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.
Abstract: We 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.
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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
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
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
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
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: In this paper, changes of absorption spectra in a polythiophene film caused by photo-excitation and electrochemical doping are studied, showing that the formation of a shallow polaron is responsible to the carrier transport.
121 citations
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85 citations
TL;DR: Les calculs ab initio au niveau Hartree Fock donnent des valeurs de barriere de rotation autour des liaisons simples de 6, 3 and 1 kcal/mole respectivement for le polyacetylene, le polythiophene and le polydiacetylene as mentioned in this paper.
Abstract: Les calculs ab initio au niveau Hartree Fock donnent des valeurs de barriere de rotation autour des liaisons simples de 6, 3 et 1 kcal/mole respectivement pour le polyacetylene, le polythiophene et le polydiacetylene suggerant que ces chai←nes devraient etre assez flexibles en solution
81 citations
TL;DR: Pernigraniline is shown to accomodate elementary excitations of soliton and polaron types having remarkable properties, in some instances markedly different from those predicted for the so-called AB polymer.
Abstract: The electronic structure of fully oxidized polyaniline, pernigraniline, is investigated in the framework of the Su-Schrieffer-Heeger Hamiltonian, making use of an original renormalization technique. Among the family of polyanilines, pernigraniline is the only form to possess a degenerate ground state. It is shown to accomodate elementary excitations of soliton and polaron types having remarkable properties, in some instances markedly different from those predicted for the so-called AB polymer. Nonlinear optical properties of the material are expected to be important.
80 citations