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Search Results: 1 - 10 of 172 matches for " Bodhaditya Santra "
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Scanning electron microscopy of cold gases
Bodhaditya Santra,Herwig Ott
Physics , 2015, DOI: 10.1088/0953-4075/48/12/122001
Abstract: Ultracold quantum gases offer unique possibilities to study interacting many-body quantum systems. Probing and manipulating such systems with ever increasing degree of control requires novel experimental techniques. Scanning electron microscopy is a high resolution technique which can be used for in situ imaging, single site addressing in optical lattices and precision density engineering. Here, we review recent advances and achievements obtained with this technique and discuss future perspectives.
Negative differential conductivity in an interacting quantum gas
Ralf Labouvie,Bodhaditya Santra,Simon Heun,Sandro Wimberger,Herwig Ott
Physics , 2014, DOI: 10.1103/PhysRevLett.115.050601
Abstract: Negative differential conductivity (NDC) is a widely exploited effect in modern electronic components. Here, a proof-of-principle is given for the observation of NDC in a quantum transport device for neutral atoms employing a multi-mode tunneling junction. The transport of the many-body quantum system is governed by the interplay between the tunnel coupling, the interaction energy and the thermodynamics of intrinsic collisions, which turn the coherent coupling into a hopping process. The resulting current voltage characteristics exhibit NDC, for which we identify a new microscopic physical mechanism. Our study opens new ways for the future implementation and control of complex neutral atom quantum circuits.
Non-equilibrium steady-states in a driven-dissipative superfluid
Ralf Labouvie,Bodhaditya Santra,Simon Heun,Herwig Ott
Physics , 2015,
Abstract: We experimentally study a driven-dissipative Josephson junction array, realized with a weakly interacting Bose Einstein condensate residing in a one-dimensional optical lattice. Engineered losses on one site act as a local dissipative process, while tunneling from the neighboring sites constitutes the driving force. We characterize the emerging steady-states of this atomtronic device. With increasing dissipation strength $\gamma$ the system crosses from a superfluid state, characterized by a coherent Josephson current into the lossy site to a resistive state, characterized by an incoherent hopping transport. For intermediate values of $\gamma$, the system exhibits bistability, where a superfluid and a resistive branch coexist. We also study the relaxation dynamics towards the steady-state, where we find a critical slowing down, indicating the presence of a non-equilibrium phase transition.
Effect of Cold-Mediated Pretreatment on Microspore Culture in Winter and Spring Wheat  [PDF]
Rituraj Khound, Meenakshi Santra, P. Stephen Baenziger, Dipak K. Santra
American Journal of Plant Sciences (AJPS) , 2013, DOI: 10.4236/ajps.2013.411278

Microspore culture of wheat generates completely homozygous (doubled haploid) plants in a single generation thereby reducing the time required for wheat variety development. Success of microspore culture in spring wheat is relatively higher than that in winter wheat. Cold mediated pretreatment was reported to improve response of microspore culture in wheat. The objective of the study was to determine and compare the influence of cold pretreatment on microspore culture in spring and winter wheat. Three spring (Chris, Express, and Macon) and three winter (Anton, Antelope, and Camelot) wheat cultivars were used. In cold pretreatment, excised anthers were incubated in solution B at 25°C-28°C for 4-5 days followed by cold treatment at 4°C for 5 days and were compared

A Bayesian Framework That Integrates Heterogeneous Data for Inferring Gene Regulatory Networks
Tapesh Santra
Frontiers in Bioengineering and Biotechnology , 2014, DOI: 10.3389/fbioe.2014.00013
Abstract: Reconstruction of gene regulatory networks (GRNs) from experimental data is a fundamental challenge in systems biology. A number of computational approaches have been developed to infer GRNs from mRNA expression profiles. However, expression profiles alone are proving to be insufficient for inferring GRN topologies with reasonable accuracy. Recently, it has been shown that integration of external data sources (such as gene and protein sequence information, gene ontology data, protein–protein interactions) with mRNA expression profiles may increase the reliability of the inference process. Here, I propose a new approach that incorporates transcription factor binding sites (TFBS) and physical protein interactions (PPI) among transcription factors (TFs) in a Bayesian variable selection (BVS) algorithm which can infer GRNs from mRNA expression profiles subjected to genetic perturbations. Using real experimental data, I show that the integration of TFBS and PPI data with mRNA expression profiles leads to significantly more accurate networks than those inferred from expression profiles alone. Additionally, the performance of the proposed algorithm is compared with a series of least absolute shrinkage and selection operator (LASSO) regression-based network inference methods that can also incorporate prior knowledge in the inference framework. The results of this comparison suggest that BVS can outperform LASSO regression-based method in some circumstances.
Modelling the Biomass Growth and Enzyme Secretion by the White Rot Fungus Phanerochaete Chrysosporium in Presence of A Toxic Pollutant  [PDF]
Kausik Sen, Kannan Pakshirajan, Sitangshu Bikas Santra
Journal of Environmental Protection (JEP) , 2012, DOI: 10.4236/jep.2012.31014
Abstract: The white rot fungus Phanerochaete chrysosporium is well known for its ability to degrade toxic pollutants owing to its efficient extracellular ligninase system. However, biomass growth and enzyme secretion in presence of toxic pollutant is not well understood. In the present study, using the model azo dye Direct Red-80, biomass growth and lignin peroxidase secretion by the fungus was studied during its degradation and a stochastic based model was applied to simulate the behavior of the fungus. Also, glucose concentration in the medium was varied in order to observe its effect on the dye degradation. Results revealed that glucose at an optimum concentration of 10 gL-1 is essential for biomass growth, LiP secretion, as well as the dye decolourization. Modeling the behavior of the fungus with the presence of both glucose and dye has shown significant similarity.
Adopsi Model Competency Based Training dalam Kewirausahaan
I Ketut Santra
Jurnal Manajemen dan Kewirausahaan , 2009,
Abstract: The aim of the research is improving the teaching method in entrepreneurship subject. This research adopted the competency based training (CBT) into the entrepreneurship. The major task in this research is formulated and designed the entrepreneurship competency. Entrepreneurship competency indicated by Personal, Strategic and Situational and Business competence. All of entrepreneurship competences are described into sub topic of competence. After designing and formulating the game and simulation the research continuing to implement the competency based training in the real class. The time consumed to implementing the CBT one semester, starting on September 2006 to early February 2007. The lesson learnt from the implementation period, the CBT could improve the student competence in Personal, Situational Strategic and Business. The three of the competencies are important for the success entrepreneur. It is a sign of application of “Kurikulum Berbasis Kompetensi”. There are many evidences to describe the achievement of the CBT in entrepreneurship subject. Firstly, physically achievement, that all of the student’s business plan could became the real business. The evidences are presented by picture of the student’s real business. Secondly theoretically achievement, that the Personal, Situational Strategic and Business competence statistically have significant relation with Business Plan even Real Business quality. The effect of the Personal, Situational Strategic and Business competence to Business Plan quality is 84.4%. and, to the Real Business quality 77.2%. The statistic’s evidence suggests that the redesign of the entrepreneurship subject is the right way. The content of the entrepreneur competence (Personal, Situational and Strategic and Business competence) have impact to the student to conduct and running for own business.
Kinetic Proofreading at Single Molecular Level: Aminoacylation of tRNAIle and the Role of Water as an Editor
Mantu Santra, Biman Bagchi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0066112
Abstract: Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNAIle which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case, respectively), in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i) the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8×102).(4.33×102) = 7.8×104, (ii) the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNAIle. The present study shows a non-michaelis type dependence of rate of reaction on tRNAIle concentration in case of valine. The overall editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNAIle whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low. We find that the presence of additional editing domain in class I editing enzyme makes the kinetic proofreading more efficient through enhanced hydrolysis of wrong product at the editing CP1 domain.
Morphology-Controlled Synthesis and Characterization of Magnetic Iron Oxide Nanocrystals and Their Potential Applications in Selective Oxidation of Alcohols and Olefins
Subhash Banerjee,Swadeshmukul Santra
Journal of Catalysts , 2013, DOI: 10.1155/2013/910489
Abstract: A protocol for the preparation of iron oxide nanocrystals of two different (nanorods and octahedrons) morphologies has been developed and the synthesized nanocrystals were well characterized by TEM and XRD. These two nanocrystals have been applied for the selectivie oxidation of aryl-methanol and vinyl-arene. Moreover, the magnetic catalysts have easily separated from reaction mixture by a magnet and are reused without appreciable loss of catalytic activity. The oxidation processes avoid the use of toxic catalysts and volatile and hazardous organic solvents. 1. Introduction Selective oxidations of aryl-methanol and vinyl-arene to aryl-aldehyde are synthetically important because of the wide applications of these products in organic reactions and also it is difficult to control the further oxidation to acid. Traditionally, oxidation of benzyl alcohol to benzaldehyde is performed with many oxidizing agents and was used in stoichiometric amount [1–3]. These oxidants are generally expensive in nature and most importantly they generate toxic heavy-metal waste and were performed in hazardous chlorinated solvents. In recent years, the oxidation reactions using hydrogen peroxide (H2O2) as reagent in combination of a catalyst has attracted much attention because H2O2 is very mild in nature, inexpensive, and produce only water as product [4–6]. For this reason, a number of methodologies have been developed for oxidation of alcohols using H2O2 as oxidant and various metal as catalyst [7–18]. Thus, there is a thrust in search for new green catalysts. Very recently, various nano-particles such as NiO2 NPs [19] and metal-oxide-supported nanogold [20] also applied as catalyst for the benzylic oxidation. Iron-based catalysts have been extensively used because they are easily accessible, inexpensive, environmentally benign, and relatively nontoxic in comparison with other transition metals. Different iron (II) [21–23] and iron (III) compounds [24–28] have been used as for the oxidation reactions. Herein, we report the synthesis and characterization of iron oxide nanomaterials of two different morphologies (namely, nanorod and octahedron) and their successful applications in the selective oxidation of aryl-methanol and vinyl-arene with H2O2 under organic solvent-free condition. 2. Results and Discussions At first, we have synthesized both the iron oxide nanorods and octahedrons using hydrogen peroxide by solvothermal technique. In a simple experimental procedure, a mixture of FeCl3 and FeCl2 was used in equimolar ratios as the precursor. Ethylenediamine and water were
Theory of x-ray absorption by laser-dressed atoms
Christian Buth,Robin Santra
Physics , 2006, DOI: 10.1103/PhysRevA.75.033412
Abstract: An ab initio theory is devised for the x-ray photoabsorption cross section of atoms in the field of a moderately intense optical laser (800nm, 10^13 W/cm^2). The laser dresses the core-excited atomic states, which introduces a dependence of the cross section on the angle between the polarization vectors of the two linearly polarized radiation sources. We use the Hartree-Fock-Slater approximation to describe the atomic many-particle problem in conjunction with a nonrelativistic quantum-electrodynamic approach to treat the photon-electron interaction. The continuum wave functions of ejected electrons are treated with a complex absorbing potential that is derived from smooth exterior complex scaling. The solution to the two-color (x-ray plus laser) problem is discussed in terms of a direct diagonalization of the complex symmetric matrix representation of the Hamiltonian. Alternative treatments with time-independent and time-dependent non-Hermitian perturbation theories are presented that exploit the weak interaction strength between x rays and atoms. We apply the theory to study the photoabsorption cross section of krypton atoms near the K edge. A pronounced modification of the cross section is found in the presence of the optical laser.
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