On the Algorithms for Vortex Element Evolution Modelling in 3D Fully Lagrangian Vortex Loops Method

2020 ◽  
Author(s):  
I.K. Marchevsky ◽  
G.A. Shcheglov ◽  
S.A. Dergachev
Keyword(s):  
Vortex Loops ◽  
Element Evolution ◽  
Vortex Element

scholarly journals Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1341-1351 ◽  
Author(s):  
I King Jordan ◽  
John F McDonald
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Negative Selection ◽  
Sequence Variation ◽  
Size Variation ◽  
Sequence Comparisons ◽  
Ty Elements ◽  
Ty Element ◽  
Amino Acid Sequence Variation ◽  
Element Evolution ◽  
High Level

Abstract The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.

The formation mechanism and shedding frequency of vortices from a sphere in uniform shear flow

1995 ◽  
Vol 287 ◽  
pp. 151-171 ◽  
Author(s):  
Hiroshi Sakamoto ◽  
Hiroyuki Haniu
Keyword(s):  
Reynolds Number ◽  
Shear Flow ◽  
Formation Mechanism ◽  
Vortex Shedding ◽  
Uniform Flow ◽  
Sphere Diameter ◽  
Uniform Shear ◽  
Uniform Shear Flow ◽  
Vortex Loops ◽  
Shear Parameter

Experiments to investigate the formation mechanism and frequency of vortex shedding from a sphere in uniform shear flow were conducted in a water channel using flow visualization and velocity measurement. The Reynolds number, defined in terms of the sphere diameter and approach velocity at its centre, ranged from 200 to 3000. The shear parameter K, defined as the transverse velocity gradient of the shear flow non-dimensionalized by the above two parameters, was varied from 0 to 0.25. The critical Reynolds number beyond which vortex shedding from the sphere occurred was found to be lower than that for uniform flow and decreased approximately linearly with increasing shear parameter. Also, the Strouhal number of the hairpin-shaped vortex loops became larger than that for uniform flow and increased as the shear parameter increased.The formation mechanism and the structure of vortex shedding were examined on the basis of series of photographs and subsequent image processing using computer graphics. The range of Reynolds number in the present investigation, extending up to 3000, could be classified into three regions on the basis of this study, and it was observed that the wake configuration did not differ substantially from that for uniform flow. Also, unlike the detachment point of vortex loops in uniform flow, which was irregularly located along the circumference of the sphere, the detachment point in shear flow was always on the high-velocity side.

Three-dimensional wake transition

1996 ◽  
Vol 328 ◽  
pp. 345-407 ◽  
Author(s):  
C. H. K. Williamson
Keyword(s):  
Shear Layer ◽  
Three Dimensional ◽  
Streamwise Vortex ◽  
Physical Structure ◽  
Small Scale ◽  
Half Cycle ◽  
Vortex Loops ◽  
Wake Transition ◽  
Mode A ◽  
Flow States

It is now well-known that the wake transition regime for a circular cylinder involves two modes of small-scale three-dimensional instability (modes A and B), depending on the regime of Reynolds number (Re), although almost no understanding of the physical origins of these instabilities, or indeed their effects on near-wake formation, have hitherto been made clear. We address these questions in this paper. In particular, it is found that the two different modes A and B scale on different physical features of the flow. Mode A has a larger spanwise wavelength of around 3–4 diameters, and scales on the larger physical structure in the flow, namely the primary vortex core. The wavelength for mode A is shown to be the result of an ‘elliptic instability’ in the nearwake vortex cores. The subsequent nonlinear growth of vortex loops is due to a feedback from one vortex to the next, involving spanwise-periodic deformation of core vorticity, which is then subject to streamwise stretching in the braid regios. This mode gives an out-of-phase streamwise vortex pattern.In contrast, mode-B instability has a distinctly smaller wavelength (1 diameter) which scales on the smaller physical structure in the flow, the braid shear layer. It is a manifestation of an instability in a region of hyperbolic flow. It is quite distinct from other shear flows, in that it depends on the reverse flow of the bluff-body wake; the presence of a fully formed streamwise vortex system, brought upstream from a previous half-cycle, in proximity to the newly evolving braid shear layer, leads to an in-phase stream-wise vortex array, in strong analogy with the ‘Mode 1’ of Meiburg & Lasheras (1988) for a forced unseparated wake. In mode B, we also observe amalgamation of streamwise vortices from a previous braid with like-sign vortices in the subsequent braid.It is deduced that the large scatter in previous measurements concerning mode A is due to the presence of vortex dislocations. Dislocations are triggered at the sites of some vortex loops of mode A, and represent a natural breakdown of the periodicity of mode A instability. By minimizing or avoiding the dislocations which occur from end contamination or which occur during wake transition, we find an excellent agreement of both critical Re and spanwise wavelength of mode A with the recent secondary stability analysis of Barkley & Henderson (1996).Wake transition is further characterized by velocity and pressure measurements. It is consistent that, when mode-A instability and large-scale dislocations appear, one finds a reduction of base suction, a reduction of (two-dimensional) Reynolds stress level, a growth in size of the formation region, and a corresponding drop in Strouhal frequency. Finally, the present work leads us to a new clarification of the possible flow states through transition. Right through this regime of Re, there exist two distinct and continuous Strouhal frequency curves: the upper one corresponds with purley small- scale instabilities (e.g. denoted as mode A), while the lower curve corresponds with a combination of small-scale plus dislocation structures (e.g. mode A*). However, some of the flow states are transient or ‘unstable’, and the natural transitioning wake appears to follow the scenario: (2D→A*→B).

scholarly journals Thrust Force Generated by Heaving Motion of a Plate: The Role of Vortex-Induced Force

2021 ◽  
Author(s):  
Kazuo Matsuuchi
Keyword(s):  
Vortex Shedding ◽  
Thrust Force ◽  
Unsteady Motion ◽  
Force Generation ◽  
Thrust Coefficient ◽  
Momentum Change ◽  
Vortex Element ◽  
Motion Characteristics ◽  
Vortex Systems

To understand the force acting on birds, insects, and fish, we take heaving motion as a simple example. This motion might deviate from the real one. However, since the mechanism of force generation is the vortex shedding due to the motion of an object, the heaving motion is important for understanding the force generated by unsteady motion. The vortices released from the object are closely related to the motion characteristics. To understand the force acting on an object, information about momentum change is necessary. However, in vortex systems, it is impossible to estimate the usual momentum. Instead of the momentum, the “virtual momentum,” or the impulse, is needed to generate the force. For calculating the virtual momentum, we traced all vortices over a whole period, which was carried out by using the vortex-element method. The force was then calculated based on the information on the vortices. We derived the thrust coefficient as a function of the ratio of the heaving to travelling velocity.

scholarly journals Probing of quantum turbulence with the emitting vortex loops

2014 ◽  
Vol 40 (12) ◽  
pp. 1116-1118 ◽  
Author(s):  
S. K. Nemirovskii
Keyword(s):  
Quantum Turbulence ◽  
Vortex Loops

scholarly journals Mating system shifts and transposable element evolution in the plant genus Capsella

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 602 ◽  
Author(s):  
J Ågren ◽  
Wei Wang ◽  
Daniel Koenig ◽  
Barbara Neuffer ◽  
Detlef Weigel ◽  
...  
Keyword(s):  
Transposable Element ◽  
Mating System ◽  
Element Evolution
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