Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics simulations reveal a clear formation of S-DNA when the B-DNA is stretched along the 3' directions of the opposite strands (OS3) and is characterized by the changes in the number of H-bonds, entropy and free energy. Stretching along 5' directions of the opposite strands (OS5) leads to force induced melting form of the DNA. Interestingly, stretching along the opposite ends of the same strand (SS) leads to a coexistence of both the S- and melted M-DNA structures. We also do the structural characterization of the S-DNA by calculating various helical parameters. We find that S-DNA has a twist of ~10 degrees which corresponds to helical repeat length of ~ 36 base pairs in close agreement with the previous experimental results. Moreover, we find that the free energy barrier between the canonical and overstretched states of DNA is higher for the same termini (SE) pulling protocol in comparison to all other protocols considered in this work. Overall, our observations not only reconcile with the available experimental results qualitatively but also enhance the understanding of different overstretched DNA structures.Comment: To be published in the The Journal of Chemical Physics (AIP

Cobb-Douglas Based Firm Production Model under Fuzzy Environment and its Solution using Geometric Programming

In this paper, we consider Cobb-Douglas production function based model in a firm under fuzzy environment, and its solution technique by making use of geometric programming. A firm may use many finite inputs such as labour, capital, coal, iron etc. to produce one single output. It is well known that the primary intention of using production function is to determine maximum output for any given combination of inputs. Also, the firm may gain competitive advantages if it can buy and sell in any quantities at exogenously given prices, independent of initial production decisions. On the other hand, in reality, constraints and/or objective functions in an optimization model may not be crisp quantities. These are usually imprecise in nature and are better represented by using fuzzy sets. Again, geometric programming has many advantages over other optimization techniques. In this paper, Cobb-Douglas production function based models are solved by applying geometric programming technique under fuzzy environment. Illustrative numerical examples further demonstrates the feasibility and efficiency of proposed model under fuzzy environment. Conclusions are drawn at last

Ionic liquids make DNA rigid

Persistence length of dsDNA is known to decrease with increase in ionic concentration of the solution. In contrast to this, here we show that persistence length of dsDNA increases dramatically as a function of ionic liquid (IL) concentration. Using all atomic explicit solvent molecular dynamics simulations and theoretical models we present, for the first time, a systematic study to determine the mechanical properties of dsDNA in various hydrated ionic liquids at different concentrations. We find that dsDNA in 50 wt% ILs have lower persistence length and stretch modulus in comparison to 80 wt% ILs. We further observe that both persistence length and stretch modulus of dsDNA increase as we increase the ILs concentration. Present trend of stretch modulus and persistence length of dsDNA with ILs concentration supports the predictions of the macroscopic elastic theory, in contrast to the behavior exhibited by dsDNA in monovalent salt. Our study further suggests the preferable ILs that can be used for maintaining DNA stability during long-term storage.Comment: 16 pages, 3 figures, Supplementary Information (Accepted for publication in the Journal of Chemical Physics, AIP (USA)

Development of a Perfectly Matched Layer Technique for a Discontinuous-Galerkin Spectral-Element Method

The numerical simulation of many aerodynamic non-periodic flows of practical interest involves discretized computational domains that often must be artificially truncated. Appropriate boundary conditions are required at these truncated domain boundaries, and ideally, these boundary conditions should be perfectly "absorbing" or "nonreflecting" so that they do not contaminate the flow field in the interior of the domain. The proper specification of these boundaries is critical to the stability, accuracy, convergence, and quality of the numerical solution, and has been the topic of considerable research. The need for accurate boundary specification has been underscored in recent years with efforts to apply higher-fidelity methods (DNS, LES) in conjunction with high-order low-dissipation numerical schemes to realistic flow configurations. One of the most popular choices for specifying these boundaries is the characteristics-based boundary condition where the linearized flow field at the boundaries are decomposed into characteristic waves using either one-dimensional Riemann or other multi-dimensional Riemann approximations. The values of incoming characteristics are then suitably modified. The incoming characteristics are specified at the in flow boundaries, and at the out flow boundaries the variation of the incoming characteristic is zeroed out to ensure no reflection. This, however, makes the problem ill-posed requiring the use of an ad-hoc parameter to allow small reflections that make the solution stable. Generally speaking, such boundary conditions work reasonably well when the characteristic flow direction is normal to the boundary, but reflects spurious energy otherwise. An alternative to the characteristic-based boundary condition is to add additional "buffer" regions to the main computational domain near the artificial boundaries, and solve a different set of equations in the buffer region in order to minimize acoustic reflections. One approach that has been used involves modeling the pressure fluctuations as acoustic waves propagating in the far-field relative to a single noise-source inside the buffer region. This approach treats vorticity-induced pressure fluctuations the same as acoustic waves. Another popular approach, often referred to as the "sponge layer," attempts to dampen the flow perturbations by introducing artificial dissipation in the buffer region. Although the artificial dissipation removes all perturbations inside the sponge layer, incoming waves are still reflected from the interface boundary between the computational domain and the sponge layer. The effect of these refkections can be somewhat mitigated by appropriately selecting the artificial dissipation strength and the extent of the sponge layer. One of the most promising variants on the buffer region approach is the Perfectly Matched Layer (PML) technique. The PML technique mitigates spurious reflections from boundaries and interfaces by dampening the perturbation modes inside the buffer region such that their eigenfunctions remain unchanged. The technique was first developed by Berenger for application to problems involving electromagnetic wave propagation. It was later extended to the linearized Euler, Euler and Navier-Stokes equations by Hu and his coauthors. The PML technique ensures the no-reflection property for all waves, irrespective of incidence angle, wavelength, and propagation direction. Although the technique requires the solution of a set of auxiliary equations, the computational overhead is easily justified since it allows smaller domain sizes and can provide better accuracy, stability, and convergence of the numerical solution. In this paper, the PML technique is developed in the context of a high-order spectral-element Discontinuous Galerkin (DG) method. The technique is compared to other approaches to treating the in flow and out flow boundary, such as those based on using characteristic boundary conditions and sponge layers. The superiority of the current PML technique over other approaches is demonstrated for a range of test cases, viz., acoustic pulse propagation, convective vortex, shear layer flow, and low-pressure turbine cascade flow. The paper is structured as follows. We first derive the PML equations from the non{linear Euler equations. A short description of the higher-order DG method used is then described. Preliminary results for the four test cases considered are then presented and discussed. Details regarding current work that will be included in the final paper are also provided

ScaleResolving Simulations of a Fundamental TrailingEdge Cooling Slot Using a DiscontinuousGalerkin SpectralElement Method

The accurate prediction of turbulent mixing in high-pressure turbines that incorporate various airfoil surface-cooling strategies is becoming increasing critical to the design of modern gas turbine engines where the quest for improved efficiency is driving compressor overall pressure ratios and turbine inlet temperatures to much higher levels than ever before. In the present paper, a recently developed computational capability for accurate and efficient scaleresolving simulations of turbomachinery is extended to study the turbulent mixing mechanism of a simplified abstraction of an airfoil trailing-edge cooling slot - a plane wall jet with finite lip thickness discharging into an ambient flow. The computational capability is based on an entropy stable, discontinuousGalerkin approach that extends to arbitrarily high orders of spatial and temporal accuracy. The numerical results show that the present simulations capture the trends observed in the experiments. Discrepancies between the simulations and experiments are believed to be due to differences in the inflow profiles and tunnel sidewall effects. The thick lip configuration leads to a thicker wake and higher unsteadiness in the wall jet compared to the thin lip. A detailed comparison of the turbulent flowfields is presented to highlight differences arising due to lip thickness variations

New limit for the half-life of double beta decay of 94^{94}Zr to the first excited state of 94^{94}Mo

Neutrinoless Double Beta Decay is a phenomenon of fundamental interest in particle physics. The decay rates of double beta decay transitions to the excited states can provide input for Nuclear Transition Matrix Element calculations for the relevant two neutrino double beta decay process. It can be useful as supplementary information for the calculation of Nuclear Transition Matrix Element for the neutrinoless double beta decay process. In the present work, double beta decay of $^{94}$Zr to the $2^{+}_{1}$ excited state of $^{94}$Mo at 871.1 keV is studied using a low background $\sim$ 230 cm$^3$ HPGe detector. No evidence of this decay was found with a 232 g.y exposure of natural Zirconium. The lower half-life limit obtained for the double beta decay of $\rm^{94}Zr$ to the $2^{+}_{1}$ excited state of $\rm^{94}Mo$ is $T_{1/2} (0\nu + 2\nu)> 3.4 \times 10^{19}$ y at 90% C.L., an improvement by a factor of $\sim$ 4 over the existing experimental limit at 90\% C.L. The sensitivity is estimated to be $T_{1/2} (0\nu + 2\nu) > 2.0\times10^{19}$ y at 90% C.L. using the Feldman-Cousins method.Comment: 11 pages, 7 figures, Accepted in Eur. Phys. J.

The role of 99mTc-DTPA retrobulbar SPECT in staging and follow-up of Graves’ orbitopathy

The pathogenesis of Graves’ orbitopathy (GO) is not completely understood. Coexistent hyperfunction of the thyroid gland is frequent; however, GO may also coexist with hypo- or euthyrodism. The course of GO is largely independent of thyroid function, although elevated serum TSH is known to negatively interfere with GO course. GO is severe in 10% of the cases; sight threatening complications may also develop. A successful therapy of GO requires the assesment of both the severity and activity of orbital inflammation. Based on relevant studies and our own experiences, the possible management choices are reviewed here. For this purpose, we compare the clinical value of imaging techniques for detecting the activity of the disease. During the last 15 years, we used 99mTc-DTPA retrobulbar SPECT routinely in more than 1400 patients to facilitate the right therapeutic decision. This diagnostic utility simplified management decisions compared to previously applied alternative techniques. We recommended the routine use of 99mTc-DTPA retrobulbar SPECT for the evaluation and follow-up of GO.The pathogenesis of Graves’ orbitopathy (GO) is not completely understood. Coexistent hyperfunction of the thyroid gland is frequent; however, GO may also coexist with hypo- or euthyrodism. The course of GO is largely independent of thyroid func­tion, although elevated serum TSH is known to negatively interfere with GO course. GO is severe in 10% of the cases; sight threatening complications may also develop. A successful therapy of GO requires the assesment of both the severity and activity of orbital inflammation. Based on relevant studies and our own experiences, the possible management choices are reviewed here. For this purpose, we compare the clinical value of imaging techniques for detecting the activity of the disease. During the last 15 years, we used 99mTc-DTPA retrobulbar SPECT routinely in more than 1400 patients to facilitate the right therapeutic decision. This diagnostic utility simplified management decisions compared to previously applied alternative techniques. We recommended the routine use of 99mTc-DTPA retrobulbar SPECT for the evaluation and follow-up of GO.

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600