Reynolds number limits for jet propulsion: A numerical study of simplified jellyfish

The Scallop Theorem states that reciprocal methods of locomotion, such as jet propulsion or paddling, will not work in Stokes flow (Reynolds number = 0). In nature the effective limit of jet propulsion is still in the range where inertial forces are significant. It appears that almost all animals that use jet propulsion swim at Reynolds numbers (Re) of about 5 or more. Juvenile squid and octopods hatch from the egg already swimming in this inertial regime. The limitations of jet propulsion at intermediate Re is explored here using the immersed boundary method to solve the two-dimensional Navier Stokes equations coupled to the motion of a simplified jellyfish. The contraction and expansion kinematics are prescribed, but the forward and backward swimming motions of the idealized jellyfish are emergent properties determined by the resulting fluid dynamics. Simulations are performed for both an oblate bell shape using a paddling mode of swimming and a prolate bell shape using jet propulsion. Average forward velocities and work put into the system are calculated for Reynolds numbers between 1 and 320. The results show that forward velocities rapidly decay with decreasing Re for all bell shapes when Re < 10. Similarly, the work required to generate the pulsing motion increases significantly for Re < 10. When compared actual organisms, the swimming velocities and vortex separation patterns for the model prolate agree with those observed in Nemopsis bachei. The forward swimming velocities of the model oblate jellyfish after two pulse cycles are comparable to those reported for Aurelia aurita, but discrepancies are observed in the vortex dynamics between when the 2D model oblate jellyfish and the organism

Leaf roll-up and aquaplaning in strong winds and floods

Flexible plants, fungi, and sessile animals are thought to reconfigure in the wind and water to reduce the drag forces that act upon them. In strong winds, for example, leaves roll up into cone shapes that reduce flutter and drag when compared to paper cut-outs with similar shapes and flexibility. During flash floods, herbaceous broad leaves aquaplane on the surface of the water which reduces drag. Simple mathematical models of a flexible beam immersed in a two-dimensional flow will also reconfigure in flow. What is less understood is how the mechanical properties of a two-dimensional leaf in a three-dimensional flow will passively allow roll up and aquaplaning. In this study, we film leaf roll-up and aquaplaning in tree and vine leaves in both strong winds and water flows

Occurrence Of Putative Endornaviruses In Non-Cultivated Plant Species And Characterization Of A Novel Endornavirus In Geranium Carolinianum

Endornaviruses are RNA viruses, which can infect plants yet cause no apparent symptoms. To date, most descriptions of endornaviruses infecting plants have been in cultivated species. A survey for endornaviruses in non-cultivated plants was initiated in 2015 and continued through 2017 in Baton Rouge, Louisiana. Two hundred and seven plant species were tested for distinctive dsRNA profiles by selective extraction and gel electrophoresis, of which seven contained endornavirus-like dsRNA. RT-PCR amplification of an endornavirus-specific sequence supported the endornavirus nature of six of the seven samples. Of the six host species, one species, Geranium carolinianum was confirmed as being infected with a novel endornavirus. The endornavirus in G. carolinianum was characterized and named Geranium carolinianum endornavirus 1 (GcEV-1). The genome of GcEV-1 is approximately 14.7 kb and is related to other endornaviruses, some infecting plants and some infecting fungi. GcEV-1 is a unique plant endornavirus containing genes closely related to fungal and bacterial genes. A GcEV-1 seed transmission test conducted in the greenhouse resulted in a 100% transmission rate. The occurrence of endornavirus-like dsRNA within G. carolinianum was evaluated at three different locations in Louisiana, two within Baton Rouge and one in Belle Chasse. Among the 184 individual plants tested, three individuals were dsRNA-free. There were no clear phenotypic differences in dsRNA-free individuals compared to those containing dsRNA. All three endornavirus-free G. carolinianum plants were collected from the same location. The discovery of only six putative endornaviruses after testing 207 plant species suggests that endornaviruses are not very common in non-cultivated plant species. The results of this study provide a foundation for future research investigating the origin of endornaviruses and the effect endornaviruses have on plants

Force-induced misfolding in RNA

RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of its importance in modern biophysics, the current understanding of RNA folding kinetics is limited by the complex interplay between the weak base-pair interactions that stabilize the native structure and the disordering effect of thermal forces. The possibility of mechanically pulling individual molecules offers a new perspective to understand the folding of nucleic acids. Here we investigate the folding and misfolding mechanism in RNA secondary structures pulled by mechanical forces. We introduce a model based on the identification of the minimal set of structures that reproduce the patterns of force-extension curves obtained in single molecule experiments. The model requires only two fitting parameters: the attempt frequency at the level of individual base pairs and a parameter associated to a free energy correction that accounts for the configurational entropy of an exponentially large number of neglected secondary structures. We apply the model to interpret results recently obtained in pulling experiments in the three-helix junction S15 RNA molecule (RNAS15). We show that RNAS15 undergoes force-induced misfolding where force favors the formation of a stable non-native hairpin. The model reproduces the pattern of unfolding and refolding force-extension curves, the distribution of breakage forces and the misfolding probability obtained in the experiments.Comment: 28 pages, 11 figure