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Search Results: 1 - 10 of 2754 matches for " Garima Mishra "
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An Introduction to Numerical Methods for the Solutions of Partial Differential Equations  [PDF]
Manoj Kumar, Garima Mishra
Applied Mathematics (AM) , 2011, DOI: 10.4236/am.2011.211186
Abstract: Partial differential equations arise in formulations of problems involving functions of several variables such as the propagation of sound or heat, electrostatics, electrodynamics, fluid flow, and elasticity, etc. The present paper deals with a general introduction and classification of partial differential equations and the numerical methods available in the literature for the solution of partial differential equations.
Force induced stretched state: Effects of temperature
Sanjay Kumar,Garima Mishra
Physics , 2007, DOI: 10.1103/PhysRevE.78.011907
Abstract: A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction co-ordinate) may increase or decrease with the temperature depending upon the applied force. The simple model developed here which incorporates semi-microscopic details of base direction provide an explanation of the force induced transitions in ssDNA as observed in experiments.
Statistical Mechanics of DNA unzipping under periodic force: Scaling behavior of hysteresis loop
Sanjay Kumar,Garima Mishra
Quantitative Biology , 2012, DOI: 10.1103/PhysRevLett.110.258102
Abstract: A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it is possible to bring DNA from the zipped/unzipped state to a new dynamic (hysteretic) state by varying the frequency of the applied force. Our studies reveal that the area of the hystersis loop grows with the same exponents as of the isotropic spin systems. These exponents are amenable to verification in the force spectroscopic experiments.
Drugs impact on CYP-450 enzyme family: A pharmacogenetical study of response variation
Kalra Kapil,Jarmal Garima,Mishra Neeti
Indian Journal of Human Genetics , 2009,
Abstract: Pharmacogenetics is the study of genetic basis in the individual response to drugs. A thorough knowledge of this will lead to a future where tailor-made drugs, suiting an individual, can be used. Scandinavian countries have been known for wide usage of pharmacogenetics and the most widely used application is for genotyping CYP2D6 in treating psychiatric illness. The CYP-450 enzyme, a super family of microsomal drug-metabolizing enzymes, is the most important of enzymes that catalyzes phase-I drug metabolism reaction. CYP2D6 is a member of this family and it has been most intensively studied and the best example of pharmacogenetics variation in drug metabolism. Neuro-transmitter and drug acting CNS viz. codeine, dextromethorphan, metoprolol and tryptyline etc. are well metabolized by this enzyme. Thus, CYP2D6 is one of the most important and responsible enzymes which regulates bioavailability and metabolism of drug. Presently 75 alleles of CYP2D6 have been described which are responsible for variance of metabolism and toxicity of drugs. Thus, by determining variance of CYP2D6 using molecular approaches viz., PCR, real-time PCR, DNA micro-array and molecular docking can determine the adverse effects, drug toxicity, bioavailability and therapeutic potential of new drug.
Stretching of a single-stranded DNA: Evidence for structural transition
Garima Mishra,Debaprasad Giri,Sanjay Kumar
Physics , 2009, DOI: 10.1103/PhysRevE.79.031930
Abstract: Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction co-ordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model, qualitatively reproduces the experimentally observed features. The multi-step plateau in the F-x curve is a signature of structural change in ssDNA.
Scaling of hysteresis loop of interacting polymers under a periodic force
Rakesh Kumar Mishra,Garima Mishra,Debaprasad Giri,Sanjay Kumar
Physics , 2013, DOI: 10.1063/1.4809985
Abstract: Using Langevin Dynamics simulations, we study a simple model of interacting-polymer under a periodic force. The force-extension curve strongly depends on the magnitude of the amplitude $(F)$ and the frequency ($\nu$) of the applied force. In low frequency limit, the system retraces the thermodynamic path. At higher frequencies, response time is greater than the external time scale for change of force, which restrict the biomolecule to explore a smaller region of phase space that results in hysteresis of different shapes and sizes. We show the existence of dynamical transition, where area of hysteresis loop approaches to a large value from nearly zero area with decreasing frequency. The area of hysteresis loop is found to scale as $F^{\alpha} \nu^{\beta}$ for the fixed length. These exponents are found to be the same as of the mean field values for a time dependent hysteretic response to periodic force in case of the isotropic spin.
Effect of shear force on the separation of double stranded DNA
Rakesh Kumar Mishra,Garima Mishra,M. S. Li,Sanjay Kumar
Physics , 2011, DOI: 10.1103/PhysRevE.84.032903
Abstract: Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and approaches to the asymptotic value in accordance with the experiment. The qualitative nature of these curves almost remains same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (back bone) under the shear force.
Role of loop entropy in the force induced melting of DNA hairpin
Garima Mishra,D. Giri,M. S. Li,S. Kumar
Physics , 2010, DOI: 10.1063/1.3609970
Abstract: Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the phase diagram differs significantly with the theoretical prediction.
Dynamical phase transition of a periodically driven DNA
Garima Mishra,Poulomi Sadhukhan,Somendra M Bhattacharjee,Sanjay Kumar
Physics , 2012, DOI: 10.1103/PhysRevE.87.022718
Abstract: Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA under a periodic drive in non-equilibrium conditions are studied. A steady state phase diagram of a driven DNA is proposed which is experimentally verifiable. As a two state system, we also compare the results of DNA with that of an Ising magnet under an asymmetrical variation of magnetic field.
Rapid and accurate detection of Cyanobacterial toxin microcystin-LR using fiber-optic long-period grating based immunosensor
Saurabh Mani Tripathi,Wojtek J. Bock,Predrag Mikulic,Garima Mishra
Physics , 2014,
Abstract: In this paper we present a label-free, stable and highly sensitive fiber-optic sensor for detection of environmental toxin microcystin-LR (MC-LR). Thiolated MC-LR-targeting aptamer covalently immobilized on dual-resonance long-period fiber gratings (DR-LPFG) is used as MC-LR recognition element and the spectral response of the DR-LPFG is monitored for various concentrations of MC-LR. Sensitivity of the DR-LPFG is optimized by coating an appropriate thickness of gold layer to the fiber surface. Gold coating serves two purposes, first it locally supports a surface-Plasmon mode associated with the modified cladding modes and second it helps covalently immobilize the MC-LR targeting aptamer to the sensor surface. Monitoring both the resonance wavelengths of our ultra sensitive DR-LPFGs (3891.5 nm/RIU) we study the aptamer and MC-LR binding to the sensor surface. Real-time, efficient MC-LR molecular binding to the sensor surface is also confirmed using atomic force microscopy. The detection limit of our sensor, limited by the molecule size of MC-LR, its fractional surface coverage of the sensor, and sensor length, is 5 ng/mL, which can be further improved by increasing the fractional MC-LR coverage on the sensor surface by (i) reducing the LPFG length (ii) increasing grating strength, (iii) increasing the LPFG sensitivity by coupling to even higher order cladding modes by reducing the grating period.
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