Abstract

Autism and dyslexia are both developmental disorders of neural origin. As we still do not understand the neural basis of these disorders fully, technology can take two approaches in helping those affected. The first is to compensate externally for a known difficulty and the other is to achieve the same function using a completely different means. To demonstrate the first option, we are developing a system to compensate for the auditory processing difficulties in case of dyslexia and to demonstrate the second option we propose a system for autism where we remove the need for traditional languages and instead use pictures for communication.

Abstract

Automatic object extraction from urban areas using high resolution satellite images remains an open research area. High variability in object features like color, shape and scale makes the urban scene classification challenging. Though significant amount of work has been done on detecting buildings, roads and other objects individually, not much work is present for complete urban scene classification. This paper proposes an algorithm that makes use of color as an important cue along with geometry and shadow information for complete urban scene classification.

Abstract

We solve instances of a general class of problems de- ned as follows: Preprocess a set S of possibly weighted colored geometric objects (e.g. points/orthogonal seg- ments/rectangles) in Rd, d  1 such that given a query orthogonal range q, we can report eciently for each dis- tinct color c of the points in S \q, the tuple < c;F(c) > where F(c) is a function (e.g. weighted sum, bounding box etc.) of the objects of color c in q.

Abstract

Water bodies, the aquatic systems on land, are one of the important store houses for variety of wildlife as well as nesting and breeding sites for different kind of avifauna. Currently these water bodies are under tremendous human pressure due to rapid urbanization. The lakes and reservoirs, across the country, are in varying degrees of environmental degradation due to various anthropogenic activities. In this context a study was carried out in and around the city, covering an area of about 7800 km2 to identify the impact of expanding urbanization process on water bodies of the Hyderabad city using 1989 and 2001 satellite data. The results of the study showed reduction in water bodies both in the area (19%) as well as in number. A negative change was observed in the status of water bodies towards NE and NW directions of the city. Most of the water bodies either were encroached by urban expansion or reduced in size due to eutrophication process. The expanding IT sector and developments in real estate, acted as major driving forces that converted agricultural lands into residential plots and there by exerting pressure on the nearby water bodies. The change study here provides us with vital clues towards understanding the change in water bodies’ vis-à-vis the urban needs, economic growth, and its location characteristics within a rapidly urbanization region.

Abstract

Forests are depleted drastically at higher rates to cope up the needs of increasing population. The present study was carried out to assess the impact of anthropogenic and natural disturbances (tsunami) on the vegetation of North Andaman islands using three different satellite images of different time period by visual image interpretation technique. A higher proportion of land cover and vegetation converted into agriculture, settlement, sand and water. Assessment of overall forest change from 1976 to 2005 is 117 Km 2 , with forest loss at the rate of 3.8 Km 2 / year. Simulation study for future forest scenario predicted an increase in agriculture / settlement area to be 196, 296, 392 and 492 Km 2 for the next 25, 50, 75 and 100 years, coupled with the conversion of forest areas of 131, 227, 320 and 427 Km 2 . Finally by the end of 100 years the estimated forest area of 1271 Km 2 (1999 data) reduces to 846 Km 2 if proper conservative actions are not taken.

Abstract

Macrocyclic trienes are important precursors for the synthesis of several biologically relevant molecules such as steroids. These molecules undergo (4+2) cycloaddition to form tricyclic compounds, which has four newly formed stereocenters. The stereochemistry at these four carbon centers has been shown to be largely controlled by the reaction energy barriers, and the conformational preferences of the macrocycle. Molecular dynamics (MD) simulation is a highly efficient approach for studying conformational properties of chemical molecules and biological macromolecules. MP2/6-31G* method was used to obtain potential energy surfaces corresponding to appropriate model compounds and used as the target data. The force field parameters were refined to accurately represent the target data involving all the model compounds chosen. Using the refined molecular mechanics force field, MD simulations were performed on six possible 14-membered symmetric trienes at different temperatures. We have also used replica exchange MD (RexMD) simulations with eight replicas between 300 and 370 K. The molecules were found to sample a larger conformational space in the RexMD simulation compared to the regular MD simulations. The probability distributions corresponding to the dihedral angles, and distances between the reaction centers have been analyzed. The relationship between the conformational sampling of the macrocyclic trienes vis-à-vis their reactivity will be discussed. Additionally, clustering of the structures from the MD trajectories was done to identify all unique conformations using a new approach.

Abstract

Sac7d is a protein present in Sulfolobus acidocaldarius, a hyperthermophilic archaeon, which is stable at extreme conditions. It is a chromosomal protein, which is capable of binding DNA thereby increasing its melting temperature. It was suggested to stabilize central 3 to 5 base pair steps in DNA. It binds to the minor groove of the DNA causing a kink in the helix without any sequential preference. We have used molecular dynamics (MD) simulations to study the binary complexes of Sac7d bound to DNA at 300 and 360 K. The objective is to understand the atomic detailed mechanism of the capability of Sac7d in facilitating DNA stability at higher temperature. As has been shown before, the structure of the protein is highly stable both at 300 and 360 K. The DNA duplex was found to be stable at 300 K and is similar to the X-ray crystal structure. Consistent with experiments, at least the central four base pairs of the DNA were found to be base paired during most of the simulation at 360 K. The dynamic properties of the protein in the protein-DNA complexes remained unchanged compared to when the protein is unbound. Interestingly, B- to A-form transitions occur in both the DNA molecules when bound to Sac7d, which was confirmed by sugar puckering angles, and backbone dihedral angles. Detailed examination of the protein-DNA interactions reveals that the stabilization of the DNA molecules is mostly due to the favorable interaction of the protein with the backbone of the DNA.

Abstract

Base flipping is a process by which one of the bases of the DNA swings out from its helical position to an extrahelical form. Several proteins such as methyltransferases, glycosylases and endonucleases employ this phenomenon in order to gain access to the target base for chemical modification. Even in the absence of protein, base pair opening occurs in nucleic acids in solution. X-ray crystal studies, fluorescence spectroscopy and NMR imino proton exchange experiments have been extensively employed to study the structures and dynamics involved in this fascinating event. We have employed molecular dynamics simulations to study base flipping both in presence and absence of the protein. The free energy pathways obtained using potential of mean force calculations will be presented. The base pair opening dynamics of AT and GC base pairs was investigated by calculating the equilibrium constants corresponding to the equilibrium between the base pair open and closed states, and compared with experimental data. Our calculations showed that the contribution to the overall equilibrium constants of the base pair opening is primarily from the purine bases. The methodological issues such as sufficient sampling and force field parameters will be addressed. In another study, the role of THR250 HhaI methyltransferase in base flipping will be discussed. THR250 is a highly conserved residue in methyltransferases and was proposed to be crucial for the correct placement of flipped cytosine for methylation. Previous computational studies have shown that the protein actively facilitates the base flipping process. Free energy calculations of base flipping in the presence of the wild type and T250G, T250A and T250D mutants of the protein were computed. The free energy profiles, structural changes and the energetic parameters for the base flipping process will be presented.

Abstract

Urea concentration dependent denaturation of proteins and nucleic acids has been widely used in obtaining (un)folding pathways and in calculating the free energies. Molecular dynamics simulations were performed on a 22-nt RNA hairpin in aqueous solution environment and in different concentrations (1-8M) of urea. The energetic and structural aspects of the role of urea in denaturating the RNA hairpin were investigated. In agreement with experimental studies, the RNA undergoes denaturation at higher concentrations of urea (> 6M). Surprisingly, the hairpin was observed to be more stable at lower concentrations of urea (1-2M) even compared to the RNA in aqueous environment. Various structural, energetic and solvation properties were analyzed to understand the mechanism of the interaction of urea with the hairpin. It was observed that urea does not directly facilitate the opening of the base pairs that leads to denaturation at higher concentrations. Instead, the open states of the RNA are stabilized by via hydrogen bonding interactions and stacking interactions thereby stabilizing the denatured form of the RNA.

Abstract

Transannular Diels-Alder reaction (TADA) combines traditional pericyclic and intramolecular reactions, and has been shown to be one of the most efficient chemical transformations for synthesizing complicated natural products. TADA reactions occur in (x+y+2)-membered triene macrocycles, which contain both the diene and the dienophile, to form A.B.C[x.6.y] type tricyclic compounds. In addition, these macrocycles were shown to interconvert among its isomers via [1,5]-sigmatropic hydrogen shifts. The stereochemical outcome of the TADA reactions depends on the energetics of various possible transition states. Initially, a validation study was undertaken to assess the performance of various ab initio (HF, MPx, and CC) and hybrid density functional B3LYP methods using a variety of basis sets. Comparison of the reaction barriers, and reaction energies from various methods indicate that B3LYP/6-31G* level is appropriate enough for accurately modeling this class of reactions. All possible reaction pathways involving the TADA and 1,5-sigmatropic reactions of six different 14-membered triene molecules were studied using B3LYP/cc-pVTZ were calculated. Based on the reaction energy barriers and conformational properties of the reactants, the reactivities of these molecules will be discussed.