Journal ArticleDOI

A density-matrix-based simulated annealing (sa) technique for locating minimum energy structures on the neutral polythiophene potential energy surface

01 Oct 2008-Journal of Theoretical and Computational Chemistry (World Scientific Publishing Company)-Vol. 07, Iss: 05, pp 977-987

TL;DR: In this paper, a modified version of the Su-Schrieffer-Heeger Hamiltonian is used to generate the PES and the unitary transformation of the density variables as the bond lengths change during random reconfiguring moves.

AbstractWe use the elements of the single particle density matrix in the atomic orbital basis as the basic variables and the simulated annealing method as the optimization tool to locate the global minima on the potential surfaces of polythiophene and polyselenophene oligomers (PT)n, (PS)n with n up to 100. A modified version of the Su–Schrieffer–Heeger Hamiltonian is used to generate the PES and the unitary transformation of the density variables as the bond lengths change during random reconfiguring moves. The cost effectiveness of the method is analyzed.

Citations
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Journal ArticleDOI
TL;DR: In this article, 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).
Abstract: 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.

28 citations

Journal ArticleDOI
TL;DR: It is shown that even noisy time series allow the identification of the stability parameters at remarkable accuracy, and this method will be useful to obtain the DNA stacking and hydrogen bonding free energies from single bubble breathing assays rather than equilibrium data.
Abstract: 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.

23 citations

Journal ArticleDOI
TL;DR: In this article, the authors explored the use of stochastic optimizer, namely simulated annealing (SA) followed by density function theory (DFT)-based strategy for evaluating the structure and infrared spectroscopy of (H2O) clusters where n = 1 − 6.
Abstract: In this paper, we explore the use of stochastic optimizer, namely simulated annealing (SA) followed by density function theory (DFT)-based strategy for evaluating the structure and infrared spectroscopy of (H2O) n OH− clusters where n = 1–6. We have shown that the use of SA can generate both global and local structures of these cluster systems. We also perform a DFT calculation, using the optimized coordinate obtained from SA as input and extract the IR spectra of these systems. Finally, we compare our results with available theoretical and experimental data. There is a close correspondence between the computed frequencies from our theoretical study and available experimental data. To further aid in understanding the details of the hydrogen bonds formed, we performed atoms in molecules calculation on all the global minimum structures to evaluate relevant electron densities and critical points.

14 citations

Journal ArticleDOI
TL;DR: In this article, the authors demonstrate how the stochastic global optimization scheme of simulated annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics and demonstrate that the method overcomes even large noise in the input surrogate data.
Abstract: 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, the denaturation bubbles in double-stranded DNA being 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.

9 citations

Journal ArticleDOI
TL;DR: The method is further tested successfully with optimization of the geometry of bipolaron-doped long PT chains and the robustness and the performance levels of variants of the algorithm are analyzed and compared with those of other derivative free methods.
Abstract: A density matrix based soft-computing solution to the quantum mechanical problem of computing the molecular electronic structure of fairly long polythiophene (PT) chains is proposed. The soft-computing solution is based on a "random mutation hill climbing" scheme which is modified by blending it with a deterministic method based on a trial single-particle density matrix [P((0))(R)] for the guessed structural parameters (R), which is allowed to evolve under a unitary transformation generated by the Hamiltonian H(R). The Hamiltonian itself changes as the geometrical parameters (R) defining the polythiophene chain undergo mutation. The scale (λ) of the transformation is optimized by making the energy [E(λ)] stationary with respect to λ. The robustness and the performance levels of variants of the algorithm are analyzed and compared with those of other derivative free methods. The method is further tested successfully with optimization of the geometry of bipolaron-doped long PT chains.

9 citations

References
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TL;DR: Experimental studies of the simulated annealing method are presented and its computational efficiency when applied to graph partitioning and traveling salesman problems are presented.
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TL;DR: The role of excitonic coupling on the nature of photoexcitations in the conjugated polymer regioregular poly(3-hexylthiophene) is addressed by means of temperature-dependent absorption and photoluminescence spectroscopy.
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788 citations