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At least 109 records · Page 6

Case Study: Can you find Delftia?

Delftia is a genus of bacteria with a bunch of cool features! The best studied species, Delftia acidovorans can produce gold nanoparticles from gold ions in solution. This bacteria has been found living in biofolms with Cupriavidis metallidurans on gold nuggets. It is also found in soil, in sinks and in rhizospheres of different plants where it promotes their growth. Delftia acidovorans forms gold nuggets by producing a short nonribosomal peptide called delftibactin. The 16 genes responsible for the production of delftibactin are called the del cluster (delA-delP). These genes were originally discovered in Delftia acidovorans SPH-1, but our research shows that the del cluster appears to be present across the genus. We'll start with a number of raw reads, clean them up and do a little taxonomy to figure out what we might be able to assemble. Next, we'll assemble the reads using 4 different methods and pick out the best assembly. Then we'll take those reads and sort them by genome and assess the quality of those genomes. We'll select the high quality genomes to annotate and insert into phylogenetic trees to find relatives.

59 BASIC BIOLOGICAL SCIENCES↗

HydroChrono: An Open-Source Hydrodynamics Package for Project Chrono

In this paper we present the development and verification of HydroChrono, a hydrodynamics package for the Project Chrono physics engine. This package includes the implementation of hydrodynamics equations, the added mass for multibody systems, the development of I/O functions as well as a Python API, and comparison against standard reference cases and other existing tools. HydroChrono provides a flexible, fully open-source solution for simulating wave energy converters (WECs), floating offshore wind turbines (FOWTs) platforms, and other hydrodynamic systems. Here we show, via comparisons with existing tools for benchmark verification cases, that HydroChrono accurately models hydrodynamic forces - making it a useful tool for the design and optimization of these systems. Additionally, the integration of HydroChrono with Project Chrono offers access to finite element modeling capabilities and high-fidelity modelling - with Chrono's existing coupling to CFD and SPH codes. This provides numerical modelers with a multifidelity simulation framework for designing and validating these systems. The development of HydroChrono provides a new, open-source solution for simulating hydrodynamic systems. Its compatibility with other simulation tools enables a more streamlined and efficient design process, advancing the field and providing new opportunities for innovation in this area.

BEM↗

New pre-Paleozoic nannofossils from the Stoer Formation /Torridonian/, northwest Scotland.

The nature of the sph eroidal unicellular fossils 10 to 62 micrometers in diameter that are abundant in black shales referred to the Stoer Formation of lower Torridonian age at Stoer Bay, in northwest Scotland, is examined. It is shown that their biological affinities are obscure; it is, however, not unlikely that many or most of them are independent unicellular members of the marine phytoplankton.

Cloud, P.↗

Modular liquid-cooled helmet liner for thermal comfort

A modular liquid-cooled helmet liner made of eight form-fitting neoprene patches was constructed. The liner was integrated into the sweatband of an Army SPH-4 helicopter aircrew helmet. This assembly was tested on four subjects seated in a hot (47 C), humid (40%) environment. Results indicate a marked reduction in the rate of increase of physiological body functions. Rectal temperature, weight loss, heart rate, and strain indices are all reduced to approximately 50% of uncooled levels. The cooling liner removed from 10% to 30% of total metabolic heat produced. This study also demonstrated the technical feasilibity of using a cooling liner in conjunction with a standard hard helmet. Potential applications of the cooling liner in thermally stressful environments are numerous, notably for helicopter and other aircrews.

Williams, B. A.↗

Interior noise and vibration measurements on operational military helicopters and comparisons with various ride quality criteria

The results of physical measurements of the interior noise and vibration obtained within eight operational military helicopters are presented. The data were extensively analyzed and are presented in the following forms: noise and vibration spectra, overall root-mean-square acceleration levels in three linear axes, peak accelerations at dominant blade passage frequencies, acceleration exceedance data, and overall and ""A'' weighted sound pressure levels. Peak acceleration levels were compared to the ISO 1-hr reduced comfort and fatigue decreased proficiency boundaries and the NASA discomfort criteria. The ""A'' weighted noise levels were compared to the NASA annoyance criteria, and the overall noise spectra were compared to MIL-STD-1294 (""Acoustical Noise Limits in Helicopters''). Specific vibration components at blade passage frequencies for several aircraft exceeded both the ISO reduced comfort boundary and the NASA passenger discomfort criteria. The ""A'' weighted noise levels, corrected for SPH-4 helmet attenuation characteristics, exceeded the NASA annoyance threshold for several aircraft.

Clevenson, S. A.↗

Effects of a giant impact on Uranus

The effects of a giant impact on Uranus with respect to the axis tilt of Uranus and its satellites are discussed. The simulations of possible giant impacts were carried out using Cray supercomputers. The technique used is called smooth particle hydrodynamics (SPH). In this technique, the material in the proto-Uranus planet and in the impactor is divided into a large number of particles which can overlap one another so that local averages over these particles determine density and pressure in the problem, and the particles themselves have their own temperatures and internal energies. During the course of the simulation, these particles move around under the influence of the forces acting on them: gravity and pressure gradients. The results of model simulations are presented.

Slattery, W. L.↗

Tidal disruption of inviscid protoplanets

Roche showed that equilibrium is impossible for a small fluid body synchronously orbiting a primary within a critical radius now termed the Roche limit. Tidal disruption of orbitally unbound bodies is a potentially important process for planetary formation through collisional accumulation, because the area of the Roche limit is considerably larger then the physical cross section of a protoplanet. Several previous studies were made of dynamical tidal disruption and different models of disruption were proposed. Because of the limitation of these analytical models, we have used a smoothed particle hydrodynamics (SPH) code to model the tidal disruption process. The code is basically the same as the one used to model giant impacts; we simply choose impact parameters large enough to avoid collisions. The primary and secondary both have iron cores and silicate mantles, and are initially isothermal at a molten temperature. The conclusions based on the analytical and numerical models are summarized.

Boss, Alan P.↗

Models of the Cartwheel ring galaxy: Spokes and starbursts

Recent observations of this famous ring galaxy, including optical and near-infrared CCD surface photometry, and VLA radio continuum and 21 cm line mapping (Higdon 1992b, in prep.), have inspired a renewed modeling effort. Toomre's (1978, in The Large-scale Structure of the Universe, eds. Longair and Einasto) series of restricted three-body simulations demonstrated how the multiple rings could be produced in a nearly head-on galaxy collision. New models with a halo-dominated potential based on the 21 cm rotation curve are able to reproduce such details as the spacing between rings, ring widths, offset of the nucleus, and several kinematical features, thus providing strong support for the collisional theory. The new observations have shown there are little or no old stars in Cartwheel; it may consist almost entirely of gas and stars produced as a result of compression in the ring wave. To model this process Smooth Particle Hydrodynamics (SPH) simulations of the Cartwheel disk have been performed. Fixed gravitational potentials were used to represent the Cartwheel and a roughly 30 percent mass collision partner. The interaction dynamics was treated as in the usual restricted three-body approximation, and the effects of local self-gravity between disk particles were calculated. We are particularly interested in testing the theory that enhanced star formation in waves is the result of gravitational instability in the compressed region (see e.g. Kennicutt 1989, ApJ 344, 685). The gas surface density in a number of simulations was initialized to a value slightly below the threshold for local gravitational instability throughout most of the disk. The first ring wave produces relatively modest compressions (a factor of order a few), triggering instability in a narrow range of wavelengths. Self-gravity in the disk is calculated over a comparable range of scales. Simulations were run with isothermal, adiabatic, and adiabatic with radiative cooling characterized by a relatively short timescale. The isothermal approximation is good except in the vicinity of the strong second (inner) ring, and several snapshots from one case are shown in the figure below. Flocculent spiral segments are present before the collision, and these are compressed into dense knots in the ring wave. These knots are likely to be sites of vigorous star formation. In the strong rarefaction behind the outer ring most of the knots are radially stretched and sheared, giving rise to spoke-like features. A few dense knots are evidently very tightly bound, because they retain their coherence and are stretched relatively little through the rarefaction. This is in accord with evidence for continuing star formation in some spokes (Marcum, Appleton and Higdon 1992). The number and spacing of spokes is a direct function of the scale of the gravitational instability in the disk. Thus, the gravitational instability theory, together with the hypothesis that massive stars are only formed in dense knots of gas, can account for most of the distinct morphology of the Cartwheel.

Struck-Marcell, Curtis↗

Dissipative merging of galaxies

The galaxy merging is investigated with hydrodynamical processes taken into account. For this purpose, the 3D calculations are performed by the use of a smoothed particle hydrodynamics (SPH) scheme combined with an N-body scheme. In these calculations, we find a new merging criterion and the dependence of the central phase space density of merger remnants upon the gas fraction in progenitors. It is concluded that ellipticals can be formed just by merging of fairly gas-rich primordial galaxies, not ordinary spiral galaxies.

Umemura, M.↗

Some cautionary remarks about smoothed particle hydrodynamics

Potential difficulties with smoothed particle hydrodynamics are discussed. In particular, empirical tests are used to demonstrate that the errors resulting from the use of variable smoothing can be much larger than commonly believed. Fortunately, however, these errors, which are normally small, do not appear to promote instability on small scales, such as fragmentation in self-gravitating fluids. Still, while SPH remains a useful tool for many problems of astrophysical interest, a rigorous formulation of it, which is adaptive but still satisfies conservation properties, is clearly wanting.

Hernquist, Lars↗

Gas dynamics for accretion disk simulations

The behavior of accretion disks can largely be understood in terms of the basic physical processes of mass, energy, and momentum conservation. Despite this, detailed modeling of these systems using modern computational techniques is challenging and controversial. Disturbing differences exist between methods used widely in astrophysics, namely Eulerian finite-difference techniques and particle codes such as SPH. Therefore neither technique is fully satisfactory for accretion disk simulations. This paper describes a new fully Lagrangian method designed to resolve these difficulties.

Whitehurst, R.↗

Shoemaker-Levy 9 and the tidal disruption of comets

The break-up of Periodic Comet Shoemaker-Levy 9 into multiple pieces following its grazing encounter with Jupiter in July 1992 can be used to study tidally-induced fracture in comets. This spectacular event allows us not only to set limits on the size, strength and density of Shoemaker-Levy 9 itself, but provides invaluable guidance to numerical modeling of such encounters. In an extensive treatment of tidal breakup which assumed self-gravitating, homogeneous, perfectly elastic bodies, Dobrovolskis derived simple analytical expressions for the tidally-induced surface and central stresses. Both can be cast in such a way that Poisson's ratio is the only material dependent constant entering these expressions. Whether both surface and central failure must be initiated as a criterion for breakup, or either one of them is sufficient, remains a subject of disagreement. To resolve this debate, we model the details of cometary breakup using a three-dimensional Smooth Particle Hydrodynamics (SPH) code modified to simulate fracture in small solid objects. At lower stresses associated with brittle failure, we use a rate-dependent strength based on the nucleation of incipient flaws whose number density is given by a Weibull distribution.

Benz, W.↗

Merging neutron stars. 1. Initial results for coalescence of noncorotating systems

We present three-dimensional Newtonian simulations of the coalescence of two neutron stars, using a smoothed particle hydrodynamics (SPH) code. We begin the simulations with the two stars in a hard, circular binary, and have them spiral together as angular momentum is lost through gravitational radiation at the rate predicted by modeling the system as two point masses. We model the neutron stars as hard polytropes (gamma = 2.4) of equal mass, and investigate the effect of the initial spin of the two stars on the coalescence. The process of coalescence, from initial contact to the formation of an axially symmetric object, takes only a few orbital periods. Some of the material from the two neutron stars is shed, forming a thick disk around the central, coalesced object. The mass of this disk is dependent on the initial neutron star spins; higher spin rates result in greater mass loss and thus more massive disks. For spin rates that are most likely to be applicable to real systems, the central coalesced object has a mass of 2.4 solar mass, which is tantalizingly close to the maximum mass allowed by any neutron star equation of state for an object that is supported in part by rotation. Using a realistic nuclear equation of state, we estimate the temperature of the material after the coalescence. We find that the central object is at a temperature of approximately 10 MeV, while the disk is heated by shocks to a temperature of 2 to 4 MeV.

Davies, M. B.↗

Galactic scale gas flows in colliding galaxies: 3-dimensional, N-body/hydrodynamics experiments

We present some results from three dimensional computer simulations of collisions between models of equal mass galaxies, one of which is a rotating, disk galaxy containing both gas and stars and the other is an elliptical containing stars only. We use fully self consistent models in which the halo mass is 2.5 times that of the disk. In the experiments we have varied the impact parameter between zero (head on) and 0.9R (where R is the radius of the disk), for impacts perpendicular to the disk plane. The calculations were performed on a Cray 2 computer using a combined N-body/smooth particle hydrodynamics (SPH) program. The results show the development of complicated flows and shock structures in the direction perpendicular to the plane of the disk and the propagation outwards of a density wave in both the stars and the gas. The collisional nature of the gas results in a sharper ring than obtained for the star particles, and the development of high volume densities and shocks.

Lamb, Susan A.↗

Nonaxisymmetric evolution in protostellar disks

We present a two-dimensional, multigridded hydrodynamical simulation of the collapse of an axisymmetric, rotating, 1 solar mass protostellar cloud, which forms a resolved, hydrotastic disk. The code includes the effects of physical viscosity, radiative transfer and radiative acceleration but not magnetic fields. We examine how the disk is affected by the inclusion of turbulent viscosity by comparing a viscous simulation with an inviscid model evolved from the same initial conditions, and we derive a disk evolutionary timescale on the order of 300,000 years if alpha = 0.01. Effects arising from non-axisymmetric gravitational instabilities in the protostellar disk are followed with a three-dimensional SPH code, starting from the two-dimensional structure. We find that the disk is prone to a series of spiral instabilities with primary azimulthal mode number m = 1 and m = 2. The torques induced by these nonaxisymmetric structures elicit material transport of angular momentum and mass through the disk, readjusting the surface density profile toward more stable configurations. We present a series of analyses which characterize both the development and the likely source of the instabilities. We speculate that an evolving disk which maintains a minimum Toomre Q-value approximately 1.4 will have a total evolutionary span of several times 10(exp 5) years, comparable to, but somewhat shorter than the evolutionary timescale resulting from viscous turbulence alone. We compare the evolution resulting from nonaxisymmetric instabilities with solutions of a one-dimensional viscous diffusion equation applied to the initial surface density and temperature profile. We find that an effective alpha-value of 0.03 is a good fit to the results of the simulation. However, the effective alpha will depend on the minimum Q in the disk at the time the instability is activated. We argue that the major fraction of the transport characterized by the value of alpha is due to the action of gravitational torques, and does not arise from inherent viscosity within the smoothed particle hydrodynamics method.

Laughlin, Gregory↗

Two-fluid simulations of galaxy formation

We investigate the formation of galaxies and larger structure with a simulation modeling two gravitationally coupled fluids representing dark matter and baryons. The baryon gas dynamics are calculated with a smoothed particle hydrodynamics (SPH) method, and the physics modeled includes thermal pressure, shock heating, and radiative cooling. We simulate a 16 Mpc periodic cube with 64(exp 3) particles in each fluid and 10% baryon mass fraction. We confirm, for the first time experimentally, disk formation as a natural consequence of hierarchical clustering in a large-scale cosmological environment. The majority of isolated galaxies exhibit centrifugally supported disks. A power-law relation between cold baryonic mass and maximum rotation velocity is found, M varies as nu(sub rot)(exp alpha) with alpha = 2.5 after correcting for differential numerical resolution. Both the spatial and velocity distributions of the simulated galaxies are biased with respect to the dark matter. A counts-in-cells analysis indicates that an unphysical degree of merging in the central cluster is likely responsible for the antibias signal in the correlation function. A robust, scale-dependent velocity bias is measured. The ratio of galaxy to dark matter pairwise velocity dispersions on a scale of 1 Mpc is 0.7. The amplitude is only mildly dependent on redshift or mass cutoff and scales with separation as r(exp 0.2). The degree to which these results depend on numerical parameters is discussed. Mass resolution plays a key role in controlling the resulting fraction of cold, dense baryons. The mass fraction associated with galaxies decreases by a factor of approximately greater than 3 when the mass per particle is increased by a factor 8. Photoionization and energy input from supernova will have to be included to determine more carefully the fraction of highly dissipated material and the characteristics of the stellar component of galaxies.

Evrard, August E.↗

Postexplosion hydrodynamics of supernovae in red supergiants

Shock propagation, mixing, and clumping are studied in the explosion of red supergiants as Type II supernovae using a two-dimensional smooth particle hydrodynamic (SPH) code. We show that extensive Rayleigh-Talor instabilities develop in the ejecta in the wake of the reverse shock wave. In all cases, the shell structure of the progenitor is obliterated to leave a clumpy, well-mixed supernova remnant. However, the occurrence of mass loss during the lifetime of the progenitor can significantly reduce the amount of mixing. These results are independent of the Type II supernova explosion mechanism.

Herant, Marc↗

Large ejecta fragments from asteroids

The asteroid 4 Vesta, with its unique basaltic crust, remains a key mystery of planetary evolution. A localized olivine feature suggests excavation of subcrustal material in a crater or impact basin comparable in size to the planetary radius (R(sub vesta) is approximately = 280 km). Furthermore, a 'clan' of small asteroids associated with Vesta (by spectral and orbital similarities) may be ejecta from this impact 151 and direct parents of the basaltic achondrites. To escape, these smaller (about 4-7 km) asteroids had to be ejected at speeds greater than the escape velocity, v(sub esc) is approximately = 350 m/s. This evidence that large fragments were ejected at high speed from Vesta has not been reconciled with the present understanding of impact physics. Analytical spallation models predict that an impactor capable of ejecting these 'chips off Vesta' would be almost the size of Vesta! Such an impact would lead to the catastrophic disruption of both bodies. A simpler analysis is outlined, based on comparison with cratering on Mars, and it is shown that Vesta could survive an impact capable of ejecting kilometer-scale fragments at sufficient speed. To what extent does Vesta survive the formation of such a large crater? This is best addressed using a hydrocode such as SALE 2D with centroidal gravity to predict velocities subsequent to impact. The fragmentation outcome and velocity subsequent to the impact described to demonstrate that Vesta survives without large-scale disassembly or overturning of the crust. Vesta and its clan represent a valuable dataset for testing fragmentation hydrocodes such as SALE 2D and SPH 3D at planetary scales. Resolution required to directly model spallation 'chips' on a body 100 times as large is now marginally possible on modern workstations. These boundaries are important in near-surface ejection processes and in large-scale disruption leading to asteroid families and stripped cores.

Asphaug, E.↗