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At least 1,531 records · Page 85

Approximation of periodic Green's operator in real space using numerical integration and its use in fast Fourier transform-based micromechanical models

In this work, we propose an expression for the periodic first derivative of Green's function in real space. The proposed expression allows an alternative way of computing the periodic Green's operator based on periodically summing the free-space Green's operator in terms of an appropriate quadrature rule. We provide computational examples, which show the accuracy of the proposed approach, together with reduced spurious oscillations in the solution fields.

42 ENGINEERING↗

Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: Application to enzyme adenylate kinase

Biomolecular simulations at millisecond and longer time-scales can provide vital insights into functional mechanisms. Because post-simulation analyses of such large trajectory datasets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA) (Ramanathan et al., PLoS One 2011;6:e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub-states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth-order statistics for characterizing atomic fluctuations. In this article, we extend QAA for analyzing long time-scale simulations online. In particular, we present HOST4MD—a higher-order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub-states, and (3) identifies conformational transitions that enable the protein to access those sub-states. We demonstrate HOST4MD on microsecond timescale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three subdomains (LID, CORE, and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate that HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time-scale simulations.

Ramanathan, Arvind↗

Assessing the mechanisms governing the daytime evolution of marine stratocumulus using large‐eddy simulation

Large‐eddy simulation (LES) output for a case of thin stratocumulus off the coast of California is examined in a mixed‐layer analysis framework to identify the specific mechanisms responsible for governing the evolution of the cloud system. An equation for cloud‐base height tendency isolates the individual cloud‐modulating mechanisms that control the evolution of boundary‐layer liquid‐water static energy ( S l ) and total water mixing ratio ( q T ). With a suitable spin‐up procedure, the control simulation performs admirably compared with observed estimates of liquid water content, vertical velocity variance, and radiative fluxes sampled during an aircraft field campaign. Investigation of the cloud response to various environmental forcing scenarios was addressed through a suite of sensitivity simulations, including variations in subsidence velocity, surface fluxes, wind shear near the inversion, and radiative forcing. In the control simulation, rising cloud‐base tendencies are associated with entrainment warming/drying and short‐wave absorption, whereas lowering cloud‐base tendencies are driven by long‐wave cooling. Even in the presence of substantial afternoon solar heating, entrainment fluxes remained active. The thin cloud demonstrated unexpected resiliency, with mixed‐layer analysis indicating that, as the short‐wave flux decreases later in the afternoon, the relative contribution of long‐wave cooling often becomes large enough to offset entrainment warming/drying and result in a reversal of cloud‐base tendency. The evolution of cloud‐base tendency is found to be insensitive to the net radiative flux divergence for most of the simulations (liquid water path ranging from ~10–50 g/m 2 ). Error analysis in comparison with LES S l and q T budgets suggests that our method of entrainment flux calculation could be improved by a more complete understanding of entrainment‐layer physics.

McMichael, Lucas A.↗

Imaging the Thickness of Passivation Layers for Crystalline Silicon with Micron‐Scale Spatial Resolution Using Spectral Photoluminescence

Thin films deposited on crystalline silicon surfaces are critical components of many silicon‐based devices, including high‐efficiency photovoltaic cells. Knowledge of their optical and electronic properties is important in designing and fabricating efficient solar cells, especially as the device complexity increases and includes micron‐scale features. Here, a camera‐based photoluminescence (PL) technique is developed to image the thickness of specific passivating films on silicon wafers. The technique is entirely contactless and nondestructive, requires minimal sample preparation, and provides a large dynamic range in terms of field of view, with micron‐scale spatial resolution possible. It retains the advantages of PL imaging, a mainstream technique for photovoltaic material and device characterization, and it has some extra capabilities similar to those of ellipsometry. This newly developed technique is demonstrated on hydrogenated amorphous silicon and silicon nitride films, two important passivation technologies for high‐efficiency silicon solar cells.

Nguyen, Hieu T.↗

Analysis of axial‐induction‐based wind plant control using an engineering and a high‐order wind plant model

Abstract Wind turbines are typically operated to maximize their performance without considering the impact of wake effects on nearby turbines. Wind plant control concepts aim to increase overall wind plant performance by coordinating the operation of the turbines. This paper focuses on axial‐induction‐based wind plant control techniques, in which the generator torque or blade pitch degrees of freedom of the wind turbines are adjusted. The paper addresses discrepancies between a high‐order wind plant model and an engineering wind plant model. Changes in the engineering model are proposed to better capture the effects of axial‐induction‐based control shown in the high‐order model. Copyright © 2015 John Wiley & Sons, Ltd.

Annoni, Jennifer↗