On the genuine bound states of a non-relativistic particle in a linear finite range potential

We explore the energy spectrum of a non-relativistic particle bound in a linear finite range, attractive potential, envisaged as a quark-confining potential. The intricate transcendental eigenvalue equation is solved numerically to obtain the explicit eigen-energies. The linear potential, which resembles the triangular well, has potential significance in particle physics and exciting applications in electronics.Comment: Latex, 8 pages, 1 Table, 1 Figur

Development of a Laminar Construction Quadrupole Ion Trap

The three-dimensional quadrupole ion trap (QIT) is an extraordinary device. It functions both as an ion store in which gaseous ions can be confined for a period of time and as a mass spectrometer of considerable mass range and variable mass resolution. Over the past few decades, it has evolved into a powerful tool for both research and routine analysis. The basic objective of this thesis is the development of a three-dimensional quadrupole ion trap with cylindrical symmetry in laminar approximation. The laminar construction allows hyperbolic geometry to be well approximated with minimal construction effort and also provides more access into the trap through interlaminar spaces without disruption of the field. The performance of the trap is examined in the mass selective trapping mode and mass-selective instability mode. Fourier detection is also done. Resolution of our instrument is limited by the external hardware. There is not good enough data quality and so not a good enough spectrum to predict its resolution accurately. A few changes to the instrumentation of the trap will improve the resolution

Analysis of nucleosomal DNA patterns around transcription factor binding sites

Nucleosomes are ~147bp DNA wrapped around the histone octamer which are involved in regulating gene transcription. They have the ability to disassemble depending on the process they are involved in and the nucleosome positioning controls the output of the genome. Therefore, it is important to understand the nucleosome positioning and how its positioning affects the binding of transcription factors (TFs) and gene expression thereby regulating the transcription outcome of the genome. Many studies suggest that TFs and nucleosomes compete with each other for genome accessibility. However, the majority of the studies focus on the nucleosome organization rather than underlying DNA sequences and its patterns which might actually be playing an important role in understanding the regulatory role of nucleosomes in gene transcription. This research study focuses on identifying the specific sequence patterns at or around TF binding sites. The study specifically focuses on identifying the fraction of nucleosomes with WW/SS and anti - WW/SS sequence patterns as they might be responsible for maintaining the stability of the nucleosomes. This will provide a new molecular mechanism underlying NDR formation around TF binding sites and pioneer TF-induced chromatin opening

Buttressing a new paradigm in protein folding: experimental tools to distinguish between downhill and multi-state folding mechanisms

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biologíoa Molecular. Fecha de lectura: 15-07-2014Many single-domain proteins fold in milliseconds or longer. However, the advent of fast folding kinetic techniques has permitted to identify many other proteins that fold in the order of (few) microseconds and thus very closely to the folding speed limit. This suggests that the proteins that fold in microsecond timescale either cross a marginal single free energy barrier, multiple very small barriers (multi-state), or no barrier at all (downhill). This results in the potential observation of broad complex unfolding transitions in these ultrafast folding proteins (in contrast to simple two-state behavior). Many of the ultrafast folding proteins have small size and fold into simple alpha helix-bundle topologies. Theoretical studies support the size scaling of protein folding barriers. Engrailed homeodomain, a 61-residue α-helical domain with a helixturn- helix topology folds in microseconds and exhibits an apparently complex (un)folding process. The observed complexity in the (un)folding behavior of engrailed homeodomain rules out a simple two-state model, but the folding mechanism of this protein has been interpreted with a conventional three-state model. The current work aims to develop a set of experimental and analytical methods that can determine unambiguously whether an apparently complex folding process of a fast folding protein is downhill or multi-state using engrailed homeodomain as a model. A large-scale multiple probe approach that combines equilibrium, fast-folding measurement and single molecule measurements has been used to provide critical information to unravel the mechanistic details of the folding mechanism of this protein. Double perturbation measurement on engrailed, in which the protein was unfolded by both chemical denaturant and temperature, showed complex results. Multi-probe equilibrium thermal and chemical unfolding measurements on engrailed revealed differences in the melting temperature and chemical denaturation midpoints respectively. All these signatures conformed to downhill folding mechanism or existence of low-barrier(s). The estimated overall barrier height was ~ 0.5 RT near Tm, by globally fitting the entire equilibrium thermal unfolding data to Mean Field Model. Multi-probe temperature jump studies resulted in single exponential relaxations by infrared and non-exponential relaxations by fluorescence and probe-dependent kinetic amplitudes for the slow rates. This result could still be explained by a downhill behavior by globally fitting both the equilibrium and the kinetic data using the same model. Single molecule FRET measurements explored the transition path of engrailed near Cm and further confirmed the existence of downhill behavior with the estimated marginal barrier of < 1 RT. These results emphasize the importance of multi-probe measurements and appropriate utilization of statistical mechanical for analysis for fast-folding protein

Documentation of Indigenous Knowledge on Folk Medicine in Doddakavalande Doddakavalande Hobli, Nanjangud Taluk of Mysore District, Karnataka

An ethnobotanical survey was conducted to collect information from traditional healers on the use of herbal medicine in Doddakavalande Hobli, Nanjangud taluk of Mysore District. The indigenous knowledge of local healers was documented through questionnaire and personal interviews. In the present study, about 19 respondents of age group between 50 to 89 yrs gave information of traditional medicines used to cure different ailments. Of about 35 plant species belonging to 26 families were used for the treatment of human ailments. In which family Fabaceae and Polygonaceae contained 3 plant species, followed by Acanthaceae, Amaranthaceae, Apocynaceae, Cucurbitaceae, Poaceae contained 2 species each, and the rest of the families Amaryllidaceae, Anacardiaceae, Apiaceae, Aristolochiaceae, Asteraceae, Cleastraceae, Crassulaceae, Lamiaceae, Lecythidaceae,&nbsp; Meliaceae,&nbsp; Olaceae, Phylanthaceae, Piperaceae,&nbsp; Plumbaginaceae, Poaceae, Polygonaceae, Rutaceae,&nbsp; Smilacaceae, Solanaceae,&nbsp; Styracaceae and Zingiberaceae. Habit wise analysis of medicinal plant species used indicated that herbs (19 species) were the most preferred life form followed by trees (8 species), shrubs (5 species) and climbers (3 species) for drug formulation. Herbal formulations were administrated either internally or applied externally depending on the type of ailment. Local people in the study area possess traditional knowledge of medicinal plants to treat various human ailments, therefore it is necessary to preserve the indigenous knowledge on traditional medicines by proper documentation, identification of plant species used, and herbal preparation. Keywords: Ethnobotany, Traditional knowledge, Medicinal plants, Mysore district