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Homology modeling and ligand interaction of human trafficking protein particle complex subunit 3-like protein and its correlation with Alzheimer’s disease
Venkata Sri Krishna K,Uday Kiran M,Siva Rama Prasad D,Anusha G
Journal of Medical and Allied Sciences , 2011,
Abstract: In order to understand the mechanism of molecular interactions at active sites of trafficking protein particle complex (TRAPPC) subunit 3-like protein (Accession number Q5T215) homology modeling and docking studies were taken up. We generated a three-dimensional (3D) model of target protein based on the Crystal structure of Human BET3 protein (PDB code 1SZ7) using modeller software. Under the process of homology modeling 25 models were generated, and the model having the lowest modeler objective function value was chosen for further assessment. The generated model was assessed and validated using PROCHECK software and found to be reliable.With the generated model, we carried out a flexible docking study using the FlexX docking tool available on the Sybyl Software in order to find better antagonist site for drug binding. We carried out a flexible docking with the Palmatic acid and Donepezil as ligands; these were found to bind at LEU87, LYS84 and THR90 residues on given generated protein in our studies. We therefore concluded that the above mentioned residues were the key residue sites for ligand binding showing strong hydrogen bonding contacts.The target protein is more prevalently seen in the amygdala region of brain which forms one of the key subunit of TRAPP complex. As per functional similarity with BET3, target protein might play key role in trafficking abnormally folded A-beta and tau proteins along endoplasmic reticulum to Golgi apparatus there by leading to formation of senile plaques in various regions of brain, whose accumulation causes Alzheimer’s disease.
A Review of Epilepsy Diagnosis Using PET Parameters  [PDF]
Yadalam Kiran Kumar, Shashi Bhushan Mehta, Uday Patil
Journal of Behavioral and Brain Science (JBBS) , 2012, DOI: 10.4236/jbbs.2012.23049
Abstract: Epilepsy is caused by abnormal excessive electric discharges from the neurons in the brain. Epileptic seizures are non- specific responses of the brain to many types of insults. The structural abnormalities causing epilepsy can be identified using various state of art imaging methods. Through a combination of brain activity monitoring, imaging and mapping techniques, physicians can locate the specific area in the brain causing epileptic discharges and identify its location in relation to those areas in the brain controlling vital functions. Positron Emission Tomography (PET) has emerged as a useful tool to identify abnormal metabolic activity of the epileptogenic foci. Parameters like asymmetric index, stan- dard uptake value (SUV) etc obtained by PET are processed and analyzed for identifying the origin of epileptic sei- zures. This paper discuss the techniques used to diagnose in general and to localize the epileptogenic regions using post-processing other features on PET imaging.
Entromics -- thermodynamics of sequence dependent base incorporation into DNA reveals novel long-distance genome organization
Petr Pancoska,Zdenek Moravek,Uday Kiran Para,Jaroslav Nesetril
Quantitative Biology , 2012,
Abstract: Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously uncharacterized physical property of DNA, the incorporation reaction chemical potential {\Delta}{\mu}. We use the combination of graph theory and statistical thermodynamics to derive entromics - a series of results providing the thermodynamic model of {\Delta}{\mu}. We also show that {\Delta}{\mu}i is quantitatively characterized as incorporation entropy. We present formulae for computing {\Delta}{\mu} from the genome DNA sequence. We then derive important restrictions on DNA properties and genome assembly that follow from thermodynamic properties of {\Delta}{\mu}. Finally, we show how these genome assembly restrictions lead directly to the evolution of detectable coherences in incorporation entropy along the entire genome. Examples of entromic applications, demonstrating functional and biological importance are shown.
Effect of Losartan and Ramipril on Oxidative stress and Anti-oxidant Status in South Indian Hypertensive Patients
V. Uday Kiran,N. Venkat Rajaiah,D. Rama Krishna,Y. Narsimha Reddy
International Journal of Pharmacology , 2010,
Abstract: Over production of oxygen free radicals, which is mainly mediated by super oxide, occurs in human hypertension. Ramipril and losartan are the drugs which found to be more prescribed drugs for hypertension patients. In the present study, an attempt has been made to evaluate the levels of serum Glutathione, Total anti-oxidant status, lipid peroxidation (malondialdehide) and liver function parameters like serum glutamate oxaloacetate transaminase and serum glutamate pyruvate transaminase. Total 75 subjects were selected for study. Out of 75 subjects 25 were normal healthy volunteers and 50 subjects were patients who are untreated with hypertension. The patients both male and female within the age group of 25-65 years were selected. Glutathione, total anti oxidant status, lipid peroxidation, serum glutamate oxaloacetate transaminase and serum glutamate pyruvate transaminase levels in plasma were estimated by using reported methods. Individual methods were standardized first and standard graphs were plotted and the parameters were measured significantly decreased values of glutathione, total anti oxidant status and malondialdehide were observed (p<0.001) in untreated hypertension patients as compared with normal healthy volunteers. After therapy there was significant (p<0.001) increase in the glutathione, total oxidant status and malondialdehide as compared with untreated patients. The results indicates that further extensive studies are required to understand the molecular level mechanism of losartan and ramipril in oxidative stress in hypertensive patients.
Studies of fractal structures and processes using methods of fractional calculus
Kiran M. Kolwankar
Physics , 1998,
Abstract: The thesis deals with applications of fractional calculus to fractals. It introduces the notion of local fractional derivative (LFD). Fractal and multifractal functions have been studied in the thesis using LFD. New kind of equations are introduced which involve LFD and one example, local fractional Fokker-Planck equation, is studied in detail.
Recursive Local Fractional Derivative
Kiran M. Kolwankar
Physics , 2013,
Abstract: The definition of the local fractional derivative has been generalised to the orders beyond the critical order. This makes it possible to retain more terms in the local fractional Taylor expansion leading to better approximation. This also extends the validity of the product rule.
Brownian motion of fractal particles: Levy flights from white noise
Kiran M. Kolwankar
Physics , 2005,
Abstract: We generalise the Langevin equation with Gaussian white noise by replacing the velocity term by a local fractional derivative. The solution of this equation is a Levy process. We further consider the Brownian motion of a fractal particle, for example, a colloidal aggregate or a biological molecule and argue that it leads to a Levy flight. This effect can also be described using the local fractional Langevin equation. The implications of this development to other complex data series are discussed.
Local Fractional Calculus: a Review
Kiran M. Kolwankar
Physics , 2013,
Abstract: The purpose of this article is to review the developments related to the notion of local fractional derivative introduced in 1996. We consider its definition, properties, implications and possible applications. This involves the local fractional Taylor expansion, Leibnitz rule, chain rule, etc. Among applications we consider the local fractional diffusion equation for fractal time processes and the relation between stress and strain for fractal media. Finally, we indicate a stochastic version of local fractional differential equation.
Separable local fractional differential equations
Kiran M. Kolwankar
Mathematics , 2015,
Abstract: The concept of local fractional derivative was introduced in order to be able to study the local scaling behavior of functions. However it has turned out to be much more useful. It was found that simple equations involving these operators naturally incorporate the fractal sets into the equations. Here, the scope of these equations has been extended further by considering different possibilities for the known function. We have also studied a separable local fractional differential equation along with its method of solution.
Nano-Sim: A Step Wise Equivalent Conductance based Statistical Simulator for Nanotechnology Circuit Design
Bharat Sukhwani,Uday Padmanabhan,Janet M. Wang
Computer Science , 2007, DOI: 10.1109/DATE.2005.221
Abstract: New nanotechnology based devices are replacing CMOS devices to overcome CMOS technology's scaling limitations. However, many such devices exhibit non-monotonic I-V characteristics and uncertain properties which lead to the negative differential resistance (NDR) problem and the chaotic performance. This paper proposes a new circuit simulation approach that can effectively simulate nanotechnology devices with uncertain input sources and negative differential resistance (NDR) problem. The experimental results show a 20-30 times speedup comparing with existing simulators.
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