Enhancing the branching ratios in the dissociation channels for O(16)O(16)O(18) molecule by designing optimum laser pulses: A study using stochastic optimization.

We propose a strategy of using a stochastic optimization technique, namely, simulated annealing to design optimum laser pulses (both IR and UV) to achieve greater fluxes along the two dissociating channels (O(18) + O(16)O(16) and O(16) + O(16)O(18)) in O(16)O(16)O(18) molecule. We show that the integrated fluxes obtained along the targeted dissociating channel is larger with the optimized pulse than with the unoptimized one. The flux ratios are also more impressive with the optimized pulse than with the unoptimized one. We also look at the evolution contours of the wavefunctions along the two channels with time after the actions of both the IR and UV pulses and compare the profiles for unoptimized (initial) and optimized fields for better understanding the results that we achieve. We also report the pulse parameters obtained as well as the final shapes they take.

Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA.

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε(hb)(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stacking interaction ε(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.

A parallel tempering based study of Coulombic explosion and identification of dissociating fragments in charged noble gas clusters.

In this communication, we would like to test the feasibility of a parallel tempering based study of dissociation in dicationic noble gas clusters, namely, Ar(n)(2+), Kr(n)(2+), and Xe(n)(2+), where "n" is the size of the cluster units. We would like to find out the correct limit for sizes of each of these systems, above which the clusters stay intact as a single unit and does not dissociate into fragments by the process of Coulomb explosion. Moreover, we would also like to, for a specific case, i.e., Ar(n)(2+), study in detail the fragmentation patterns and point out the switchover from the non-fission way to the fission mechanism of dissociation. In all these calculations, we would like to analyse, how close we are in our predictions with that of experimental results. As a further check on the dissociating patterns found out by parallel tempering, we also conduct basin hopping based study on representative sizes of the clusters and find that parallel tempering, as used for this present work as an optimizer, is able to predict correct features when compared with other celebrated methods like the basin hopping algorithm.

Selective bond breaking mediated by state specific vibrational excitation in model HOD molecule through optimized femtosecond IR pulse: a simulated annealing based approach.

The selective control of O-H/O-D bond dissociation in reduced dimensionality model of HOD molecule has been explored through IR+UV femtosecond pulses. The IR pulse has been optimized using simulated annealing stochastic approach to maximize population of a desired low quanta vibrational state. Since those vibrational wavefunctions of the ground electronic states are preferentially localized either along the O-H or O-D mode, the femtosecond UV pulse is used only to transfer vibrationally excited molecule to the repulsive upper surface to cleave specific bond, O-H or O-D. While transferring from the ground electronic state to the repulsive one, the optimization of the UV pulse is not necessarily required except specific case. The results so obtained are analyzed with respect to time integrated flux along with contours of time evolution of probability density on excited potential energy surface. After preferential excitation from [line]0, 0> ([line]m, n> stands for the state having m and n quanta of excitations in O-H and O-D mode, respectively) vibrational level of the ground electronic state to its specific low quanta vibrational state ([line]1, 0> or [line]0, 1> or [line]2, 0> or [line]0, 2>) by using optimized IR pulse, the dissociation of O-D or O-H bond through the excited potential energy surface by UV laser pulse appears quite high namely, 88% (O-H ; [line]1, 0>) or 58% (O-D ; [line]0, 1>) or 85% (O-H ; [line]2, 0>) or 59% (O-D ; [line]0, 2>). Such selectivity of the bond breaking by UV pulse (if required, optimized) together with optimized IR one is encouraging compared to the normal pulses.

Controlling birhythmicity in a self-sustained oscillator by time-delayed feedback.

Time-delayed feedback is a practical method for controlling various nonlinear dynamical systems. We consider its influence on the dynamics of a multicycle van der Pol oscillator that is birhythmic in nature. It has been shown that depending on the strength of delay the bifurcation space can be divided into two subspaces for which the dynamical response of the system is generically distinct. We observe an interesting collapse and revival of birhythmicity with the variation of the delay time. Depending on the parameter space the system also exhibits a transition between birhythmicity and monorhythmic behavior. Our analysis of amplitude equation corroborates with the results obtained by numerical simulation of the dynamics.

Reaction-diffusion systems with stochastic time delay in kinetics.

Time delay is an important dynamical issue in a multistep chemical reaction. We present a theoretical scheme for delayed reaction-diffusion systems where the time delay in kinetics is stochastic in nature. It has been shown that a small but finite strength of delay may result in generic change in the nature of spatiotemporal instability in the dynamics. Our theoretical analysis has been corroborated by numerical simulations on two reaction-diffusion systems.

Spatial periodicity induced by a chemical wave train.

An all-chemical analog of clock-wave-front model for somitogenesis is proposed. The spatial periodicity can be obtained by arresting the homogeneous oscillations in a typical two-component reaction-diffusion system in the Hopf region by interacting with a chemical wave front. The patterns can be controlled by tuning the wave speed of the front.

Reaction-Cattaneo systems with fluctuating relaxation time.

A reaction-Cattaneo equation with fluctuating relaxation time of the diffusive flux has been explored. It has been shown that depending on the strength of fluctuations, the dynamical system exhibits new oscillatory solutions as a result of Hopf and double Hopf bifurcations leading to spatiotemporal patterns. This analysis has been applied to two model nonlinear systems.

Time-delay-induced instabilities in reaction-diffusion systems.

Time delay in the kinetic terms of reaction-diffusion systems has been investigated. It has been shown that short delay beyond a critical threshold may induce spatiotemporal instabilities. For unequal diffusivities and appropriate parameter space delay may induce Turing instability resulting in stationary patterns and also interesting Turing-Hopf transition with the formation of spirals. The theoretical scheme has been numerically explored in two different prototypical reaction-diffusion systems.

Galerkin analysis of light-induced patterns in the chlorine dioxide-iodine-malonic acid reaction-diffusion system.

The photosensitive chlorine dioxide-iodine-malonic acid reaction-diffusion system has been an experimental paradigm for the study of Turing pattern over the last several years. When subjected to illumination of varied intensity by visible light the patterns undergo changes from spots to stripes, vice versa, and their mixture. We carry out a nonlinear analysis of the underlying model in terms of a Galerkin scheme with finite number of modes to explore the nature of the stability and existence of various modes responsible for the type and crossover of the light-induced patterns.

Secant-hyperbolic instability in a reaction-diffusion system.

We have shown that the nonlinearity of the chemical reaction may induce instability on a homogenous stable steady state of a one-component reaction-diffusion system characterized by a cubic polynomial source term. This results in a growth of an asymptotically approaching inhomogeneous spatial profile of secant-hyperbolic form reminiscent of a solitary wave.

Nonlinear dynamics of finite perturbation: collapse and revival of spatial patterns.

A full-scale nonlinear stability analysis is performed on a reaction-diffusion system that includes a cubic polynomial source term and Cattaneo's modification of Fick's law of diffusion. This modification incorporates the effect of a small, finite relaxation time of flux at the macroscopic level of the description of the process. While linear stability analysis predicts the decay of small wavelength perturbations on a homogeneous steady state for large reaction time, consideration of finite perturbations leads to a spatiotemporal instability, resulting in an interesting phenomenon of periodic collapse and revival of spatial patterns. This instability is relaxation (time) driven, and the time period is determined by self-sustaining oscillations due to the limit cycle of the underlying dynamics. The nonlinear dynamics of finite perturbations may thus be generically different from what is expected from a linear stability analysis.

Temperature dependence and temperature compensation of kinetics of chemical oscillations; Belousov-Zhabotinskii reaction, glycolysis and circadian rhythms.

Based on the distribution of activation energies around the experimental mean and averaging of rate constants we propose a theoretical scheme to examine the temperature dependence and temperature compensation of time periods of chemical oscillations. The critical finite width of the distribution is characteristic of endogeneous oscillations for compensating kinetics as observed in circadian oscillations, while the vanishing width corresponds to Arrhenius temperature dependent kinetics of non-endogeneous chemical oscillation in Belousov-Zhabotinskii reaction in a CSTR or glycolysis in cell-free yeast extracts. Our theoretical analysis is corroborated with experimental data.