Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

HYDROMAGNETICS OF ADVECTIVE ACCRETION FLOWS AROUND BLACK HOLES: REMOVAL OF ANGULAR MOMENTUM BY LARGE-SCALE MAGNETIC STRESSES

We show that the removal of angular momentum is possible in the presence of large-scale magnetic stresses in geometrically thick, advective, sub-Keplerian accretion flows around black holes in steady state, in the complete absence of alpha-viscosity. The efficiency of such an angular momentum transfer could be equivalent to that of alpha-viscosity with alpha = 0.01-0.08. Nevertheless, the required field is well below its equipartition value, leading to a magnetically stable disk flow. This is essentially important in order to describe the hard spectral state of the sources when the flow is non/sub-Keplerian. We show in our simpler 1.5 dimensional, vertically averaged disk model that the larger the vertical-gradient of the azimuthal component of the magnetic field is, the stronger the rate of angular momentum transfer becomes, which in turn may lead to a faster rate of outflowing matter. Finding efficient angular momentum transfer in black hole disks via magnetic stresses alone, is very interesting when the generic origin of alpha-viscosity is still being explored.

Seismic intensity map of South India for estimated future earthquakes

In this study, an attempt has been made to prepare the seismic intensity map for south India considering the probable earthquakes in the region. Anbazhagan et al. (Nat Hazards 60:1325-1345, 2012) have identified eight probable future earthquake zones in south India based on rupture-based seismic hazard analysis. Anbazhagan et al. (Eng Geol 171:81-95, 2014) has estimated the maximum future earthquake magnitude at these eight zones using regional rupture character. In this study, the whole south India is divided into several grids of size 1(o) x 1(o) and the intensity at each grid point is calculated using the regional intensity model for the maximum earthquake magnitude at each of the eight zones. The intensity due to earthquakes at these zones is mapped and thus eight seismic intensity maps are prepared. The final seismic intensity map of south India is obtained by considering the maximum intensity at each grid point due to the estimated earthquakes. By looking at the seismic intensity map, one can expect slight to heavy damage due to the probable earthquake magnitudes. Heavy damage may happen close to the probable earthquake zones.

Photometric metallicity map of the Large Magellanic Cloud

We have estimated a metallicity map of the Large Magellanic Cloud (LMC) using the Magellanic Cloud Photometric Survey (MCPS) and Optical Gravitational Lensing Experiment (OGLE III) photometric data. This is a first of its kind map of metallicity up to a radius of 4 degrees-5 degrees, derived using photometric data and calibrated using spectroscopic data of Red Giant Branch (RGB) stars. We identify the RGB in the V, (V - I) colour-magnitude diagrams of small subregions of varying sizes in both data sets. We use the slope of the RGB as an indicator of the average metallicity of a subregion, and calibrate the RGB slope to metallicity using spectroscopic data for field and cluster red giants in selected subregions. The average metallicity of the LMC is found to be Fe/H] = -0.37 dex (sigmaFe/H] = 0.12) from MCPS data, and Fe/H] = -0.39 dex (sigmaFe/H] = 0.10) from OGLE III data. The bar is found to be the most metal-rich region of the LMC. Both the data sets suggest a shallow radial metallicity gradient up to a radius of 4 kpc (-0.049 +/- 0.002 dex kpc(-1) to -0.066 +/- 0.006 dex kpc(-1)). Subregions in which the mean metallicity differs from the surrounding areas do not appear to correlate with previously known features; spectroscopic studies are required in order to assess their physical significance.

The legacy of G. N. Ramachandran and the development of structural biology in India

G. N. Ramachandran is among the founding fathers of structural molecular biology. He made pioneering contributions in computational biology, modelling and what we now call bioinformatics. The triple helical coiled coil structure of collagen proposed by him forms the basis of much of collagen research at the molecular level. The Ramachandran map remains the simplest descriptor and tool for validation of protein structures. He has left his imprint on almost all aspects of biomolecular conformation. His contributions in the area of theoretical crystallography have been outstanding. His legacy has provided inspiration for the further development of structural biology in India. After a pause, computational biology and bioinformatics are in a resurgent phase. One of the two schools established by Ramachandran pioneered the development of macromolecular crystallography, which has now grown into an important component of modern biological research in India. Macromolecular NMR studies in the country are presently gathering momentum. Structural biology in India is now poised to again approach heights of the kind that Ramachandran conquered more than a generation ago.

Spatio-temporal Map Formation Based on a Potential Function

We revisit the problem of temporal self organization using activity diffusion based on the neural gas (NGAS) algorithm. Using a potential function formulation motivated by a spatio-temporal metric, we derive an adaptation rule for dynamic vector quantization of data. Simulations results show that our algorithm learns the input distribution and time correlation much faster compared to the static neural gas method over the same data sequence under similar training conditions.

Visualisation of charge-transfer excitations in donor-acceptor molecules using the particle-hole map: a case study

Charge-transfer (CT) excitations are essential for photovoltaic phenomena in organic solar cells. Owing to the complexity of molecular geometries and orbital coupling, a detailed analysis and spatial visualisation of CT processes can be challenging. In this paper, a new detail-oriented visualisation scheme, the particle-hole map (PHM), is applied and explained for the purpose of spatial analysis of excitations in organic molecules. The PHM can be obtained from the output of a time-dependent density-functional theory calculation with negligible additional computational cost, and provides a useful physical picture for understanding the origins and destinations of electrons and holes during an excitation process. As an example, we consider intramolecular CT excitations in Diketopyrrolopyrrole-based molecules, and relate our findings to experimental results.

Supersonic dusty-gas flows with Knudsen effect in interphase momentum exchange

On the basis of the two-continuum model of dilute gas-solid suspensions, the dynamic behavior of inertial particles in supersonic dusty-gas flows past a blunt body is studied for moderate Reynolds numbers, when the Knudsen effect in the interphase momentum exchange is significant. The limits of the inertial particle deposition regime in the space of governing parameters are found numerically under the assumption of the slip and free-molecule flow regimes around particles. As a model problem, the flow structure is obtained for a supersonic dusty-gas point-source flow colliding with a hypersonic flow of pure gas. The calculations performed using the full Lagrangian approach for the near-symmetry-axis region and the free-molecular flow regime around the particles reveal a multi-layer structure of the dispersed-phase density with a sharp accumulation of the particles in some thin regions between the bow and termination shock waves.

Wavelike patterns in one-dimensional coupled map lattices

We investigate the existence of wavelike solution for the logistic coupled map lattices for which the spatiotemporal periodic patterns can be predicted by a simple two-dimensional mapping. The existence of such wavelike solutions is proved by the implicit function theorem with constraints. We also examine the stabilities of these wave solutions under perturbations of uniform small deformation type. We show that in some specific cases these perturbations are completely general. The technique used in this paper is also applicable to investigate other space-time regular patterns.

Convective coupled map for simulating spatiotemporal chaos in flows

A coupled map lattices with convective nonlinearity or, for short, Convective Coupled Map (CCM) is proposed in this paper to simulate spatiotemporal chaos in fluid hows. It is found that the parameter region of spatiotemporal chaos can be determined by the maximal Liapunov exponent of its complexity time series. This simple model implies a similar physical mechanism for turbulence such that the route to spatiotemporal chaos in fluid hows can be envisaged.