Shape selection of surface-bound helical filaments: biopolymers on curved membranes

Motivated to understand the behavior of biological filaments interacting with membranes of various types, we study a theoretical model for the shape and thermodynamics of intrinsically-helical filaments bound to curved membranes. We show filament-surface interactions lead to a host of non-uniform shape equilibria, in which filaments progressively unwind from their native twist with increasing surface interaction and surface curvature, ultimately adopting uniform-contact curved shapes. The latter effect is due to non-linear coupling between elastic twist and bending of filaments on anisotropically-curved surfaces, such as the cylindrical surfaces considered here. Via a combination of numerical solutions and asymptotic analysis of shape equilibria we show that filament conformations are critically sensitive to the surface curvature in both the strong- and weak-binding limits. These results suggest that local structure of membrane-bound chiral filaments is generically sensitive to the curvature-radius of the surface to which it is bound, even when that radius is much larger than the filament intrinsic pitch. Typical values of elastic parameters and interaction energies for several prokaryotic and eukaryotic filaments indicate that biopolymers are inherently very sensitive to the coupling between twist, interactions and geometry and that this could be exploited for regulation of a variety of processes such as the targeted exertion of forces, signaling and self-assembly in response to geometric cues including the local mean and Gaussian curvatures

Faster Than Real Time Tsunami Warning with Associated Hazard Uncertainties

Tsunamis are unpredictable events and catastrophic in their potential for destruction of human lives and economy. The unpredictability of their occurrence poses a challenge to the tsunami community, as it is difficult to obtain from the tsunamigenic records estimates of recurrence rates and severity. Accurate and efficient mathematical/computational modeling is thus called upon to provide tsunami forecasts and hazard assessments. Compounding this challenge for warning centres is the physical nature of tsunamis, which can travel at extremely high speeds in the open ocean or be generated close to the shoreline. Thus, tsunami forecasts must be not only accurate but also delivered under severe time constraints. In the immediate aftermath of a tsunamigenic earthquake event, there are uncertainties in the source such as location, rupture geometry, depth, magnitude. Ideally, these uncertainties should be represented in a tsunami warning. However in practice, quantifying the uncertainties in the hazard intensity (i.e., maximum tsunami amplitude) due to the uncertainties in the source is not feasible, since it requires a large number of high resolution simulations. We approximate the functionally complex and computationally expensive high resolution tsunami simulations with a simple and cheap statistical emulator. A workflow integrating the entire chain of components from the tsunami source to quantification of hazard uncertainties is developed here - quantification of uncertainties in tsunamigenic earthquake sources, high resolution simulation of tsunami scenarios using the GPU version of Volna-OP2 on a non-uniform mesh for an ensemble of sources, construction of an emulator using the simulations as training data, and prediction of hazard intensities with associated uncertainties using the emulator. Thus, using the massively parallelized finite volume tsunami code Volna-OP2 as the heart of the workflow, we use statistical emulation to compute uncertainties in hazard intensity at locations of interest. Such an integration also balances the trade-off between computationally expensive simulations and desired accuracy of uncertainties, within given time constraints. The developed workflow is fully generic and independent of the source (1945 Makran earthquake) studied here

Defect Formation and Kinetics of Atomic Terrace Merging

Pairs of atomic scale terraces on a single crystal metal surface can be made to merge controllably under suitable conditions to yield steps of double height and width. We study the effect of various physical parameters on the formation of defects in a kinetic model of step doubling. We treat this manifestly non- equilibrium problem by mapping the model onto a 1-D random sequential adsorption problem and solving this analytically. We also do simulations to check the validity of our treatment. We find that our treatment effectively captures the dynamic evolution and the final state of the surface morphology. We show that the number and nature of the defects formed is controlled by a single dimensionless parameter $q$. For $q$ close to one we show that the fraction of defects rises linearly with $\epsilon \equiv 1-q$ as $0.284 \times \epsilon$. We also show that one can arrive at the final state faster and with fewer defects by changing the parameter with time.Comment: 17 pages, 8 figures. To be submitted to Phys. Rev.

Nonlinear analytical flame models with amplitude-dependent time-lag distributions

In the present work, we formulate a new method to represent a given Flame Describing Function by analytical expressions. The underlying idea is motivated by the observation that different types of perturbations in a burner travel with different speeds and that the arrival of a perturbation at the flame is spread out over time. We develop an analytical model for the Flame Describing Function, which consists of a superposition of several Gaussians, each characterised by three amplitude-dependent quantities: central time-lag, peak value and standard deviation. These quantities are treated as fitting parameters, and they are deduced from the original Flame Describing Function by using error minimisation and nonlinear optimisation techniques. The amplitude-dependence of the fitting parameters is also represented analytically (by linear or quadratic functions). We test our method by using it to make stability predictions for a burner with well-documented stability behaviour (Noiray's matrix burner). This is done in the time-domain with a tailored Green's function approach

Training manual on phytoplankton identification/taxonomy

The term 'plankton' was coined by Victor Hensen in 1887, denotes collectively all free floating and suspended bodies, both plants and animals, living or dead, that essentially move passively in a body of water. The phytoplankters are the microscopic plant life of the sea, which constitute the primary producers synthesizing the basic food. It belongs to the class Algae, which besides chlorophylls posses other characteristic pigments. The important components of phytoplankton are Diatoms (Bacillariophyceae), Dinoflagellates (Dinophyceae), Blue-green algae (Cyanophyceae), Phytoflagellates (Xanthophyceae, Chrysophyceae, Haptophyceae, Cryptophyceae) and Nannoplankters (Chlorella, Nannochloropsis etc.). In addition to these, two other Classes namely Silicoflagellates and Coccolithophores also belong to the category of phytoplankton

Larval rearing, spat production and juvenile growth of the blood clam Anadara granosa

The blood clam A d r u gmtwsa spawned in the Shdl6lsh Hatchery Laboratory, Tuf icorin on two occasions. The fertilised eggs measured 50-60~in diameter, morula larvae developed in 3 4h m and the trochophorc stage was reached in 5 hrs. The straigb t hinge stage was attained in 20-26 hrs after fertilimtion and these larvae measured 8 3I~en ah and 65.5~h eight. Advanced umbo stage was reached on day 12 (size 155.3 x 140.5~) and on day 16, majority of the larvae were in pedivcliger stage with an average size of 182.7 x 162.9~. SettIement began on day 16 and majority of the larvae were set on day 18. The growth of the spat in the hatchery is described by the exponential equation L - 0.0002739 D - where L is length in mm and D. days. On day 59, tbe spat attained an average size of 2.42 x 1.70 mm. A total of 8090 spat were produced. During tha nursery rearing in the field, the seed clam attained 20 mm average length in the following 5 months. In India, A.grund~llsecd were grodwdfor the Arst time. The significance of this study forthe mass production of the blood clam seed in the bat~herya nd its relevma to undertake blood clam culture are highlighted

Culture of live feed organisms

In any maricuUure practice, availability of seed is one of the prime requisites for sustaining growth, development and to make the activity viable ecologically and economically. As the natural source of seed is often beset with environmental / conservational problems, the dependable source is production through hatchery techniques. Uninterrupted production and supply of live feeds alone can sustain hatchery operations and to feed the emerging larvae or post larvae with different feed requirements at different stages of development / growth. Technologies developed by CMFRl in this line are given in this paper. The method of culturing important live feed organisms such as micro-algae, rotifers, cladocerans and Artemia salina along with their harvesting and preservation are briefly described in this accoun

Diffusion and binding of finite-size particles in confined geometries

Describing the diffusion of particles through crowded, confined environments with which they can interact is of considerable biological and technological interest. Under conditions where the confinement dimensions become comparable to the particle dimensions, steric interactions between particles, as well as particle-wall interactions, will play a crucial role in determining transport properties. To elucidate the effects of these interactions on particle transport, we consider the diffusion and binding of finite-size particles within a channel whose diameter is comparable to the size of the particles. Using a simple lattice model of this process, we calculate the steady-state current and density profiles of both bound and free particles in the channel. We show that the system can exhibit qualitatively different behavior depending on the ratio of the channel width to the particle size. We also perform simulations of this system, and find excellent agreement with our analytic results.Comment: 11 pages, 5 figures, Phys. Rev. E (accepted

Polymer Translocation in Crowded Environments

We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are significantly altered, leading to novel scaling behaviors of the translocation time in terms of chain length. We also observe new and qualitatively different translocation regimes depending upon the extent of crowding, transmembrane chemical potential asymmetry, and polymer length.Comment: 4 figure

Larval rearing and production of spat of the oyster Crassostrea madrasensis (Preston) in an Experimental hatchery

The Indian backwater oyster, Crassostrea madrasensis, was spawned in the laboratory at Tuticorin. The larvae were reared and the spat settled in 15-20 days. Two species of jihytoflagellates, Isochrysis galbana and Pavlova sp. were isolated from the natural environment, cultured in mass scale and given as food throughout the larval period. Early stages of the development of fertilized egg, successive stages of developing larvae, and metamorphosis to the spat have been described. The methodology of the production of cultchless spat and rearing the post-set oysters are discussed