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 studied the π*←π singlet excitations of polyacetylene, polydiacetylene and polybutatriene, polythiophene, poly(para-phenylene vinylene) and the lowest singlet of the hydrogen chain and concluded that the reduction of static polarizability when using the Vignale-Kohn functional has two origins.
Abstract: We study the π*←π singlet excitations of the π-conjugated oligomers of polyacetylene, polydiacetylene, polybutatriene, polythiophene, poly(para-phenylene vinylene), and the lowest singlet excitations of the hydrogen chain. For this we used time-dependent current-density-functional theory within the Vignale–Kohn and adiabatic local density approximations. By studying the dependence of the excitation spectrum on the chain length we conclude that the reduction of the static polarizability when using the Vignale–Kohn functional has two origins. First, the excitation energies of transitions with a large transition dipole are shifted upward. Second, the character of the transition between the lowest occupied and highest unoccupied molecular orbitals and the oscillator strength of the lowest transition within the adiabatic local density approximation is transferred to higher transitions. The lowest transitions that have a considerable oscillator strength obtained with the Vignale–Kohn functional have excitation energies that are in most cases in better agreement with available reference data than the adiabatic local density approximation.
21 citations
TL;DR: This model predicts an insulating behavior of the ordered bipolaron lattice of PT and predicts that the superlattice structure of doped PT's will be semiconductors at room temperature but with a high resistivity.
Abstract: We study here theoretically the evolution of the electronic structure of polythiophene (PT) due to bipolaron doping after modifying the \ensuremath{\sigma}-bond compressibility model. Since the electron-lattice coupling in this model alters both the site energies and the hopping integrals, effects due to the changes in the site energies on the formation of polarons and bipolarons in PT are incorporated. The inductive effect of sulfur is also considered. The ground state geometry of the neutral PT and the experimentally observed bipolaronic optical transitions are reproduced. We predict an insulating behavior of the ordered bipolaron lattice of PT. The bipolaron cluster model also fails to develop a near degeneracy of the highest occupied and the lowest unoccupied molecular orbitals at and above 20 mol % defect concentration. We attribute this to the altering of the site energies upon doping. Our model further predicts that the superlattice structure of doped PT's will be semiconductors at room temperature but with a high resistivity. \textcopyright{} 1996 The American Physical Society.
15 citations
TL;DR: In this paper, the Simulated Annealing (SAN) method was applied to the ground and the singlet 1S2S states of a few members of the He-isoelectronic sequence.
13 citations
TL;DR: A modified Su-Schrieffer-Heeger Hamiltonian-based model is used to compute the electronic and geometric structures of fairly long polythiophene (PT) chains, neutral as well as doped as discussed by the authors.
Abstract: A modified Su–Schrieffer–Heeger Hamiltonian-based model is used to compute the electronic and geometric structures of fairly long polythiophene (PT) chains, neutral as well as doped. The geometry optimization is carried out by the simulated annealing method. Both Metropolis and Glauber functions are used for sampling. It is shown that a bipolaron can be structurally represented by a fragment of the PT chain containing 14 thiophene units. As a series of bipolaronic defects are introduced in a long PT chain (50–100 rings), the highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap energy (Δ) becomes vanishingly small, a feature not present in the PT chains of similar sizes containing polaronic defects. The Fermi energy level (EF) also moves into the valency band and nonzero density of states at ϵ = EF are created. Once again, this feature is shown to be missing in PT chains containing polaronic defects. Implications of these findings are analyzed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
5 citations
TL;DR: In this paper, the hyperpolarizabilities of DMABN and DMANB in the ground and a number of excited states (vertical) have been calculated by combining the MNDO geometry optimization with finite-field SCF-CI at the CNDO/S level of approximation.
5 citations