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At least 829 records · Page 46

DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design. However, few user-friendly tools leveraging the latest deep learning technology for inter-chain contact prediction and the distance-based modelling to predict protein quaternary structures are available. To address this gap, we develop DeepComplex, a web server for predicting structures of dimeric protein complexes. It uses deep learning to predict inter-chain contacts in a homodimer or heterodimer. The predicted contacts are then used to construct a quaternary structure of the dimer by the distance-based modelling, which can be interactively viewed and analysed. The web server is freely accessible and requires no registration. It can be easily used by providing a job name and an email address along with the tertiary structure for one chain of a homodimer or two chains of a heterodimer. The output webpage provides the multiple sequence alignment, predicted inter-chain residue-residue contact map, and predicted quaternary structure of the dimer.

59 BASIC BIOLOGICAL SCIENCES↗

Developing an Empirical Model for Jet-Surface Interaction Noise

The process of developing an empirical model for jet-surface interaction noise is described and the resulting model evaluated. Jet-surface interaction noise is generated when the high-speed engine exhaust from modern tightly integrated or conventional high-bypass ratio engine aircraft strikes or flows over the airframe surfaces. An empirical model based on an existing experimental database is developed for use in preliminary design system level studies where computation speed and range of configurations is valued over absolute accuracy to select the most promising (or eliminate the worst) possible designs. The model developed assumes that the jet-surface interaction noise spectra can be separated from the jet mixing noise and described as a parabolic function with three coefficients: peak amplitude, spectral width, and peak frequency. These coefficients are fit to functions of surface length and distance from the jet lipline to form a characteristic spectra which is then adjusted for changes in jet velocity and/or observer angle using scaling laws from published theoretical and experimental work. The resulting model is then evaluated for its ability to reproduce the characteristic spectra and then for reproducing spectra measured at other jet velocities and observer angles; successes and limitations are discussed considering the complexity of the jet-surface interaction noise versus the desire for a model that is simple to implement and quick to execute.

Brown, Clifford A.↗

Developing an Empirical Model for Jet-Surface Interaction Noise

The process of developing an empirical model for jet-surface interaction noise is described and the resulting model evaluated. Jet-surface interaction noise is generated when the high-speed engine exhaust from modern tightly integrated or conventional high-bypass ratio engine aircraft strikes or flows over the airframe surfaces. An empirical model based on an existing experimental database is developed for use in preliminary design system level studies where computation speed and range of configurations is valued over absolute accuracy to select the most promising (or eliminate the worst) possible designs. The model developed assumes that the jet-surface interaction noise spectra can be separated from the jet mixing noise and described as a parabolic function with three coefficients: peak amplitude, spectral width, and peak frequency. These coefficients are t to functions of surface length and distance from the jet lipline to form a characteristic spectra which is then adjusted for changes in jet velocity and/or observer angle using scaling laws from published theoretical and experimental work. The resulting model is then evaluated for its ability to reproduce the characteristic spectra and then for reproducing spectra measured at other jet velocities and observer angles; successes and limitations are discussed considering the complexity of the jet-surface interaction noise versus the desire for a model that is simple to implement and quick to execute.

Brown, Clif↗

Material Interactions in Severe Accidents – Benchmarking the MELCOR V2.2 Eutectics Model for a BWR-3 MARK-I Station Blackout: Part I – Single Case Analysis

Here in this analysis, the two material interaction models available in the MELCOR code are benchmarked for a severe accident at a BWR under representative Fukushima Daiichi boundary conditions. This part of the benchmark investigates the impact of each material interaction model on accident progression through a detailed single case analysis. It is found that the eutectics model simulation exhibits more rapid accident progression for the duration of the accident. The slower accident progression exhibited by the interactive materials model simulation, however, allows for a greater degree of core material oxidation and hydrogen generation to occur, as well as elevated core temperatures during the ex-vessel accident phase. The eutectics model simulation exhibits more significant degradation of core components during the late in-vessel accident phase – more debris forms and relocates to the lower plenum before lower head failure. The larger debris bed observed in the eutectics model simulation also reaches higher temperatures, presenting a more significant thermal challenge to the lower head until its failure. At the end of the simulated accident scenario, however, core damage is comparable between both simulations due to significant core degradation that occurs during the ex-vessel phase in the interactive materials model simulation. A key difference between the two models’ performance is the maximum temperatures that can be reached in the core and therefore the maximum ΔT between any two components. When implementing the interactive materials model, users have the option to modify the liquefaction temperature of the ZrO 2 -interactive and UO 2 -interactive materials as a way to mimic early fuel rod failure due to material interactions. Through modification of the liquefaction of high melting point materials with significant mass, users may inadvertently limit maximum core temperatures for fuel, cladding, and debris components.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

An SYK-inspired model with density–density interactions: Spectral & wave function statistics, Green’s function and phase diagram

The Sachdev–Ye–Kitaev (SYK) model is a rare example of a strongly-interacting system that is analytically tractable. Tractability arises because the model is largely structureless by design and therefore artificial: while the interaction is restricted to two-body terms, interaction matrix elements are “randomized” and therefore the corresponding interaction operator does not commute with the local density. Unlike conventional density–density-type interactions, the SYK-interaction is, in this sense, not integrable. We here investigate a variant of the (complex) SYK model, which restores this integrability. It features a randomized single-body term and a density–density-type interaction. We present numerical investigations suggesting that the model exhibits two integrable phases separated by several intermediate phases including a chaotic one. The chaotic phase carries several characteristic SYK-signatures including in the spectral statistics and the frequency scaling of the Green’s function and therefore should be adiabatically connected to the non-Fermi liquid phase of the original SYK model. Thus, our model Hamiltonian provides a bridge from the SYK-model towards microscopic realism.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Self-consistent solar wind-LISM interaction including neutrals: A 4-fluid model

We investigate the interaction between the heliosphere and local interstellar medium, including charge-exchange self-consistently between the neutral and ionized components. The system is modelled as consisting of neutral hydrogen, protons and electrons. The electrons are assumed to contribute to the dynamics via a pressure that is everywhere equal to the proton pressure. The fluid equations for the protons and hydrogen are solved self-consistently, assuming the two species interact only via charge exchange. The protons are treated as a single isotropic fluid. The hydrogen is decomposed into three isotropic fluids: hydrogen of interstellar origin with characteristic temperature of approximately 104 K, hydrogen produced via charge exchange in the post-shock solar wind, with characteristic temperature of approximately 105 K, and hydrogen produced via charge exchange in the supersonic solar wind, relatively cool but expanding radially outward with the solar wind speed. Two-Dimensional time-dependent numerical simulations of this system are performed to calculate the number density, temperature and bulk velocity of neutral hydrogen and plasma everywhere in the heliosphere. These quantities are compared to relevant solar wind observations. Implications for the pick-up process in the supersonic solar wind, as well as heating and deceleration of the wind, are addressed.

Williams, L. L.↗

A new predictive model for determining solar wind-terrestrial planet interactions

A computational model has been developed for the determination of the gasdynamic and magnetic field properties of the solar wind flow around a magnetic planet, such as the earth, or a nonmagnetic planet, such as Venus. The procedures are based on an established single-fluid, steady, dissipationless, magnetogasdynamic model and are appropriate for the calculation of axisymmetric, supersonic, super-Alfvenic solar wind flow past a planetary magneto/ionosphere. Sample results are reported for a variety of solar wind and planetary conditions. Some of these are new applications; others are included to show that the new procedures produce the same results as previous procedures when applied to the same conditions. The new methods are completely automated and much more efficient and versatile than those employed heretofore.

Spreiter, J. R.↗

Boundary layer effects on the flowfield about flow-through nacelles

A numerical study has been made of boundary layer effects on the flowfield about flow-through nacelles. A viscous-inviscid interacting computational model for investigating the problem was constructed by coupling a three-dimensional explicit Euler solution procedure with a compressible, 'lag-entrainment' integral boundary layer solution technique. Solutions obtained with the interacting model for long-duct turbofan engine nacelles at a free stream Mach number of 0.8 and an angle of attack of 0 deg are compared with experimental data. The numerical experiments have revealed insight into the boundary layer effects on the interactions between the internal and external flows.

Compton, W. B.↗

Interactive display of molecular models using a microcomputer system

A simple, microcomputer-based, interactive graphics display system has been developed for the presentation of perspective views of wire frame molecular models. The display system is based on a TERAK 8510a graphics computer system with a display unit consisting of microprocessor, television display and keyboard subsystems. The operating system includes a screen editor, file manager, PASCAL and BASIC compilers and command options for linking and executing programs. The graphics program, written in USCD PASCAL, involves the centering of the coordinate system, the transformation of centered model coordinates into homogeneous coordinates, the construction of a viewing transformation matrix to operate on the coordinates, clipping invisible points, perspective transformation and scaling to screen coordinates; commands available include ZOOM, ROTATE, RESET, and CHANGEVIEW. Data file structure was chosen to minimize the amount of disk storage space. Despite the inherent slowness of the system, its low cost and flexibility suggests general applicability.

Egan, J. T.↗

SASHIMI-SIDM: semi-analytical subhalo modelling for self-interacting dark matter at sub-galactic scales

We combine the semi-analytical structure formation model, SASHIMI, which predicts subhalo populations in collisionless, cold dark matter (CDM), with a parametric model that maps CDM halos to self-interacting dark matter (SIDM) halos. The resulting model, SASHIMI-SIDM, generates SIDM subhalo populations down to sub-galactic mass scales, for an arbitrary input cross section, in minutes. We show that SASHIMI-SIDM agrees with SIDM subhalo populations from high-resolution cosmological zoom-in simulations in resolved regimes. Crucially, we predict that the fraction of core-collapsed subhalos peaks at a mass scale determined by the input SIDM cross section and decreases toward higher halo masses, consistent with the predictions of gravothermal models and cosmological simulations. For the first time, we also show that the core-collapsed fraction decreases toward lower halo masses. While the dependence of the collapse time on mass and concentration implies such behaviour, our semi-analytical approach allows us to quantify and illustrate this trend clearly across the full mass spectrum of subhalos, including for subhalo masses below the resolution limit of any current cosmological SIDM simulation. As a proof of principle, we apply SASHIMI-SIDM to predict the boost to the local dark matter density and annihilation rate from core-collapsed SIDM subhalos, which can be enhanced relative to CDM by an order of magnitude for viable SIDM models. Thus, SASHIMI-SIDM provides an efficient and reliable tool for scanning SIDM parameter space and testing it with astrophysical observations. The code is publicly available at https://github.com/shinichiroando/sashimi-si.

cosmological simulations↗

Full-Potential Modeling of Blade-Vortex Interactions

A study of the full-potential modeling of a blade-vortex interaction was made. A primary goal of this study was to investigate the effectiveness of the various methods of modeling the vortex. The model problem restricts the interaction to that of an infinite wing with an infinite line vortex moving parallel to its leading edge. This problem provides a convenient testing ground for the various methods of modeling the vortex while retaining the essential physics of the full three-dimensional interaction. A full-potential algorithm specifically tailored to solve the blade-vortex interaction (BVI) was developed to solve this problem. The basic algorithm was modified to include the effect of a vortex passing near the airfoil. Four different methods of modeling the vortex were used: (1) the angle-of-attack method, (2) the lifting-surface method, (3) the branch-cut method, and (4) the split-potential method. A side-by-side comparison of the four models was conducted. These comparisons included comparing generated velocity fields, a subcritical interaction, and a critical interaction. The subcritical and critical interactions are compared with experimentally generated results. The split-potential model was used to make a survey of some of the more critical parameters which affect the BVI.

Jones, Henry E.↗

Data for Responsiveness of Miscanthus and Switchgrass Yields to Stand Age and Nitrogen Fertilization: A Meta-regression Analysis

The compiled datasets include plot level observations of energy crops (miscanthus and switchgrass) from recent experimental field trials in the US including dry biomass yield, location, state, region, harvest year, growing season degree days (GDD), winter season heating degree days (HDD), growing season cumulative precipitation, annual nitrogen application rate, age of the pant when harvested, National Commodity Crop Productivity Index (NCCPI) values, and cultivar type (switchgrass) from various published and unpublished sources. The stata codes include estimation procedures for four different specifications, i.e., Model A includes deterministic effect without interaction terms; Model B includes deterministic effect with interaction terms (N2, age2, N × age, GDD2, precip2, N × NCCPI); Model C includes deterministic effect with interaction terms, study, and location random effect; Model D includes deterministic effect with interaction terms, harvest year augmented study, and location random effect.

Age↗

A stand-alone interactive graphics finite element modeling system

The finite element modeling (FEM) system described here is an interactive graphics system designed for use with an intelligent terminal. It offers an economical alternative to the conventional methods (hand compilation and remote terminals) of 2 and 3-dimensional model generation. Using local computing and local storage, this FEM system allows the operator to create and display 3-dimensional models entirely off-line from the host computer. This eliminates costly on-line computer and host-processing time, and makes the user more effective by greatly reducing computer response time. The system allows model generation by down-loading node and element data from the host computer or by using the system's model generation operations for digitizing and automatic creation. The system then generates completed model information in the desired analysis package's bulk data format and transmits it to the host computer for finite element analysis.

Gingerich, J. Z.↗

Computer modeling of solar wind interaction with Venus and Mars

The fundamental ideas, successes, and shortcomings of fluid models based on MHD theory for the interaction of the solar wind and a planetary magnetic field and/or atmosphere are reviewed, with special attention to applications to Venus and Mars. An account, including new quantitative results, is given of a number of enhancements of a basic gasdynamic convected field approximation to the magnetohydrodynamic model that incorporate features of solar wind flow past a planet not treated previously. These permit solutions to be calculated for 3D, as opposed to axisymmetric, obstacle shapes, the effects of a magnetic barrier region just exterior to the ionopause, the complete MHD equations for the special case in which the interplanetary magnetic field is aligned with the flow, the effects of mass loading by pickup of ions newly created by photoionization of atmospheric neutrals, and for the unsteady effects associated with the passage of an interplanetary shock wave. Particular emphasis is placed on the information furnished by these models that can be compared with observations, and conversely on the observational data that provide critical tests of the models.

Spreiter, John R.↗

Influence of World and Gravity Model Selection on Surface Interacting Vehicle Simulations

A vehicle simulation is surface-interacting if the state of the vehicle (position, velocity, and acceleration) relative to the surface is important. Surface-interacting simulations perform ascent, entry, descent, landing, surface travel, or atmospheric flight. Modeling of gravity is an influential environmental factor for surface-interacting simulations. Gravity is the free-fall acceleration observed from a world-fixed frame that rotates with the world. Thus, gravity is the sum of gravitation and the centrifugal acceleration due to the world s rotation. In surface-interacting simulations, the fidelity of gravity at heights above the surface is more significant than gravity fidelity at locations in inertial space. A surface-interacting simulation cannot treat the gravity model separately from the world model, which simulates the motion and shape of the world. The world model's simulation of the world's rotation, or lack thereof, produces the centrifugal acceleration component of gravity. The world model s reproduction of the world's shape will produce different positions relative to the world center for a given height above the surface. These differences produce variations in the gravitation component of gravity. This paper examines the actual performance of world and gravity/gravitation pairs in a simulation using the Earth.

Madden, Michael M.↗