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 authors present a strategy for enhancing the dissociation probability of a diatomic molecule, namely LiH, by designing an optimal laser pulse function, generated by using the stochastic optimization technique of simulated annealing.
Abstract: We present a strategy for enhancing the dissociation probability of a diatomic molecule, namely LiH, by designing optimal laser pulse. Dissociation dynamics is followed by solving time-dependent Schrodinger equation using time-dependent Fourier Grid Hamiltonian technique with optimal laser pulse function, generated by using the stochastic optimization technique of simulated annealing. We show that as we increase number of variable parameters while designing the optimal time dependent perturbation, higher dissociation is obtained. The step-wise increase in dissociation probability with the increase in complexity of designed pulse is clearly shown.
8 citations
TL;DR: It is demonstrated that the stochastic global optimization scheme of simulated annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics and 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 with the denaturation zones in double stranded DNA 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.
8 citations
TL;DR: A variational recipe in a finite basis has been invoked in one of the strategies leading to a matrix eigenvalue problem that has been solved by GA with simultaneous optimization of the basis.
Abstract: Several strategies based on Genetic Algorithms have been explored to locate the ground state energy and structure of atoms and molecules. A variational recipe in a finite basis has been invoked in one of the strategies leading to a matrix eigenvalue problem that has been solved by GA with simultaneous optimization of the basis. In the second approach, the molecular electronic Schrodinger equation has been solved by Genetic Algorithm by directly optimizing the electronic probability amplitude distribution in space. In the third approach, the single-particle density matrix in atomic orbital basis has been treated as the basic unknown quantity. The search for the optimal ground state density has been simplified by a unitary transformation on the trial density which has been optimized by GA.
6 citations
Cites methods from "A density-matrix-based simulated an..."
...The GA based search has a slight edge over the search based on Simulated Annealing Method proposed earlier [22], or the other methods which require calculation of derivatives of energy with respect to nuclear coordinates [23]....
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TL;DR: In this article, the authors seek to design optimum pulses for selective target excitation to specified excited levels using the time dependent Fourier grid Hamiltonian technique and the simulated annealing method.
Abstract: In this paper, we seek to design optimum pulses for selective target excitation to specified excited levels. We test our proposed idea for vibrational excitation in systems modelled by the Morse potential, using the time dependent Fourier grid Hamiltonian technique and the simulated annealing method.
6 citations
TL;DR: In this article, a GA-driven density matrix method for calculating the equilibrium geometry and charge storage configurations of hole-bipolaron-doped polythiophene (PT) oligomers is proposed.
Abstract: We propose a genetic algorithm (GA)-driven density matrix method for calculating the equilibrium geometry and charge storage configurations of hole(bipolaron)-doped Polythiophene (PT) oligomers. A modified version of the Su–Schrieffer–Heeger Hamiltonian is used to describe the PT chain. A population of geometry strings are used to generate the corresponding PT-Hamiltonians which act as generators of corresponding unitary transformations which transform a single trial one-electron density matrix into a population of density matrices for different geometries. As the geometry strings evolve under the action of GA operators, the density matrices also evolve on the fitness landscape. Once the fitness reaches maximum, the optimum geometry string, the corresponding Hamiltonian, and the density matrix lead to equilibrium geometry, energy, charge distribution, band gap, Fermi energy, etc. The bipolaronic defect–induced conducting state is predicted to have a symmetric lattice-like admixture of “aromatic” and “quin...
4 citations
Cites methods from "A density-matrix-based simulated an..."
...It appears that the present method has an edge over a simulated annealing driven density-based method proposed earlier [28] as the fitness evaluation step in GA can be easily parallelized....
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References
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TL;DR: There is a deep and useful connection between statistical mechanics and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters), and a detailed analogy with annealing in solids provides a framework for optimization of very large and complex systems.
Abstract: There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters). A detailed analogy with annealing in solids provides a framework for optimization of the properties of very large and complex systems. This connection to statistical mechanics exposes new information and provides an unfamiliar perspective on traditional optimization problems and methods.
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TL;DR: In this article, a unified scheme combining molecular dynamics and density-functional theory is presented, which makes possible the simulation of both covalently bonded and metallic systems and permits the application of density functional theory to much larger systems than previously feasible.
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TL;DR: In this paper, the authors present a theoretical study of soliton formation in long-chain polyenes, including the energy of formation, length, mass, and activation energy for motion.
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IBM1
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.
Abstract: Simulated annealing is a stochastic optimization procedure which is widely applicable and has been found effective in several problems arising in computeraided circuit design. This paper derives the method in the context of traditional optimization heuristics and presents experimental studies of its computational efficiency when applied to graph partitioning and traveling salesman problems.
1,808 citations
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.
Abstract: We address the role of excitonic coupling on the nature of photoexcitations in the conjugated polymer regioregular poly(3-hexylthiophene). By means of temperature-dependent absorption and photoluminescence spectroscopy, we show that optical emission is overwhelmingly dominated by weakly coupled H aggregates. The relative absorbance of the 0-0 and 0-1 vibronic peaks provides a powerfully simple means to extract the magnitude of the intermolecular coupling energy, of approximately 5 and 30 meV for films spun from isodurene and chloroform solutions, respectively.
848 citations