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At least 1,783 records · Page 99

Molecular Simulations in Astrobiology

One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides exhibit orientational flexibility with changing conditions, which may have provided a mechanism of transmitting signals between the protocell and its environment. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations identify the mechanisms by which protons move through the gate.

Pohorille, Andrew↗

Plasticity of irradiated materials at the nano and micro-scales

Here, we review here our recent work on plastic deformation in irradiated materials at the nano- and micro-scales, as revealed by Discrete Dislocation Dynamics (DDD) simulations. Two methods of including irradiation effects in the DDD framework are presented. The first directly captures the atomistic interaction mechanisms, while the second can effectively study high-dose irradiation. Computer simulations lead to new understanding of the dynamics of collective dislocation-irradiation defect interactions, as well as the quantitative analysis of the temporal and spatial characteristics associated with plastic instabilities. Based on these insights, theoretical models are developed to predict the critical conditions for dislocation channel formation. A simple probability model is proposed and demonstrated to predict the width of dislocation channels in bulk irradiated materials with good agreement with experimental data. The fundamental understanding of the origins of plastic flow localization in irradiated materials sheds light on the design of future generations of radiation-resistant materials.

36 MATERIALS SCIENCE↗

Flight instrument and telemetry response and its inversion

Mathematical models of rate gyros, servo accelerometers, pressure transducers, and telemetry systems were derived and their parameters were obtained from laboratory tests. Analog computer simulations were used extensively for verification of the validity for fast and large input signals. An optimal inversion method was derived to reconstruct input signals from noisy output signals and a computer program was prepared.

Weinberger, M. R.↗

Improved Interactive Medical-Imaging System

An improved computational-simulation system for interactive medical imaging has been invented. The system displays high-resolution, three-dimensional-appearing images of anatomical objects based on data acquired by such techniques as computed tomography (CT) and magnetic-resonance imaging (MRI). The system enables users to manipulate the data to obtain a variety of views for example, to display cross sections in specified planes or to rotate images about specified axes. Relative to prior such systems, this system offers enhanced capabilities for synthesizing images of surgical cuts and for collaboration by users at multiple, remote computing sites.

Ross, Muriel D.↗

SEDS1 mission software verification using a signal simulator

The first flight of the Small Expendable Deployer System (SEDS1) is scheduled as the secondary payload of a Delta II in late 1992. The objective of the SEDS1 mission is to collect data to validate the concept of tethered satellite systems and to verify computer simulations used to predict their behavior. A series of tests will be performed to exercise the software modules which make up the Mission Software of the SEDS Data System. These tests will be performed by using a SEDS Signal Simulator to generate signals which will simulate the inputs normally produced by sensors and circuits in the SEDS system. The SEDS Signal Simulator will be used in the debugging and in the formal verification of the SEDS1 Mission Software. The Simulator will not only emulate normal flight conditions but also exercise all modules written to handle anticipated anomalous flight conditions, conditions that would be difficult to reproduce and control with actual SEDS hardware. The simulator will help to expedite software development and to increase the confidence of the users of the Mission Software. With little modification, the Simulator should be useful in the software development of future SEDS flights.

Pierson, William E.↗

Self-assembly in the systems of magnetic anisotropic nanoparticles

This paper presents the complex investigation of the system of magnetic anisotropic nanoparticles using computer simulations in a wide range of the system’s parameters. The cluster analysis was made, various average characteristics of the formed clusters were calculated and the initial magnetic susceptibility and the radial distribution function were computed. It was shown that via changing the nanoparticles characteristics (their shape and the values of the magnetic moments) it’s possible to change macroscopic response of the system, that implements the idea of tuning and design new materials with controllable properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Localized growth and remodelling drives spongy mesophyll morphogenesis

The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other biological tissues, which remain confluent throughout development, the spongy mesophyll must develop from an initially confluent tissue into a tortuous network of cells with a large proportion of intercellular airspace. How the airspace in the spongy mesophyll develops while the tissue remains mechanically stable is unknown. Here, we use computer simulations of deformable polygons to develop a purely mechanical model for the development of the spongy mesophyll tissue. By stipulating that cell wall growth and remodelling occurs only near void space, our computational model is able to recapitulate spongy mesophyll development observed in Arabidopsis thaliana leaves. We find that robust generation of pore space in the spongy mesophyll requires a balance of cell growth, adhesion, stiffness and tissue pressure to ensure cell networks become porous yet maintain mechanical stability. The success of this mechanical model of morphogenesis suggests that simple physical principles can coordinate and drive the development of complex plant tissues like the spongy mesophyll.

Science & Technology - Other Topics↗

Separability of Mesh Bias and Parametric Uncertainty for a Full System Thermal Analysis

When making computational simulation predictions of multi-physics engineering systems, sources of uncertainty in the prediction need to be acknowledged and included in the analysis within the current paradigm of striving for simulation credibility. A thermal analysis of an aerospace geometry was performed at Sandia National Laboratories. For this analysis a verification, validation and uncertainty quantification workflow provided structure for the analysis, resulting in the quantification of significant uncertainty sources including spatial numerical error and material property parametric uncertainty. It was hypothesized that the parametric uncertainty and numerical errors were independent and separable for this application. This hypothesis was supported by performing uncertainty quantification simulations at multiple mesh resolutions, while being limited by resources to minimize the number of medium and high resolution simulations. Based on this supported hypothesis, a prediction including parametric uncertainty and a systematic mesh bias are used to make a margin assessment that avoids unnecessary uncertainty obscuring the results and optimizes computing resources.

42 ENGINEERING↗

Frequency modulation television analysis: Distortion analysis

Computer simulation is used to calculate the time-domain waveform of standard T-pulse-and-bar test signal distorted in passing through an FM television system. The simulator includes flat or preemphasized systems and requires specification of the RF predetection filter characteristics. The predetection filters are modeled with frequency-symmetric Chebyshev (0.1-db ripple) and Butterworth filters. The computer was used to calculate distorted output signals for sixty-four different specified systems, and the output waveforms are plotted for all sixty-four. Comparison of the plotted graphs indicates that a Chebyshev predetection filter of four poles causes slightly more signal distortion than a corresponding Butterworth filter and the signal distortion increases as the number of poles increases. An increase in the peak deviation also increases signal distortion. Distortion also increases with the addition of preemphasis.

Hodge, W. H.↗

Energy consumption analysis of the Venus Deep Space Station (DSS-13)

This report continues the energy consumption analysis and verification study of the tracking stations of the Goldstone Deep Space Communications Complex, and presents an audit of the Venus Deep Space Station (DSS 13). Due to the non-continuous radioastronomy research and development operations at the station, estimations of energy usage were employed in the energy consumption simulation of both the 9-meter and 26-meter antenna buildings. A 17.9% decrease in station energy consumption was experienced over the 1979-1981 years under study. A comparison of the ECP computer simulations and the station's main watt-hour meter readings showed good agreement.

Hayes, N. V.↗

Constant reverse thrust activated reorientation of liquid hydrogen with Geyser initiation

A key objective of the cryogenic fluid management of the spacecraft propulsion system is to develop the technology necessary for acquisition or positioning of liquid outflow or vapor venting. Numerical simulation of positive liquid acquisition is attempted by introducing reverse gravity acceleration, resulting from the propulsive thrust of auxiliary engines, which exceeds critical value for the initiation of geyser. Based on the computer simulation of flowfields during the course of fluid reorientation, six dimensionless parameters resulted in this study. It shows that these parameters hold near-constant values through the entire ranges of liquid filled levels, from 30-80 percent, during the course of fluid reorientation.

Hung, R. J.↗

Desktop chaotic systems: Intuition and visualization

This paper presents a dynamic study of the Wildwood Pendulum, a commercially available desktop system which exhibits a strange attractor. The purpose of studying this chaotic pendulum is twofold: to gain insight in the paradigmatic approach of modeling, simulating, and determining chaos in nonlinear systems; and to provide a desktop model of chaos as a visual tool. For this study, the nonlinear behavior of this chaotic pendulum is modeled, a computer simulation is performed, and an experimental performance is measured. An assessment of the pendulum in the phase plane shows the strange attractor. Through the use of a box-assisted correlation dimension methodology, the attractor dimension is determined for both the model and the experimental pendulum systems. Correlation dimension results indicate that the pendulum and the model are chaotic and their fractal dimensions are similar.

Bright, Michelle M.↗

Real-Time Digital Simulation of Inertial Response with Hardware-in-the-Loop Implementation on the CART3 Wind Turbine at the National Wind Technology Center

With increasing penetrations of wind power on electric grids, the stability and reliability of interconnected power systems may be impacted. In some countries that have developed renewable energy sources and systems, grid codes have been revised to require wind power plants (WPPs) to provide ancillary services to support the power system frequency in case of severe grid events. To do this, wind turbine generators (WTGs) should be deloaded to reserve a certain amount of active power for primary frequency response; however, deloading curtails annual energy production, and the market for this type of service needs to be further developed. In this report, we focus on the temporary frequency support provided by WTGs through inertial response. WTGs have potential to provide inertial response, but appropriate control methods should be implemented. With the implemented inertial control methods, wind turbines are capable of increasing their active power output by releasing some of their stored kinetic energy when a frequency excursion occurs. Active power can be temporarily boosted above the maximum power points, after which the rotor speed decelerates, and subsequently an active power output reduction restores the kinetic energy. In this report, we develop two types of models for wind power systems: the first is common, based on the wind power aerodynamic equation, and the power coefficient can be regressed using nonlinear functions; the second is much more complicated, wherein the wind turbine system is modeled using the Fatigue, Aerodynamics, Structures, and Turbulence Modeling (FAST) tool with several degrees of freedoms. A nine-bus test power system is built in Simulink and the Real-Time Digital Simulator, respectively, which are used to evaluate the frequency support performance of the WPPs. We implement two distinct types of inertial control methods in the modeled wind turbines: frequency-based inertial control (FBIC) and stepwise inertial control (SIC). We compare the performances of the two methods in terms of their frequency nadirs, rates of change of frequency, and recovery times. We conclude the results under various wind speeds and penetration cases, which provide insight into designing the inertial response of WTGs. Further, we discuss the impact of the parameters on the performance of the inertial control methods. We evaluate both the scaling factors for the FBIC method and the slope values for the TLIC methods. The simulation work shows the characteristics of different inertial responses compared to conventional synchronous generators. Based on the simulation results, we modify, improve, and test the inertial control methods under a more realistic wind turbine model based on FAST. We then validate the inertial responses under highly turbulent wind conditions generated by TurbSim, and we examine their influences on the turbine mechanical components. The extensive simulation proves the effectiveness of the proposed inertial control methods as well as the nine-bus test power system. We then reconsider the parameters. We rebuild the same test power system using Real time Simulator Computer Aided Design (RSCAD), and we implement the inertial control methods in the real Controls Advanced Research Turbine (CART3), which is prepared for the hardware-in-the-loop field-test simulation. After the setups for the hardware and software hybrid simulation platform are complete, the inertial response is further tested on a real wind turbine for the first time, in which CART3 release the controlled inertial response against the emulated frequency excursion, provided by the real-time simulated power system test bed in RTDS.

17 WIND ENERGY↗

Design and Analysis of Multifidelity Finite Element Simulations

Abstract The numerical accuracy of finite element analysis (FEA) depends on the number of finite elements used in the discretization of the space, which can be varied using the mesh size. The larger the number of elements, the more accurate the results are. However, the computational cost increases with the number of elements. In current practice, the experimenter chooses a mesh size that is expected to produce a reasonably accurate result, and for which the computer simulation can be completed in a reasonable amount of time. Improvements to this approach have been proposed using multifidelity modeling by choosing two or three mesh sizes. However, mesh size is a continuous parameter, and therefore, multifidelity simulations can be performed easily by choosing a different value for the mesh size for each of the simulations. In this article, we develop a method to optimally find the mesh sizes for each simulation and satisfy the same time constraints as a single or a double mesh size experiment. A range of different mesh sizes used in the proposed method allows one to fit multifidelity models more reliably and predict the outcome when meshes approach infinitesimally small, which is impossible to achieve in actual simulations. We illustrate our approach using an analytical function and a cantilever beam finite element analysis experiment.

Engineering↗

Design of coupled mace filters for optical pattern recognition using practical spatial light modulators

Spatial light modulators (SLMs) are being used in correlation-based optical pattern recognition systems to implement the Fourier domain filters. Currently available SLMs have certain limitations with respect to the realizability of these filters. Therefore, it is necessary to incorporate the SLM constraints in the design of the filters. The design of a SLM-constrained minimum average correlation energy (SLM-MACE) filter using the simulated annealing-based optimization technique was investigated. The SLM-MACE filter was synthesized for three different types of constraints. The performance of the filter was evaluated in terms of its recognition (discrimination) capabilities using computer simulations. The correlation plane characteristics of the SLM-MACE filter were found to be reasonably good. The SLM-MACE filter yielded far better results than the analytical MACE filter implemented on practical SLMs using the constrained magnitude technique. Further, the filter performance was evaluated in the presence of noise in the input test images. This work demonstrated the need to include the SLM constraints in the filter design. Finally, a method is suggested to reduce the computation time required for the synthesis of the SLM-MACE filter.

Rajan, P. K.↗

Simulation of pseudo-CT images based on deformable image registration of ultrasound images: A proof of concept for transabdominal ultrasound imaging of the prostate during radiotherapy

Purpose: Imaging of patient anatomy during treatment is a necessity for position verification and for adaptive radiotherapy based on daily dose recalculation. Ultrasound (US) image guided radiotherapy systems are currently available to collect US images at the simulation stage (US{sub sim}), coregistered with the simulation computed tomography (CT), and during all treatment fractions. The authors hypothesize that a deformation field derived from US-based deformable image registration can be used to create a daily pseudo-CT (CT{sub ps}) image that is more representative of the patients’ geometry during treatment than the CT acquired at simulation stage (CT{sub sim}). Methods: The three prostate patients, considered to evaluate this hypothesis, had coregistered CT and US scans on various days. In particular, two patients had two US–CT datasets each and the third one had five US–CT datasets. Deformation fields were computed between pairs of US images of the same patient and then applied to the corresponding US{sub sim} scan to yield a new deformed CT{sub ps} scan. The original treatment plans were used to recalculate dose distributions in the simulation, deformed and ground truth CT (CT{sub gt}) images to compare dice similarity coefficients, maximum absolute distance, and mean absolute distance on CT delineations and gamma index (γ) evaluations on both the Hounsfield units (HUs) and the dose. Results: In the majority, deformation did improve the results for all three evaluation methods. The change in gamma failure for dose (γ{sub Dose}, 3%, 3 mm) ranged from an improvement of 11.2% in the prostate volume to a deterioration of 1.3% in the prostate and bladder. The change in gamma failure for the CT images (γ{sub CT}, 50 HU, 3 mm) ranged from an improvement of 20.5% in the anus and rectum to a deterioration of 3.2% in the prostate. Conclusions: This new technique may generate CT{sub ps} images that are more representative of the actual patient anatomy than the CT{sub sim} scan.

60 APPLIED LIFE SCIENCES↗

Simple Ion Channels: From Structure to Electrophysiology and Back

A reliable way to establish whether our understanding of a channel is satisfactory is to reproduce its measured ionic conductance over a broad range of applied voltages in computer simulations. In molecular dynamics (MD), this can be done by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive, we have developed a markedly more efficient alternative in which MD is combined with the electrodiffusion (ED) equation. In this approach, the assumptions of the ED equation can be rigorously tested, and the precision and consistency of the calculated conductance can be determined. We have demonstrated that the full current/voltage dependence and the underlying free energy profile for a simple channel can be reliably calculated from equilibrium or non-equilibrium MD simulations at a single voltage. To carry out MD simulations, a structural model of a channel has to be assumed, which is an important constraint, considering that high-resolution structures are available for only very few simple channels. If the comparison of calculated ionic conductance with electrophysiological data is satisfactory, it greatly increases our confidence that the structure and the function are described sufficiently accurately. We examined the validity of the ED for several channels embedded in phospholipid membranes - four naturally occurring channels: trichotoxin, alamethicin, p7 from hepatitis C virus (HCV) and Vpu from the HIV-1 virus, and a synthetic, hexameric channel, formed by a 21-residue peptide that contains only leucine and serine. All these channels mediate transport of potassium and chloride ions. It was found that the ED equation is satisfactory for these systems. In some of them experimental and calculated electrophysiological properties are in good agreement, whereas in others there are strong indications that the structural models are incorrect.

molecular dynamics (MD↗