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.

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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.

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For a reaction to proceed via tunneling mechanism, it is essential that the reactants will cross the potential barrier (E P ), where its initial energy (E 0 ) is below the potential barrier E P . Tunneling probability s is defined as the probability of having momentum higher than k m , where k m 5 ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi ð2mE P Þ p . In the momentum basis representation, s can be directly calculated by integrating jwðkÞj 2 from the limit k m to infinity, where wðkÞ is the wave function in the momentum space. Instead of the continuous basis, if we chose momentum grid space, s can be expressed as s5 P 1 ki5km jwðk i Þj 2 . Our target here is to increase this s by applying a polychromatic field, so that the reaction rate can be enhanced. By applying Simulated Annealing technique we have designed some polychromatic electric fields, spatially symmetric and asymmetric type, which enhances the tunneling rate in symmetric double well system and Eckart barrier confined in an infinite well. K E Y W O R D S Eckart barrier, momentum representation, SDWP, simulated annealing, tunneling probability Int J Quantum Chem. 2017;117:e25388.