Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach

We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic Gillespie scheme with the denaturation zones in double stranded DNA studied as a single molecule time series. Simulated Annealing is used to find the optimum value of the activation energy for which the equilibrium bubble size distribution matches with a given value. It is demonstrated that the method overcomes even large noise in the input surrogate data.Comment: 9 pages, 4 figures, iop article package include

Ultra-relativistic oscillon collisions

In this short note we investigate the ultra-relativistic collisions of small amplitude oscillons in 1+1 dimensions. Using the amplitude of the oscillons and the inverse relativistic boost factor $\gamma^{-1}$ as the perturbation variables, we analytically calculate the leading order spatial and temporal phase shifts, and the change in the amplitude of the oscillons after the collisions. At leading order, we find that only the temporal phase shift receives a nonzero contribution, and that the collision is elastic. This work is also the first application of the general kinematic framework for understanding ultra-relativistic collisions (arXiv:1308.0606) to intrinsically time-dependent solitons.Comment: 12 pages, 3 figures, version 2, added one reference and matching the version to appear on PR

Optimal operating conditions and characteristics of acetone/CaF_2 detector for inverse photoemission spectroscopy

Performance and characteristics of a band-pass photon detector using acetone gas and CaF_2 window (acetone/CaF_2) have been studied and compared with an ethanol/MgF_2 detector. The optimal operating conditions are found to be 4 mbar acetone pressure and 745+/-20 V anode voltage. The count rate obtained by us is about a factor of 3 higher than what has been reported earlier for the acetone detector. Unlike other gas filled detectors, this detector works in the proportional region with very small dead time (4 micro sec). A detector band-pass of 0.48+/-0.01 eV FWHM is obtained.Comment: Review of Scientific Instruments 76, 066102 (2005

Photogrammetry-Based Analysis of the On-Orbit Structural Dynamics of the Roll-Out Solar Array

The Roll-Out Solar Array (ROSA) flight experiment was launched to the International Space Station (ISS) on June 3rd, 2017. ROSA is an innovative, lightweight solar array with a flexible substrate that makes use of the stored strain energy in its composite structural members to provide deployment without the use of motors. This paper will discuss the results of various structural dynamics experiments conducted on the ISS during the weeks following launch. Data gathered from instrumentation on the solar array wing during the experiments was previously compared with pre-flight predictions from two different Finite Element Modeling (FEM) efforts. In this paper, data generated from photogrammetry is compared with accelerometer data and used to extend previous conclusions. Whereas previous analyses were only able to track the accelerations of six discrete points on the structure and photovoltaic (PV) blanket of ROSA, the photogrammetry analysis makes available displacements for dozens of points distributed throughout the array. This larger data set makes it possible to compare higher-order PV blanket modes with FEM predictions, in addition to verifying conclusions reached using accelerometer data. The goal in this effort was to better understand the performance of ROSA and to improve modeling efforts for future designs of similar solar arrays

Structural Analysis Methods for the Roll-Out Solar Array Flight Experiment

The Roll-Out Solar Array (ROSA) flight experiment was launched to the International Space Station (ISS) on June 3rd, 2017. ROSA is an innovative, lightweight solar array with a flexible substrate that makes use of the stored strain energy in its composite structural members to provide deployment without the use of motors. This paper discusses the effort to model the structural dynamics of ROSA using finite element modeling. Two distinct and agnostic approaches were used by separate teams to assess the structural dynamics of the solar array prior to ground vibrational testing and flight testing. Results from each approach are compared to measured dynamics from accelerometers and photogrammetry data gathered on orbit. Advantages and disadvantages of each approach are discussed as are preliminary efforts to calibrate the models to the empirical data for the benefit of future modeling efforts on similar space structures

Observation and analysis of Fano-like lineshapes in the Raman spectra of molecules adsorbed at metal interfaces

Surface enhanced Raman spectra from molecules (bipyridyl ethylene) adsorbed on gold dumbells are observed to become increasingly asymmetric (Fano-like) at higher incident light intensity. The electronic temperature (inferred from the anti-Stokes (AS) electronic Raman signal increases at the same time while no vibrational AS scattering is seen. These observations are analyzed by assuming that the molecule-metal coupling contains an intensity dependent contribution (resulting from light-induced charge transfer transitions as well as renormalization of the molecule metal tunneling barrier). We find that interference between vibrational and electronic inelastic scattering routes is possible in the presence of strong enough electron-vibrational coupling and can in principle lead to the observed Fano-like feature in the Raman scattering profile. However the best fit to the observed results, including the dependence on incident light intensity and the associated thermal response is obtained from a model that disregards this coupling and accounts for the structure of the continuous electronic component of the Raman scattering signal. The temperatures inferred from the Raman signal are argued to be only of qualitative value.Comment: 20 pages, 12 figure

Diazotrophic activity and ferric phosphate mineralizing ability in estuarine sulfate reducing bacteria

Twenty strainsofsulfate reducing bacteria were isolated from water and sediments of Cochin backwaters, India. Five of them were identified as Desulfovibrio desulfuricans and fifteen as Desulfotomaculum orientis. All the Desulfovibrio were isolated from sediments whereas Desulfotomaculum was present in both water and sediment. All the bacteria grew at pH of slightly alkaline reaction and lowered the Eh from -105 to - 270 m V of the growth medium. Complete reduction of sulfate to sulfide by the bacteria was evidenced by blackening of Post gate culture media. All isolates were able to fix dinitrogen in anaerobic N-free modified Postgate broth. In addition to nitrogen fixing ability, 5 of the Desulfotomaculum and 3 of the Desulfovibrio were able to produce soluble phosphorus in growth medium from insoluble FePO4. A scheme for FePO4 mineralization in marine and estuarine sediments has been proposed

Chitinolytic bacteria in Penaeus indicus

Quantitative distribution of chitinolytic bacteria from the hepatopancreas, stomach and intestine of a commercially important marine prawn Penaeus indicus was studied. Twenlyfive representative bacteria were isolated from colonies forming well defined clear zones on chitin agar medium and were identified. Eighteen of the isolates were members of the genus Vibrio and the rest were members of the genus Pseudomonas

Epitaxial Electrodeposition Of Ordered Inorganic Materials

Conspectus The quality of technological materials generally improves as the crystallographic order is increased. This is particularly true in semiconductor materials, as evidenced by the huge impact that bulk single crystals of silicon have had on electronics. Another approach to producing highly ordered materials is the epitaxial growth of crystals on a single-crystal surface that determines their orientation. Epitaxy can be used to produce films and nanostructures of materials with a level of perfection that approaches that of single crystals. It may be used to produce materials that cannot be grown as large single crystals due to either economic or technical constraints. Epitaxial growth is typically limited to ultrahigh vacuum (UHV) techniques such as molecular beam epitaxy and other vapor deposition methods. In this Account, we will discuss the use of electrodeposition to produce epitaxial films of inorganic materials in aqueous solution under ambient conditions. In addition to lower capital costs than UHV deposition, electrodeposition offers additional levels of control due to solution additives that may adsorb on the surface, solution pH, and, especially, the applied overpotential. We show, for instance, that chiral morphologies of the achiral materials CuO and calcite can be produced by electrodepositing the materials in the presence of chiral agents such as tartaric acid. Inorganic compound materials are electrodeposited by an electrochemical-chemical mechanism in which solution precursors are electrochemically oxidized or reduced in the presence of molecules or ions that react with the redox product to form an insoluble species that deposits on the electrode surface. We present examples of reaction schemes for the electrodeposition of transparent hole conductors such as CuI and CuSCN, the magnetic material Fe3O4, oxygen evolution catalysts such as Co(OH)2, CoOOH, and Co3O4, and the n-type semiconducting oxide ZnO. These materials can all be electrodeposited as epitaxial films or nanostructures onto single-crystal surfaces. Examples of epitaxial growth are given for the growth of films of CuI(111) on Si(111) and nanowires of CuSCN(001) on Au(111). Both are large mismatch systems, and the epitaxy is explained by invoking coincidence site lattices in which x unit meshes of the film overlap with y unit meshes of the substrate. We also discuss the epitaxial lift-off of single-crystal-like foils of metals such as Au(111) and Cu(100) that can be used as flexible substrates for the epitaxial growth of semiconductors. The metals are grown on a Si wafer with a sacrificial SiOx interlayer that can be removed by chemical etching. The goal is to move beyond the planar structure of conventional Si-based chips to produce flexible electronic devices such as wearable solar cells, sensors, and flexible displays. A scheme is shown for the epitaxial lift-off of wafer-scale foils of the transparent hole conductor CuSCN. Finally, we offer some perspectives on possible future work in this area. One question we have not answered in our previous work is whether these epitaxial films and nanostructures can be grown with the level of perfection that is achieved in UHV. Another area that is ripe for exploration is the epitaxial electrodeposition of metal-organic framework materials from solution precursors