Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization

We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local denaturation zones (bubbles). On the basis of the reconstructed bubble size distribution, this is achieved through stochastic optimization of the free energies in terms of simulated annealing. In particular, it is shown that even noisy time series allow the identification of the stability parameters at remarkable accuracy. This method will be useful to obtain the DNA stacking and hydrogen bonding free energies from single bubble breathing assays rather than equilibrium data.     

Structural,spectroscopic aspects,and electronic properties of (TiO2)n clusters: A study based on the use of natural algorithms in association with quantum chemical methods

In this article, we propose a stochastic search‐based method, namely genetic algorithm (GA) and simulated annealing (SA) in conjunction with density functional theory (DFT) to evaluate global and local minimum structures of (TiO₂)_n clusters with n = 1–12. Once the structures are established, we evaluate the infrared spectroscopic modes, cluster formation energy, vertical excitation energy, vertical ionization potential, vertical electron affinity, highest occupied molecular orbital (HOMO)‐lowest unoccupied molecular orbital (LUMO) gaps, and so forth. We show that an initial determination of structure using stochastic techniques (GA/SA), also popularly known as natural algorithms as their working principle mimics certain natural processes, and following it up with density functional calculations lead to high‐quality structures for these systems. We have shown that the clusters tend to form three‐dimensional networks. We compare our results with the available experimental and theoretical results. The results obtained from SA/GA‐DFT technique agree well with available theoretical and experimental data of literature. © 2013 Wiley Periodicals, Inc.     

Structure,spectroscopy and electronic properties of neutral lattice-like (MgO) n clusters: a study based on a blending of DFT with stochastic algorithms inspired by natural processes

In this article, we explore the feasibility of using stochastic optimization techniques, which are inspired by natural processes, namely simulated annealing (SA) and genetic algorithm (GA) in association with DFT, to find out the global minimum structures of (MgO) _n clusters with n being in the range of 2–15. To check whether the structures are indeed the correct ones, we proceed to do several property calculations like IR-spectroscopic modes, vertical excitation energy, cluster-formation energy, vertical ionization potential, the HOMO–LUMO gap as well as polarizability and hyperpolarizability—both static and dynamic. We emphasize on the point that an initial determination of structure using SA/GA leads to very quick relaxation to structures which are very close to the structures predicted from quantum chemical calculations done from the outsets like DFT. The general pattern of these systems to form beautiful three-dimensional lattice networks is also evident from our study.     

Microwave absorption studies of MgB2 superconductor

Microwave absorption studies have been carried out on MgB₂ superconductor using a standard X-band EPR spectrometer. The modulated low-field microwave absorption signals recorded for polycrystalline (grain size ∼ 10 μm) samples suggested the absence of weak-link character. The field dependent direct microwave absorption has been found to obey a ✓H dependence with two different slopes, which indicated a transition from strongly pinned lattice to flux flow regime.     

The radio frequency conductivity of some aliphatic alcohols at different temperatures

Activation energies for viscous flow and conductivity are computed from experimental values of RF conductivity (frequency 400 kHz) at different temperatures for eight polar liquids. It is observed that for aliphatic alcohols the activation energy for conductivity is greater than that for viscous flow. However, their ratio is slightly greater than unity and is different for different alcohols whereas for nonassociating polar liquids the ratio is almost equal to unity. The dependence of conductivity on viscosity for the liquid alcohols does not follow the Walden’s law but can be well represented by Adamczewskis relation.     

Motion of drops on a surface induced by thermal gradient and vibration

It is well known that a liquid drop with a low contact angle (approximately 45 degrees ) and low wetting hysteresis moves toward the colder region of a temperature gradient substrate as a result of the thermal Marangoni force. A moderately sized water drop, however, usually does not move on such a surface because of the overwhelming effect of hysteresis. The water drop can, however, be forced to move when it is vibrated on a temperature gradient surface with its velocity exhibiting maxima at the respective Rayleigh frequencies. A simple model is presented that captures the dependence of drop velocity on hysteresis, vibration amplitude, and the forcing and resonance frequencies of vibration.     

The dynamics of intermittent strand separation in double-stranded DNA

The transient rupture and reformation of hydrogen bonds between base pairs on distinct chains of double-stranded DNA ("bubble" dynamics) is modeled in terms of the fluctuating distance between the bases. The fluctuations in the distance are assumed to be governed by a simple Langevin equation with a quadratic potential under conditions of high friction. A critical distance of separation L must be achieved before a bubble defect is considered to have been formed. The decay of the dynamic correlations between states of the DNA that have such defects and those that do not has been calculated from the above model and has been found to reproduce the trends in experimental measurements of the same quantity.     

Shear-induced adhesive failure of a rigid slab in contact with a thin confined film

A rigid-glass prism (square or rectangular base, rectangular cross-section) is sheared off a thin film of silicone elastomer bonded to a glass plate by applying a tangential force at various distances above the prism/elastomer interface. At a given tangential force, the prism starts to slide on the elastomeric film. As the sliding velocity, thus the frictional force, is progressively increased, an elastic instability develops at the interface that results in the formation of numerous bubbles. These bubbles, the lateral dimension of which is comparable to the thickness of the film, move across the interface with speeds 1000 times faster than the overall sliding speed of the glass prism against the PDMS film. It is found that the glass prism continues to slide on the elastomeric film as long as the applied shear stress is less than a critical value. During sliding, however, a normal stress is developed at the interface that decays from the front (i.e. where the force is applied) to the rear end of the prism. When the normal stress reaches a critical value, the prism comes off the film. The critical shear stress of fracture increases with the modulus of the film, but decreases with the thickness following a square root relationship, as is the case with the removal of rigid punches from thin elastomeric films by normal pull-off forces.     

Model of fluorescence intermittency in single enzymes

The intermittent emission of fluorescent light from single enzymes, quantum dots, and other nanoscale systems is often characterized by statistical correlations in the emitted signal. A one-dimensional model of such correlations in enzymes, based on a model of protein conformational fluctuations developed by Kou and Xie (Phys. Rev. Lett. 2004, 93, 180603), is formulated in the present paper in terms of the dynamics of a particle moving stochastically between "on" and "off" states under the action of fractional Gaussian noise. The model yields predictions for the short and long time behavior of the following quantities: the time correlation function, C(t), of the fluctuations of the signal intensity, the distribution, f(t), of time intervals between intensity fluctuations, and the Mandel parameter, Q(t), describing the extent of bunching or anti-bunching in the signal. At short times, C(t) and f(t) are found to decay exponentially, while, at long times, they are found to decay as power laws, the exponents being functions solely of the nature of the temporal correlations in the noise. The results are in good qualitative agreement with results from single-molecule experiments on fluorescence intermittency in the enzyme cholesterol oxidase carried out by Xie and co-workers (Science 1998, 282, 1877). The Mandel parameter, Q(t), for this model is positive at short and long times, indicating super-Poisson statistics in these limits, consistent with bunching of the fluorescent signal.     

Quantum control of the hyperfine spin of a Cs atom ensemble

We demonstrate quantum control of a large spin angular momentum associated with the F=3 hyperfine ground state of 133Cs. Time-dependent magnetic fields and a static tensor light shift are used to implement near-optimal controls and map a fiducial state to a broad range of target states, with yields in the range 0.8-0.9. Squeezed states are produced also by an adiabatic scheme that is more robust against errors. Universal control facilitates the encoding and manipulation of qubits and qudits in atomic ground states and may lead to the improvement of some precision measurements.