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At least 1,135 records · Page 63

Quantifying Energetic and Entropic Pathways in Molecular Systems

When examining dynamics occurring at nonzero temperatures, both energy and entropy must be taken into account to describe activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe different metastable states and the transition mechanisms between them. Here we use a physics-based machine learning method called state predictive information bottleneck (SPIB) to find nonlinear reaction coordinates for three systems of varying complexity. SPIB is able to correctly predict an entropic bottleneck for an analytical flat-energy double-well system and identify the entropy- and energy-dominated pathways for an analytical four-well system. Lastly, for a simulation of benzoic acid permeation through a lipid bilayer, SPIB is able to discover the entropic and energetic barriers to the permeation process. Given these results, we thus establish that SPIB is a reasonable and robust method for finding the important entropy, energy, and enthalpy barriers in physical systems, which can then be used to enhance the understanding and sampling of different activated mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Initial Land Use/Cover Distribution Substantially Affects Global Carbon and Local Temperature Projections in the Integrated Earth System Model

Initial land cover distribution varies among Earth system models, an uncertainty in initial conditions that can substantially affect carbon and climate projections. We use the integrated Earth System Model to show that a 3.9 M km2 difference in 2005 global forest area (9–14% of total forest area) generates uncertainties in initial atmospheric CO2 concentration, terrestrial carbon, and local temperature that propagate through a future simulation following the Representative Concentration Pathway 4.5. By 2095, the initial 6 ppmv uncertainty range increases to 9 ppmv and the initial 26 PgC uncertainty range in terrestrial carbon increases to 33 PgC. The initial uncertainty range in annual average local temperature of -0.74 to 0.96 °C persists throughout the future simulation, with a seasonal maximum in Dec-Jan-Feb. These results highlight the importance of accurately characterizing historical land use and land cover to reduce overall initial condition uncertainty.

Di Vittorio, Alan↗

Uncertainty Analysis in Multi‐Sector Systems: Considerations for Risk Analysis, Projection, and Planning for Complex Systems

Abstract Simulation models of multi‐sector systems are increasingly used to understand societal resilience to climate and economic shocks and change. However, multi‐sector systems are also subject to numerous uncertainties that prevent the direct application of simulation models for prediction and planning, particularly when extrapolating past behavior to a nonstationary future. Recent studies have developed a combination of methods to characterize, attribute, and quantify these uncertainties for both single‐ and multi‐sector systems. Here, we review challenges and complications to the idealized goal of fully quantifying all uncertainties in a multi‐sector model and their interactions with policy design as they emerge at different stages of analysis: (a) inference and model calibration; (b) projecting future outcomes; and (c) scenario discovery and identification of risk regimes. We also identify potential methods and research opportunities to help navigate the tradeoffs inherent in uncertainty analyses for complex systems. During this discussion, we provide a classification of uncertainty types and discuss model coupling frameworks to support interdisciplinary collaboration on multi‐sector dynamics (MSD) research. Finally, we conclude with recommendations for best practices to ensure that MSD research can be properly contextualized with respect to the underlying uncertainties.

54 ENVIRONMENTAL SCIENCES↗

Energy landscapes and functions of supramolecular systems

By means of two supramolecular systems—peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps—we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. Furthermore, these competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function.

36 MATERIALS SCIENCE↗

Cyber‐physical system testbed for power system monitoring and wide‐area control verification

The electric power system is intrinsically a cyber‐physical system (CPS) with power flowing inthe physical system and information flowing in the cyber‐network. Testbeds arecrucial for understanding the cyber‐physical interactions and provideenvironments for prototyping novel applications. This study proposes afour‐layer architecture for CPS testbeds with emphases on communication networkemulation and networked physical components. A configurable software‐definednetwork is employed to bridge physical components with wide‐area applicationsfor closed‐loop control. In order to distribute physically coupled devices intomultiple software simulations, this study proposes a data broker setup based ona distributed messaging environment to achieve low‐latency data streaming. Thedecoupled design with data streaming allows for building testbed components asmodules and running them in a distributed manner. Case studies verify the databroker setup for low‐latency sensing and actuation, as well as the communicationemulation setup for the desired network latency. Also illustrated is a replayattack scenario using synchrophasors in the Western Electricity CoordinatingCouncil (WECC) 181‐bus system for demonstrating the closed‐loop cyber‐physicalsimulation capability of the testbed.

Cui, Hantao↗

Evolution of the Data Quality Monitoring and Prompt Processing System in the proto DUNE-SP experiment

The DUNE Collaboration currently operates an experimental program based at CERN which includes a beam test and an extended cosmic ray run of two large-scale prototypes of the massive Liquid Argon Time Projection Chamber (LArTPC) for the DUNE Far Detector. The volume of data collected by the single-phase prototype (protoDUNE-SP) amounts to 3PB and the sustained rate of data sent to mass storage is O(100) MB/s. Data Quality Monitoring was implemented by directing a fraction of the data stream to the protoDUNE prompt processing system (p3s) which is optimized for continuous low-latency calculation of the vital detector metrics and various graphics including event displays. It served a crucial role throughout the life cycle of the experiment. We present our experience in leveraging the CERN computing environment and operating the system over an extended period of time, while adapting to evolving requirements and computing platform.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Classification of attractors for systems of identical coupled Kuramoto oscillators

We present a complete classification of attractors for networks of coupled identical Kuramoto oscillators. In such networks, each oscillator is driven by the same first-order trigonometric function, with coefficients given by symmetric functions of the entire oscillator ensemble. For N≠3 oscillators, there are four possible types of attractors: completely synchronized fixed points or limit cycles, and fixed points or limit cycles where all but one of the oscillators are synchronized. The case N = 3 is exceptional; systems of three identical Kuramoto oscillators can also posses attracting fixed points or limit cycles with all three oscillators out of sync, as well as chaotic attractors. Our results rely heavily on the invariance of the flow for such systems under the action of the three-dimensional group of Möbius transformations, which preserve the unit disc, and the analysis of the possible limiting configurations for this group action.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cryogenic System for the Cryomodule Test Facility at Fermilab

This paper provides an overview of the current progress and near-future plans for the cryogenic system at the new Cryomodule Test Facility (CMTF) at Fermilab, which includes the helium compressors, refrigerators, warm vacuum compressors, gas and liquid storage, and a distribution system. CMTF will house the Project X Injector Experiment (PXIE), which is the front end of the proposed Project X. PXIE includes one 162.5 MHz half wave resonator (HWR) cryomodule and one 325 MHz single spoke resonator (SSR) cryomodule. Both cryomodules contain superconducting radio-frequency (SRF) cavities and superconducting magnets operated at 2.0 K. CMTF will also support the Advanced Superconducting Test Accelerator (ASTA), which is located in the adjacent New Muon Lab (NML) building. A cryomodule test stand (CMTS1) located at CMTF will be used to test 1.3 GHz cryomodules before they are installed in the ASTA cryomodule string. A liquid helium pump and transfer line will be used to provide supplemental liquid helium to ASTA.

White, Michael↗

Linac cryogenic distribution system maintenance and upgrades at JLab

The Central Helium Liquefier (CHL) distribution system to the CEBAF and FEL linacs at Jefferson Lab (JLab) experienced a planned warm up during the late summer and fall of 2012 for the first time after its commissioning in 1991. Various maintenance and modifications were performed to support high beam availability to the experimental users, meet 10 CFR 851 requirements for pressure systems, address operational issues, and prepare the cryogenic interfaces for the high-gradient cryomodules needed for the 12 GeV upgrade. Cryogenic maintenance and installation work had to be coordinated with other activities in the linacs and compete for manpower from other department installation activities. With less than a quarter of the gas storage capacity available to handle the boil-off from the more than 40 cryomodules, 35,000 Nm{sup 3} of helium was re-liquefied and shipped to a vendor via a liquid tanker trailer. Nearly 200 u-tubes had to be removed and stored while seals were replaced on related equipment such as vacuum pump outs, bayonet isolation and process valves.

42 ENGINEERING↗

Chaotic vibrations of the duffing system with fractional damping

We examined the Duffing system with a fractional damping term. Calculating the basins of attraction, we demonstrate a broad spectrum of non-linear behaviour connected with sensitivity to the initial conditions and chaos. To quantify dynamical response of the system, we propose the statistical 0-1 test as well as the maximal Lyapunov exponent; the application of the latter encounter a few difficulties because of the memory effect due to the fractional derivative. The results are confirmed by bifurcation diagrams, phase portraits, and Poincaré sections.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

GL(3,C) invariance of type B 3-fold supersymmetric systems

Type B 3-fold supersymmetry is a necessary and sufficient condition for a quantum Hamiltonian to admit three linearly independent local solutions in closed form. We show that any such a system is invariant under GL(3,C) homogeneous linear transformations. In particular, we prove explicitly that the parameter space is transformed as an adjoint representation of it and that every coefficient of the characteristic polynomial appeared in 3-fold superalgebra is algebraic invariants. In the type A case, it includes as a subgroup the GL(2,C) projective transformation studied in the literature. We argue that any N-fold supersymmetric system has a GL(N,C) invariance for an arbitrary integral N.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Parameter estimation for chaotic systems using a hybrid adaptive cuckoo search with simulated annealing algorithm

This paper introduces a novel hybrid optimization algorithm to establish the parameters of chaotic systems. In order to deal with the weaknesses of the traditional cuckoo search algorithm, the proposed adaptive cuckoo search with simulated annealing algorithm is presented, which incorporates the adaptive parameters adjusting operation and the simulated annealing operation in the cuckoo search algorithm. Normally, the parameters of the cuckoo search algorithm are kept constant that may result in decreasing the efficiency of the algorithm. For the purpose of balancing and enhancing the accuracy and convergence rate of the cuckoo search algorithm, the adaptive operation is presented to tune the parameters properly. Besides, the local search capability of cuckoo search algorithm is relatively weak that may decrease the quality of optimization. So the simulated annealing operation is merged into the cuckoo search algorithm to enhance the local search ability and improve the accuracy and reliability of the results. The functionality of the proposed hybrid algorithm is investigated through the Lorenz chaotic system under the noiseless and noise condition, respectively. The numerical results demonstrate that the method can estimate parameters efficiently and accurately in the noiseless and noise condition. Finally, the results are compared with the traditional cuckoo search algorithm, genetic algorithm, and particle swarm optimization algorithm. Simulation results demonstrate the effectiveness and superior performance of the proposed algorithm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Integrable and superintegrable Hamiltonian systems with four dimensional real Lie algebras as symmetry of the systems

We construct integrable and superintegrable Hamiltonian systems using the realizations of four dimensional real Lie algebras as a symmetry of the system with the phase space R{sup 4} and R{sup 6}. Furthermore, we construct some integrable and superintegrable Hamiltonian systems for which the symmetry Lie group is also the phase space of the system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analyzing the errors of DFT approximations for compressed water systems

We report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchange-correlation functionals, and we characterize their errors before and after correction for 1- and 2-body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm{sup 3} where the experimental pressure is 15 kilobars; second, thermal samples of compressed water clusters from the trimer to the 27-mer. For the liquid, we report four first-principles molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1- and 2-body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutron-diffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2-body and beyond-2-body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond-2-body errors of DFT make a substantial contribution to the overall errors, so that correction for 1- and 2-body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3-body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput. 9, 1103 (2013)] gives a reasonably good way of correcting for beyond-2-body errors, after which the remaining errors are typically 0.5 mE{sub h} ≃ 15 meV/monomer for the liquid and the clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonlinear phase field model for electrodeposition in electrochemical systems

A nonlinear phase-field model has been developed for describing the electrodeposition process in electrochemical systems that are highly out of equilibrium. Main thermodynamic driving forces for the electrode-electrolyte interface (EEI) evolution are limited to local variations of overpotential and ion concentration. Application of the model to Li-ion batteries describes the electrode interface motion and morphology change caused by charge mass transfer in the electrolyte, an electrochemical reaction at the EEI and cation deposition on the electrode surface during the charging operation. The Li electrodeposition rate follows the classical Butler-Volmer kinetics with exponentially and linearly depending on local overpotential and cation concentration at the electrode surface, respectively. Simulation results show that the Li deposit forms a fiber-like shape and grows parallel to the electric field direction. The longer and thicker deposits are observed both for higher current density and larger rate constant where the surface reaction rate is expected to be high. The proposed diffuse interface model well captures the metal electrodeposition phenomena in plenty of non-equilibrium electrochemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultra-high vacuum compatible optical chopper system for synchrotron x-ray scanning tunneling microscopy

High-speed beam choppers are a crucial part of time-resolved x-ray studies as well as a necessary component to enable elemental contrast in synchrotron x-ray scanning tunneling microscopy (SX-STM). However, many chopper systems are not capable of operation in vacuum, which restricts their application to x-ray studies with high photon energies, where air absorption does not present a significant problem. To overcome this limitation, we present a fully ultra-high vacuum (UHV) compatible chopper system capable of operating at variable chopping frequencies up to 4 kHz. The lightweight aluminum chopper disk is coated with Ti and Au films to provide the required beam attenuation for soft and hard x-rays with photon energies up to about 12 keV. The chopper is used for lock-in detection of x-ray enhanced signals in SX-STM.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗