Sharavathi River Basin Flora Information System(SRFIS)

The INFORMATION SYSTEM with user friendly GUI’s (Graphical user Interface) is developed to maintain the flora data and generate reports for Sharavathi River Basin. The database consists of the information related to trees, herbs, shrubs and climbers. The data is based on the primary field survey and the information available in flora of Shimoga, Karnataka and Hassan flora. User friendly query options based on dichotomous keys are provided to help user to retrieve the data while data entry options aid in updating and editing the database at family, genus and species levels.

Steady-State Stability of Current-Mode Active-Clamp ZVS DC-DC Converters

Active-clamp dc-dc converters are pulsewidth-modulated converters having two switches featuring zero-voltage switching at frequencies beyond 100 kHz. Generalized equivalent circuits valid for steady-state and dynamic performance have been proposed for the family of active-clamp converters. The active-clamp converter is analyzed for its dynamic behavior under current control in this paper. The steady-state stability analysis is presented. On account of the lossless damping inherent in the active-clamp converters, it appears that the stability region in the current-controlled active-clamp converters get extended for duty ratios, a little greater than 0.5 unlike in conventional hard-switched converters. The conventional graphical approach fails to assess the stability of current-controlled active-clamp converters, due to the coupling between the filter inductor current and resonant inductor current. An analysis that takes into account the presence of the resonant elements is presented to establish the condition for stability. This method correctly predicts the stability of the current-controlled active-clamp converters. A simple expression for the maximum duty cycle for subharmonic-free operation is obtained. The results are verified experimentally.

Stability of control systems with time delay

To find the approximate stability limit on the forward gain in control systems with small time delay, this note suggests approximating the exponential in the characteristic equation by the first few terms of its series and using the Routh–Hurwitz criterion. This approximation avoids all the time-consuming graphical work and gives a somewhat pessimistic maximum bound for the gain constant.

Quaternary association in beta-prism I fold plant lectins: Insights from X-ray crystallography, modelling and molecular dynamics

Dimeric banana lectin and calsepa, tetrameric artocarpin and octameric heltuba are mannose-specific beta-prism I fold lectins of nearly the same tertiary structure. MD simulations on individual subunits and the oligomers provide insights into the changes in the structure brought about in the protomers on oligomerization, including swapping of the N-terminal stretch in one instance. The regions that undergo changes also tend to exhibit dynamic flexibility during MD simulations. The internal symmetries of individual oligomers are substantially retained during the calculations. Energy minimization and simulations were also carried out on models using all possible oligomers by employing the four different protomers. The unique dimerization pattern observed in calsepa could be traced to unique substitutions in a peptide stretch involved in dimerization. The impossibility of a specific mode of oligomerization involving a particular protomer is often expressed in terms of unacceptable steric contacts or dissociation of the oligomer during simulations. The calculations also led to a rationale for the observation of a heltuba tetramer in solution although the lectin exists as an octamer in the crystal, in addition to providing insights into relations among evolution, oligomerization and ligand binding.

Computer simulation of liquid crystals

In this article we review the current status in the modelling of both thermotropic and lyotropic Liquid crystal. We discuss various coarse-graining schemes as well as simulation techniques such as Monte Carlo (MC) and Molecular dynamics (MD) simulations.In the area of MC simulations we discuss in detail the algorithm for simulating hard objects such as spherocylinders of various aspect ratios where excluded volume interaction enters in the simulation through overlap test. We use this technique to study the phase diagram, of a special class of thermotropic liquid crystals namely banana liquid crystals. Next we discuss a coarse-grain model of surfactant molecules and study the self-assembly of the surfactant oligomers using MD simulations. Finally we discuss an atomistically informed coarse-grained description of the lipid molecules used to study the gel to liquid crystalline phase transition in the lipid bilayer system.

Minor mergers and their impact on the kinematics of old and young stellar populations in disk galaxies

By means of N-body simulations we investigate the impact of minor mergers on the angular momentum and dynamical properties of the merger remnant. Our simulations cover a range of initial orbital characteristics and gas-to-stellar mass fractions (from 0 to 20%), and include star formation and supernova feedback. We confirm and extend previous results by showing that the specific angular momentum of the stellar component always decreases independently of the orbital parameters or morphology of the satellite, and that the decrease in the rotation velocity of the primary galaxy is accompanied by a change in the anisotropy of the orbits. However, the decrease affects only the old stellar population, and not the new population formed from gas during the merging process. This means that the merging process induces an increasing difference in the rotational support of the old and young stellar components, with the old one lagging with respect to the new. Even if our models are not intended specifically to reproduce the Milky Way and its accretion history, we find that, under certain conditions, the modeled rotational lag found is compatible with that observed in the Milky Way disk, thus indicating that minor mergers can be a viable way to produce it. The lag can increase with the vertical distance from the disk midplane, but only if the satellite is accreted along a direct orbit, and in all cases the main contribution to the lag comes from stars originally in the primary disk rather than from stars in the satellite galaxy. We also discuss the possibility of creating counter-rotating stars in the remnant disk, their fraction as a function of the vertical distance from the galaxy midplane, and the cumulative effect of multiple mergers on their creation.

Unzipping and binding of small interfering RNA with single walled carbon nanotube: A platform for small interfering RNA delivery

In an effort to design efficient platform for siRNA delivery, we combine all atom classical and quantum simulations to study the binding of small interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our results show that siRNA strongly binds to SWCNT surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the SWCNTs. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the SWCNT surface. However, molecular dynamics (MD) simulations of double strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This interesting difference is due to smaller interaction energy of thymidine of dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by dispersion corrected density functional theory (DFT) methods. After the optimal binding of siRNA to SWCNT, the complex is very stable which serves as one of the major mechanisms of siRNA delivery for biomedical applications. Since siRNA has to undergo unwinding process with the effect of RNA-induced silencing complex, our proposed delivery mechanism by SWCNT possesses potential advantages in achieving RNA interference. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3682780]

PAMAM Dendrimer-Drug Interactions: Effect of pH on the Binding and Release Pattern

Understanding the dendrimer-drug interaction is of great importance to design and optimize the dendrimer-based drug delivery system. Using atomistic molecular dynamics (MD) simulations, we have analyzed the release pattern of four ligands (two soluble drugs, namely, salicylic acid (Sal), L-alanine (Ala), and two insoluble drugs, namely, phenylbutazone (Pbz) and primidone (Prim)), which were initially encapsulated inside the ethylenediamine (EDA) cored polyamidoamine (PAMAM) dendrimer using the docking method. We have computed the potential of mean force (PMF) variation with generation 5 (G5)-PAMAM dendrimer complexed with drug molecules using umbrella sampling. From our calculated PMF values, we observe that soluble drugs (Sal and Ala) have lower energy barriers than insoluble drugs (Pbz and Prim). The order of ease of release pattern for these drugs from G5 protonated PAMAM dendrimer was found to be Ala > Sal > Prim > Pbz. In the case of insoluble drugs (Prim and Pbz), because of larger size, we observe much nonpolar contribution, and thus, their larger energy barriers can be reasoned to van der Waals contribution. From the hydrogen bonding analysis of the four PAMAM drug complexes under study, we found intermolecular hydrogen bonding to show less significant contribution to the free energy barrier. Another interesting feature appears while calculating the PMF profile of G5NP (nonprotonated)-PAMAM Pbz and G5NP (nonprotonated)-PAMAM-Sal complex. The PMF was found to be less when the drug is bound to nonprotonated dendrimer compared to the protonated dendrimer. Our results suggest that encapsulation of the drug molecule into the host PAMAM dendrimer should be carried out at higher pH values (near pH 10). When such complex enters the human body, the pH is around 7.4 and at that physiological pH, the dendrimer holds the drug tightly. Hence the release of drug can occur at a controlled rate into the bloodstream. Thus, our findings provide a microscopic picture of the encapsulation and controlled release of drugs in the case of dendrimer-based host-guest systems.

Dielectric properties of DC reactive magnetron sputtered Al2O3 thin films

Alumina (Al2O3) thin films were sputter deposited over well-cleaned glass and Si < 100 > substrates by DC reactive magnetron sputtering under various oxygen gas pressures and sputtering powers. The composition of the films was analyzed by X-ray photoelectron spectroscopy and an optimal O/Al atomic ratio of 1.59 was obtained at a reactive gas pressure of 0.03 Pa and sputtering power of 70 W. X-ray diffraction results revealed that the films were amorphous until 550 degrees C. The surface morphology of the films was studied using scanning electron microscopy and the as-deposited films were found to be smooth. The topography of the as-deposited and annealed films was analyzed by atomic force microscopy and a progressive increase in the rms roughness of the films from 3.2 nm to 4.53 nm was also observed with increase in the annealing temperature. Al-Al2O3-Al thin film capacitors were then fabricated on glass substrates to study the effect of temperature and frequency on the dielectric property of the films. Temperature coefficient of capacitance. AC conductivity and activation energy were determined and the results are discussed. (C) 2011 Elsevier B.V. All rights reserved.

Early protein malnutrition disrupts cerebellar development and impairs motor coordination

Maternal malnutrition affects every aspect of fetal development. The present study asked the question whether a low-protein diet of the mother could result in motor deficits in the offspring. Further, to examine whether cerebellar pathology was correlated with motor deficits, several parameters of the postnatal development of the cerebellum were assayed. This is especially important because the development of the cerebellum is unique in that the time scale of development is protracted compared with that of the cortex or hippocampus. The most important result of the study is that animals born to protein-deficient mothers showed significant delays in motor development as assessed by rotarod and gait analysis. These animals also showed reduced cell proliferation and reduced thickness in the external granular layer. There was a reduction in the number of calbindin-positive Purkinje cells (PC) and granular cells in the internal granular layer. However, glial fibrillary acidic protein-positive population including Bergmann glia remained unaffected. We therefore conclude that the development of the granular cell layer and the PC is specifically prone to the effects of protein malnutrition potentially due to their protracted developmental period from approximately embryonic day 11 to 13 until about the third postnatal week.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. (c) 2012 Wiley Periodicals, Inc.