Integrable motion of a vortex dipole in an axisymmetric flow

The evolution of a self-propelling vortex dipole, embedded in an external nondivergent flow with constant potential vorticity, is studied in an equivalent-barotropic model commonly used in geophysical, astrophysical and plasma studies. In addition to the conservation of the Hamiltonian for an arbitrary point vortex dipole, it is found that the angular momentum is also conserved when the external flow is axisymmetric. This reduces the original four degrees of freedom to only two, so that the solution is expressed in quadratures. In particular, the scattering of antisymmetric dipoles approaching from the infinity is analyzed in the presence of an axisymmetric oceanic flow typical for the vicinity of isolated seamounts

Role of deposit-feeding sea cucumbers in integrated multitrophic aquaculture: progress, problems, potential and future challenges

There is significant commercial and research interest in the application of sea cucumbers as nutrient recyclers and processors of particulate waste in polyculture or integrated multitrophic aquaculture (IMTA) systems. The following article reviews examples of existing IMTA systems operating with sea cucumbers, and details the role and effect of several sea cucumber species in experimental and pilot IMTA systems worldwide. Historical observations and quantification of impacts of sea cucumber deposit-feeding and locomotion are examined, as is the development and testing of concepts for the application of sea cucumbers in sediment remediation and site recovery. The extension of applied IMTA systems is reported, from basic piloting through to economically viable farming systems operating at commercial scales. The near-global recognition of the ecological and economic value of deposit-feeding sea cucumbers in IMTA applications within existing and developing aquaculture industries is discussed. Predictions and recommendations are offered for optimal development of sea cucumber IMTA globally. Future directions within the industry are indicated, and key areas of ecological, biological and commercial concern are highlighted to be kept in mind and addressed in a precautionary manner as the industry develops

Interaction between a surface quasi-geostrophic buoyancy anomaly jet and internal vortices

This paper addresses the dynamical coupling of the ocean's surface and the ocean's interior. In particular, we investigate the dynamics of an oceanic surface jet, and its interaction with vortices at depth. The jet is induced by buoyancy (density) anomalies at the surface. We first focus on the jet alone. The linear stability indicates there are two modes of instability: the sinuous and the varicose modes. When a vortex in present below the jet, it interacts with it. The velocity field induced by the vortex perturbs the jet and triggers its destabilisation. The jet also influences the vortex by pushing it under a region of co-operative shear. Strong jets may also partially shear out the vortex. We also investigate the interaction between a surface jet and a vortex dipole in the interior. Again, strong jets may partially shear out the vortex structure. The jet also modifies the trajectory of the dipole. Dipoles travelling towards the jet at shallow incidence angles may be reflected by the jet. Vortices travelling at moderate incidence angles normally cross below the jet. This is related to the displacement of the two vortices of the dipole by the shear induced by the jet. Intense jets may also destabilise early and form streets of billows. These billows can pair with the vortices and separate the dipole.PostprintPeer reviewe

Ribosome rearrangements at the onset of translational bypassing.

Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of gene 60 of bacteriophage T4. The nascent peptide in the exit tunnel anchors the P-site peptidyl-tRNAGly to the ribosome and locks an inactive conformation of the peptidyl transferase center (PTC). The mRNA forms a short dynamic hairpin in the decoding site. The ribosomal subunits adopt a rolling conformation in which the rotation of the small subunit around its long axis causes the opening of the A-site region. Together, PTC conformation and mRNA structure safeguard against premature termination and read-through of the stop codon and reconfigure the ribosome to a state poised for take-off and sliding along the noncoding mRNA gap

A switch from α‐helical to β‐strand conformation during co‐translational protein folding

Cellular proteins begin to fold as they emerge from the ribosome.The folding landscape of nascent chains is not only shaped by theiramino acid sequence but also by the interactions with the ribo-some. Here, we combine biophysical methods with cryo-EM struc-ture determination to show that folding of aβ-barrel proteinbegins with formation of a dynamicα-helix inside the ribosome. Asthe growing peptide reaches the end of the tunnel, the N-terminalpart of the nascent chain refolds to aβ-hairpin structure thatremains dynamic until its release from the ribosome. Contactswith the ribosome and structure of the peptidyl transferase centerdepend on nascent chain conformation. These results indicate thatproteins may start out asα-helices inside the tunnel and switchinto their native folds only as they emerge from the ribosome.Moreover, the correlation of nascent chain conformations withreorientation of key residues of the ribosomal peptidyl-transferasecenter suggest that protein folding could modulate ribosome activity

Hetonic quartets in a two-layer quasi-geostrophic flow : V-states and stability

M.A.S. and X.C. were supported by RFBR/CNRS (PRC Grant No. 16-55-150001/1069). M.A.S. was supported also by RFBR (Grant No. 16-05-00121), RSF (Grant No. 14-50-00095, geophysical applications) and MESRF (Grant No. 14.W.03.31.0006, numerical simulation, vortex dynamics).We investigate families of finite core vortex quartets in mutual equilibrium in a two- layer quasi-geostrophic flow. The finite core solutions stem from known solutions for discrete (singular) vortex quartets. Two vortices lie in the top layer and two vortices lie in the bottom layer. Two vortices have a positive potential vorticity anomaly while the two others have negative potential vorticity anomaly. The vortex configurations are therefore related to the baroclinic dipoles known in the literature as hetons. Two main branches of solutions exist depending on the arrangement of the vortices: the translating zigzag-shaped hetonic quartets and the rotating zigzag- shaped hetonic quartets. By addressing their linear stability, we show that while the rotating quartets can be unstable over a large range of the parameter space, most translating quartets are stable. This has implications on the longevity of such vortex equilibria in the oceans.PostprintPeer reviewe

The construction of exact multipolar equilibria of the two-dimensional Euler equations

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Vortex merger near a topographic slope in a homogeneous rotating fluid

This work is a contribution to the PHYSINDIEN research program. It was supported by CNRS-RFBR contract PRC 1069/16-55-150001.The effect of a bottom slope on the merger of two identical Rankine vortices is investigated in a two dimensional, quasi-geostrophic, incompressible fluid. When two cyclones initially lie parallel to the slope, and more than two vortex diameters away from the slope, the critical merger distance is unchanged. When the cyclones are closer to the slope, they can merge at larger distances, but they lose more mass into filaments, thus weakening the efficiency of merger. Several effects account for this: the topographic Rossby wave advects the cyclones, reduces their mutual distance and deforms them. This along shelf wave breaks into filaments and into secondary vortices which shear out the initial cyclones. The global motion of fluid towards the shallow domain and the erosion of the two cyclones are confirmed by the evolution of particles seeded both in the cyclone sand near the topographic slope. The addition of tracer to the flow indicates that diffusion is ballistic at early times. For two anticyclones, merger is also facilitated because one vortex is ejected offshore towards the other, via coupling with a topographic cyclone. Again two anticyclones can merge at large distance but they are eroded in the process. Finally, for taller topographies, the critical merger distance is again increased and the topographic influence can scatter or completely erode one of the two initial cyclones. Conclusions are drawn on possible improvements of the model configuration for an application to the ocean.PostprintPeer reviewe

Geostrophic tripolar vortices in a two-layer fluid : linear stability and nonlinear evolution of equilibria

We investigate equilibrium solutions for tripolar vortices in a two-layer quasi-geostrophic flow. Two of the vortices are like-signed and lie in one layer. An opposite-signed vortex lies in the other layer. The families of equilibria can be spanned by the distance (called separation) between the two like-signed vortices. Two equilibrium configurations are possible when the opposite-signed vortex lies between the two other vortices. In the first configuration (called ordinary roundabout), the opposite signed vortex is equidistant to the two other vortices. In the second configuration (eccentric roundabouts), the distances are unequal. We determine the equilibria numerically and describe their characteristics for various internal deformation radii. The two branches of equilibria can co-exist and intersect for small deformation radii. Then, the eccentric roundabouts are stable while unstable ordinary roundabouts can be found. Indeed, ordinary roundabouts exist at smaller separations than eccentric roundabouts do, thus inducing stronger vortex interactions. However, for larger deformation radii, eccentric roundabouts can also be unstable. Then, the two branches of equilibria do not cross. The branch of eccentric roundabouts only exists for large separations. Near the end of the branch of eccentric roundabouts (at the smallest separation), one of the like-signed vortices exhibits a sharp inner corner where instabilities can be triggered. Finally, we investigate the nonlinear evolution of a few selected cases of tripoles.PostprintPeer reviewe

Steady late quaternary slip rate on the Cinarcik section of the North Anatolian fault near Istanbul, Turkey

The distribution of plate motion between multiple fault strands and how this distribution may evolve remain poorly understood, despite the key implications for seismic hazards. The North Anatolian Fault in northwest Turkey is a prime example of a multistranded continental transform. Here we present the first constraints on late Quaternary slip rates on its northern branch across the Cinarcik Basin in the eastern Marmara Sea. We use both deep penetration and high‐resolution multichannel seismic reflection data with a stratigraphic age model to show that a depocenter has persisted near the fault bend responsible for that transform basin. Successively older depocenters have been transported westward by fault motion relative to Eurasia, indicating a uniform right‐lateral slip rate of 18.5 mm/yr over the last 500,000 years, compared to overall GPS rates (23–24 mm/yr). Thus, the northern branch has slipped at a nearly constant rate and has accounted for most of the relative plate motion between Eurasia and Anatolia since ~0.5 Ma