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. © 2008 World Scientific Publishing Company.

PINAKI CHAUDHURY

Chemistry

S NANDY

R SHARMA

S P BHATTACHARYYA

University of Calcutta (informally known as Calcutta University or CU) is a collegiate public state university located in Kolkata, West Bengal, India.&nbsp;Within India it is recognized as a &quot;Five-Star University&quot; and accredited &quot;A&quot; Grade by National Assessment and Accreditation Council.

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The University of Calcutta has secured the Fifth position among the Universities of India in the prestigious &quot;Indian University Ranking 2019&quot; list, released by the NIRF of the Ministry of Human Resource Development, Government of India.

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It was established on 24 January 1857, and was one of the first institutions in Asia to be established as a multidisciplinary and Western-style university. Its alumni and faculty include several heads of state, heads of government, social reformers, prominent artists, only academy award winner and Dirac medal winner in India, many Fellows of the Royal Society and five Nobel laureates as of 2019 which is highest in South Asia.

University Of Calcutta

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

Journal of Theoretical and Computational Chemistry

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. © 2012 IACS.

Indian Journal of Physics

A simulated annealing based study to design optimum pulses for selective target excitation in vibrational levels

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. © 2011 American Institute of Physics.

Fulltext

Journal of Chemical Physics

Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization

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 quininoid regions and is characterized by nonzero density of states at Fermi energy and low band gaps. Copyright © Taylor &amp; Francis Group, LLC.

Materials and Manufacturing Processes

A density-genetic algorithm method for computing electronic structures of doped and undoped polythiophene oligomers: A modified su-schrieffer-heeger hamiltonian-based study

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. © 2009 IOP Publishing Ltd.

Journal of Physics A: Mathematical and Theoretical

Finding the optimum activation energy in DNA breathing dynamics: A simulated annealing approach

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.

Journal	Journal of Theoretical and Computational Chemistry
Publisher	WORLD SCIENTIFIC PUBL CO PTE LTD
ISSN	0219-6336