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Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca 2 UO 2 (CO 3 ) 3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.
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S -Adenosyl-l-methionine (SAM) dependent xanthosine methyltransferase (XMT) is the key enzyme that catalyzes the first methyl transfer in the caffeine biosynthesis pathway to produce the intermediate 7-methylxanthosine (7mXR). Although XMT has been a subject of extensive discussions, the catalytic mechanism and nature of the substrate involved in the catalysis are still unclear. Here in this paper, quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy (potential of mean force or PMF) simulations are undertaken to determine the catalytic mechanism of the XMT-catalyzed reaction. Both xanthosine and its monoanionic form with N3 deprotonated are used as the substrates for the methylation. It is found that while the methyl group can be transferred to the monoanionic form of xanthosine with a reasonable free energy barrier (about 17 kcal/mol), that is not the case for the neutral xanthosine. The results suggest that the substrate for the first methylation step in the caffeine biosynthesis pathway is likely to be the monoanionic form of xanthosine rather than the neutral form as widely adopted. This conclusion is supported by the p K a value on N3 of xanthosine both measured in aqueous phase and calculated in the enzymatic environment. As a result, the structural and dynamics information from both the X-ray structure and MD simulations is also consistent with the monoanionic xanthosine scenario. Finally, we discuss the implications of this conclusion for caffeine biosynthesis.
This simulation study adapts and applies the general framework described in BESTEST-EX (Judkoff et al 2010) for self-testing residential building energy model calibration methods. BEopt/DOE-2.2 is used to evaluate four mathematical calibration methods in the context of monthly, daily, and hourly synthetic utility data for a 1960's-era existing home in a cooling-dominated climate. The home's model inputs are assigned probability distributions representing uncertainty ranges, random selections are made from the uncertainty ranges to define 'explicit' input values, and synthetic utility billing data are generated using the explicit input values. The four calibration methods evaluated in this study are: an ASHRAE 1051-RP-based approach (Reddy and Maor 2006), a simplified simulated annealing optimization approach, a regression metamodeling optimization approach, and a simple output ratio calibration approach. The calibration methods are evaluated for monthly, daily, and hourly cases; various retrofit measures are applied to the calibrated models and the methods are evaluated based on the accuracy of predicted savings, computational cost, repeatability, automation, and ease of implementation.
This simulation study adapts and applies the general framework described in BESTEST-EX (Judkoff et al 2010) for self-testing residential building energy model calibration methods. BEopt/DOE-2.2 is used to evaluate four mathematical calibration methods in the context of monthly, daily, and hourly synthetic utility data for a 1960's-era existing home in a cooling-dominated climate. The home's model inputs are assigned probability distributions representing uncertainty ranges, random selections are made from the uncertainty ranges to define "explicit" input values, and synthetic utility billing data are generated using the explicit input values. The four calibration methods evaluated in this study are: an ASHRAE 1051-RP-based approach (Reddy and Maor 2006), a simplified simulated annealing optimization approach, a regression metamodeling optimization approach, and a simple output ratio calibration approach. The calibration methods are evaluated for monthly, daily, and hourly cases; various retrofit measures are applied to the calibrated models and the methods are evaluated based on the accuracy of predicted savings, computational cost, repeatability, automation, and ease of implementation.
Due to the inherent complexity of multi-dimensional solutions for transient conduction in a multilayered building element, most heat balance-based algorithms assume that conduction occurs only in one dimension—through the building element between the inside and outside environments. Usually, since the length and width of the elements are much greater than the thickness of the element, this is a valid assumption. However, there are some cases such as hydronic radiant slabs where this assumption may not lead to an accurate estimate of the energy consumption of the system. In a hydronic radiant slab, water tubes are embedded in a slab, and hot or chilled water is circulated to meet any heating or cooling loads. The energy consumption of such a system will depend highly on the temperature of the water being sent to the slab (i.e., produced by the boiler or chiller). The temperature of the water that must be sent to the slab will depend on the spacing of the tubes, the multilayer construction of the building element, and the boundary conditions to which the construction is exposed. Thus, to accurately predict the energy consumption of such a system, a transient two-dimensional heat conduction model must be integrated with a heat balance-based simulation. This paper demonstrates the potential loss of accuracy associated with the one-dimensional radiant system models by providing a comparison of one- and two-dimensional solutions using EnergyPlus.
Vertical-axis wind turbines (VAWTs) have been the subject of research and development for nearly a century. However, this turbine architecture has fallen in and out of favor on multiple occasions. Beginning in the late 1970s, the U.S. Department of Energy sponsored an extensive experimental program through Sandia National Laboratories which produced a mass of experimental data from several highly instrumented turbines. Turbines designed, built, and tested include the 2 meter, 5 meter, 17 meter, and 34 meter and their respective configurations. This program kicked off a commercial collaboration and resulted in the FloWind turbines. The FloWind turbines had several notable design changes from the experimental turbines that, in conjunction with a general lack of understanding regarding predicting fatigue at the time, led to the majority of the turbines failing prematurely during the late 80s.
This presentation describes the ExaWind project and the team's progress in creating a suite of performance-portable codes designed for predictive simulations of wind farms on next-generation exascale-class supercomputers. Such simulations will require the resolution of scales spanning many orders of magnitude, from blade boundary layers to wind farm flow structures. In the U.S., the first exascale systems will be GPU accelerated, and different GPU manufacturers have been chosen for the different systems. At the heart of the ExaWind software is a hybrid-solver approach based on the codes Nalu-Wind and AMR-Wind, which are computational fluid dynamics solvers for the incompressible Navier-Stokes equations. Nalu-Wind is an unstructured-grid code used to resolve wind turbine geometry and blade boundary layers, whereas AMR-Wind is a structured-grid background solver for atmospheric turbulent flow and turbine wake propagation. The models are coupled with overset meshes and global linear systems are approximated through a loose-coupling algorithm. Results will include validation-quality high-fidelity simulations and strong/weak scaling results from the Summit supercomputer.
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Neutron multiplicity analysis is used for many applications, including nonproliferation and criticality safety. Multiplicity detectors have advantages over total neutron counting as they provide the ability to assess both multiplication and mass in fissionable material. In addition, multiplicity detectors can generate real-time information, e.g., dose estimation. The ability to evaluate the detector efficiency in each application is of primary importance in producing meaningful analyses. Multiplicity detectors usually house 3 He tubes within a polyethylene moderator. If the tubes are located behind different thickness of polyethylene, they will have different energy responses. This paper assesses 3 He tube efficiency as a function of neutron energy for a specific multiplicity detector.
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A radiation effects experimental program was performed, in which second surface mirror type thermal control coatings were exposed to ultraviolet radiation, electrons, and protons simultaneously. Stability was assessed by making periodic spectral reflectance measurements in situ (and in air after testing for comparison). Solar absorption coefficients were derived by computer. Many of the exposed materials showed large amounts of degradation in reflectance absorptance, principally due to the electron exposure. A series of tests was conducted, leading to the identification of a modified second surface mirror that shows considerable improvement and promise for stability during thermal control applications in a charged particle space radiation environment.
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