration completed during the fall of 2013 on the Fontana, California, study circuit, which includes a total of 4.5 MW of interconnected utility-scale rooftop PV systems. The demonstration included operating a 2-MW PV system at an off-unity power factor that had been determined during previously completed distribution system modeling and PV impact assessment analyses. Data on the distribution circuit and PV system operations were collected during the 2-week demonstration period. This demonstration reinforces the findings of previous laboratory testing that showed that utility-scale PV inverters are capable of operating at off-unity power factor to mitigate PV impacts; however, because of difficulties setting and retaining PV inverter power factor set points during the field demonstration, it was not possible to demonstrate the effectiveness of off-unity power factor operation to mitigate the voltage impacts of high-penetration PV integration. Lessons learned from this field demonstration are presented to inform future field demonstration efforts.

14 SOLAR ENERGY↗

Effects of gravity-gradient torque on the rotational motion of a triaxial satellite in a precessing elliptic orbit.

A method of general perturbations, based on the use of Lie series to generate approximate canonical transformations, is applied to study the effects of gravity-gradient torque on the rotational motion of a triaxial, rigid satellite. The center of mass of the satellite is constrained to move in an elliptic orbit about an attracting point mass. The orbit, which has a constant inclination, is free to precess and spin. The method of general perturbations is used to obtain the Hamiltonian for the nonresonant secular and long-period rotational motion of the satellite. The differential equations derivable from the transformed Hamiltonian are integrable, and the solution for the long-term motion may be expressed in terms of Jacobian elliptic functions and elliptic integrals. Geometrical aspects of the long-term rotational motion are discussed, and a comparison of theoretical results with observations is made.

Cochran, J. E.↗

Long-term motion in a restricted problem of rotational motion

A method of general perturbations, based on the use of Lie series to generate approximate canonical transformations, is applied to study the long-term effects of gravity-gradient torque and orbital evolution on the rotational motion of a triaxial, rigid satellite. The center of mass of the satellite is constrained to move in an elliptic orbit about an attracting point mass. The orbit, which has a constant inclination, is constrained to precess and spin with constant rates. The method of general perturbations is used to obtain the Hamiltonian for the nonresonant secular and long-period rotational motion of the satellite to second order in n/omega sub 0, where n is the orbital mean motion of the center of mass and omega sub 0 is a reference value of the magnitude of the satellite's rotational angular velocity. The differential equations derivable from the transformed Hamiltonian are integrable, and the solution for the long-term motion may be expressed in terms of Jacobian elliptic functions and elliptic integrals. Geometrical aspects of the long-term rotational motion are discussed, and a comparison of theoretical results with observations is made.

Cochran, J. E.↗

Wall boundary equations with slip and catalysis for multicomponent, nonequilibrium gas flows

Boundary equations obtained for a low Reynolds number, high enthalpy gas flow in regions of velocity slip and temperature jump are presented. The formulation treats, through a first-order distribution function used to include multicomponent diffusion, a multicomponent gas mixture that may be in nonequilibrium with finite-rate catalytic recombination occurring on the wall. In the boundary equations, which are obtained for use in flow-field calculations applicable to low-density flow regimes, a simplified gas/wall interaction is assumed wherein individual atoms or molecules either reflect specularly off the wall or stick and are fully accommodated. Fluxes in terms of evaluated integrals over the distribution function and integrals necessary for determining fluxes are given.

Scott, C. D.↗

Boolean differentiation and integration using Karnaugh maps

Algorithms are presented for differentiation and integration of Boolean functions by means of Karnaugh maps. The algorithms are considered simple when the number of variables is six or less; in this case Boolean differentiation and integration is said to be as easy as the Karnaugh map method of simplifying switching functions. It is suggested that the algorithms would be useful in the analysis of faults in combinational systems and in the synthesis of asynchronous sequential systems which utilize edge-sensitive flip-flops.

Tucker, J. H.↗

Shadow energy functionals and potentials in Born–Oppenheimer molecular dynamics

In Born–Oppenheimer molecular dynamics (BOMD) simulations based on the density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which, in practice, never is fully converged. The calculated energies and forces are, therefore, only approximate, which may lead to an unphysical energy drift and instabilities. Here, we discuss an alternative shadow BOMD approach that is based on backward error analysis. Instead of calculating approximate solutions for an underlying exact regular Born–Oppenheimer potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow Born–Oppenheimer potential energy surface. In this way, the calculated forces are conservative with respect to the approximate shadow potential and generate accurate molecular trajectories with long-term energy stabilities. We show how such shadow Born–Oppenheimer potentials can be constructed at different levels of accuracy as a function of the integration time step, δt, from the constrained minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each energy functional, there is a corresponding ground state Born–Oppenheimer potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original “zeroth-level” shadow energy functionals and potentials used in extended Lagrangian BOMD. The proposed shadow energy functionals and potentials are useful only within this extended dynamical framework, where also the electronic degrees of freedom are propagated as dynamical field variables together with the atomic positions and velocities. The theory is quite general and can be applied to MD simulations using approximate DFT, Hartree–Fock, or semi-empirical methods, as well as to coarse-grained flexible charge models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Active control of the forced and transient response of a finite beam

Structural vibrations from a point force are modelled on a finite beam. This research explores the theoretical limit on controlling beam vibrations utilizing another point source as an active controller. Three different types of excitation are considered, harmonic, random, and transient. For harmonic excitation, control over the entire beam length is possible only when the excitation frequency is near a resonant frequency of the beam. Control over a subregion may be obtained even between resonant frequencies at the cost of increasing the vibration outside of the control region. For random excitation, integrating the expected value of the displacement squared over the required interval, is shown to yield the identical cost function as obtained by integrating the cost function for harmonic excitation over all excitation frequencies. As a result, it is always possible to reduce the cost function for random excitation whether controlling the entire beam or just a subregion, without ever increasing the vibration outside the region in which control is desired. The last type of excitation considered is a single, transient pulse. The form of the controller is specified as either one or two delayed pulses, thus constraining the controller to be casual. The best possible control is examined while varying the region of control and the controller location. It is found that control is always possible using either one or two control pulses.

Post, John T.↗

Multi-technology Investigation of the Atomic Structure of Calcium Silicate Hydrates

In this study, synthetic C-S-H samples were investigated to reveal the feature at atomic scale. Rietveld refinement was applied to high resolution X-ray scattering data, yielding the lattice constants of the pseudocrystal structure, as well as the crystallinity along three axes. Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra was collected at calcium L3,2-edge. Evolution of calcium coordination symmetry were studied by investigating spectra characteristics. Pair Distribution Function (PDF) study yields the statistics of atom pair distribution. Coordination number of Ca and Si were obtained by integrating Radial distribution function. Atomic model based on dimeric structure were discussed and compared with experimental data. Synthetic C-S-H samples with increasing Ca/Si ratio exhibit pseudo-crystal structure, resembling Dreierketten configuration similar to natural tobermorite structure. Along c-axis, the repeated structure could not survives two layers in case of low Ca/Si ratio (0.70, 1.05). But in high Ca/Si ratio (1.42) case, the crystallinity along c-axis is much bigger. The coordination number of Ca decreases with increasing Ca/Si ratio. Octahedrally coordinated Ca are observed in sample with Ca/Si ratio of 1.42. Various dimeric models are compared with experimental data. In case of Ca/Si ratio of 1.42, SiO4 tetrahedron chain needs to be shortened in linkage, most probably by substituting bridging SiO4 tetrahedron with CaO6 octahedron. These octahedrons in interlayer space act like pins to join two adjacent layer structures together. The crystallinity is thus increased along c-axis, and average coordination number is therefore reduced. In case of Ca/Si 1.05, crystallinity is low along c-axis since, indicating that not too many Ca ions exist in interlayer space to hold two layers together. Instead, negative charge of end oxygen could be balanced by proton. Ca/Si 0.70 has long tetrahedron chain linkage within layer while the linkage between adjacent layers are not strong, resulting in low crystallinity along c-axis. Neither Ca/Si ratio 0.70 nor 1.42 sample contains any Ca in octahedral symmetry, as indicated by the weak crystal field splitting of NEXAFS spectra.

Atomic Configuration↗

Structural optimization of rotor blades with integrated dynamics and aerodynamics

The problem of structural optimization of helicopter rotor blades with integrated dynamic and aerodynamic design considerations is addressed. Results of recent optimization work on rotor blades for minimum weight with constraints on multiple coupled natural flap-lag frequencies, blade autorotational inertia and centrifugal stress has been reviewed. A strategy has been defined for the ongoing activities in the integrated dynamic/aerodynamic optimization of rotor blades. As a first step, the integrated dynamic/airload optimization problem has been formulated. To calculate system sensitivity derivatives necessary for the optimization recently developed, Global Sensitivity Equations (GSE) are being investigated. A need for multiple objective functions for the integrated optimization problem has been demonstrated and various techniques for solving the multiple objective function optimization are being investigated. The method called the Global Criteria Approach has been applied to a test problem with the blade in vacuum and the blade weight and the centrifugal stress as the multiple objectives. The results indicate that the method is quite effective in solving optimization problems with conflicting objective functions.

Chattopadhyay, Aditi↗