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, the authors present a new method of electrochemical polymerization of poly(thiophene) using dithiophene as the starting material, from which they obtain a high-quality film with a sharp interband absorption edge.
Abstract: We present a new method of electrochemical polymerization of poly(thiophene) using dithiophene as the starting material, from which we obtain a high-quality film with a sharp interband absorption edge. An in situ study of the absorption spectrum during the electrochemical doping process has been carried out. In the dilute regime, the results are in detailed agreement with charge storage via bipolarons; weakly confined soliton pairs with confinement parameter $\ensuremath{\gamma}\ensuremath{\cong}0.1\ensuremath{-}0.2$. At the highest doping levels, the data are characteristic of the free-carrier absorption expected for a metal. From a parallel electrochemical voltage spectroscopy study, we find evidence of charge injection near the band edge and charge removal from the bipolaron gap states. In the dilute regime, the position of the chemical potential is consistent with charge storage in weakly confined bipolarons. The high Coulombic recovery over a charge-discharge cycle indicates that poly (thiophene) may be an excellent cathode-active material in battery applications.
550 citations
TL;DR: In this article, the synthesis and physical properties of poly(thiophene) with a molecular weight of approximately 4000 consisting of 46-47 thiophene rings (184- 188 carbons along the backbone).
296 citations
TL;DR: It is demonstrated that the dominant photocarriers generated in polythiophene with excitation above the energy gap E sub g are charged bipolarons (spin zero) from photoinduced absorption and light induced electron spin resonance.
Abstract: From photoinduced absorption and light-induced electron-spin resonance, we demonstrate that the dominant photocarriers generated in polythiophene with excitation above the energy gap (${E}_{g}$) are charged bipolarons (spin 0). The observation of bipolarons (${B}^{2\ifmmode\pm\else\textpm\fi{}}$) rather than polarons (${P}^{\ifmmode\pm\else\textpm\fi{}}$) as the dominant photoexciations demonstrates that the Coulomb contribution to the bipolaron energy (${U}_{B}$) is sufficiently small that ${P}^{\ifmmode\pm\else\textpm\fi{}}$+${P}^{\ifmmode\pm\else\textpm\fi{}}$\ensuremath{\rightarrow}${B}^{\ifmmode\pm\else\textpm\fi{}2}$. From the analysis of the spectra, we find ${U}_{B}$/${E}_{g}$\ensuremath{\simeq}0.12. .AE
207 citations
TL;DR: In this article, the optical transitions in α-conjugated oligothiophenes are investigated on the basis of a theoretical approach, including correlation effects; the authors consider both the neutral and doped states.
Abstract: The optical transitions in α‐conjugated oligothiophenes are investigated on the basis of a theoretical approach, including correlation effects; the authors consider both the neutral and doped states. The results are able to provide a coherent interpretation of the sometimes contradictory experimental data. For the neutral oligomers, the authors report the evolution of the lowest energy, dipole‐allowed triplet–triplet transition with increasing chain length.
156 citations
TL;DR: In this paper, band-structure calculations for different lattice conformations of doped polyacetylene and polythiophene were presented for different polaron lattice conformation, and the results of these calculations were compared with results of the Takayama, Lin-Liu, and Maki (TLM) model.
Abstract: Band-structure calculations are presented for different lattice conformations of doped polyacetylene and polythiophene. At intermediate doping levels, the intraband transition energies are found to be in good agreement with experimental optical-absorption data for a soliton lattice conformation in polyacetylene and a bipolaron lattice conformation in polythiophene. At high doping levels, where both polymers exhibit a metalliclike behavior, we find the best agreement with observed optical-absorption and magnetic data to occur for a polaron lattice conformation. Important qualitative differences are found between the polaron lattice conformations obtained in this work and those reported previously. The polaron lattice band structures for polyacetylene and polythiophene are calculated to be very similar to one another, which is also consistent with the experimental trends. The evolutions of the \ensuremath{\pi}-${\ensuremath{\pi}}^{\mathrm{*}}$ and the \ensuremath{\pi}-to-soliton band energy gaps for polyacetylene are studied and compared with results of the Takayama, Lin-Liu, and Maki (TLM) model. We find that, in comparison with optical data probing these transitions, the valence effective Hamiltonian results are superior to the results of the TLM model. We stress that our results do not constitute a proof of the existence of polaron lattice conformation at high doping levels but indicate that the presence of such a conformation is in agreement with a large number of experimental (ir, optical conductivity, magnetic, electron-energy-loss spectroscopy) data.
123 citations