Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach

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.Comment: 9 pages, 4 figures, iop article package include

On the ground state of solids with strong electron correlations

We formulate the calculation of the ground-state wavefunction and energy of a system of strongly correlated electrons in terms of scattering matrices. A hierarchy of approximations is introduced which results in an incremental expansion of the energy. The present approach generalizes previous work designed for weakly correlated electronic systems.Comment: 17 pages, Latex(revtex

Modified conjugated gradient method for diagonalising large matrices

We present an iterative method to diagonalise large matrices. The basic idea is the same as the conjugated gradient (CG) method, i.e, minimizing the Rayleigh quotient via its gradient and avoiding reintroduce errors to the directions of previous gradients. Each iteration step is to find lowest eigenvector of the matrix in a subspace spanned by the current trial vector and the corresponding gradient of the Rayleigh quotient, as well as some previous trial vectors. The gradient, together with the previous trail vectors, play a similar role of the conjugated gradient of the original CG algorithm. Our numeric tests indicate that this method converges significantly faster than the original CG method. And the computational cost of one iteration step is about the same as the original CG method. It is suitably for first principle calculations.Comment: 6 Pages, 2EPS figures. (To appear in Phys. Rev. E

Convergence improvement for coupled cluster calculations

Convergence problems in coupled-cluster iterations are discussed, and a new iteration scheme is proposed. Whereas the Jacobi method inverts only the diagonal part of the large matrix of equation coefficients, we invert a matrix which also includes a relatively small number of off-diagonal coefficients, selected according to the excitation amplitudes undergoing the largest change in the coupled cluster iteration. A test case shows that the new IPM (inversion of partial matrix) method gives much better convergence than the straightforward Jacobi-type scheme or such well-known convergence aids as the reduced linear equations or direct inversion in iterative subspace methods.Comment: 7 pages, IOPP styl

Daubechies wavelets as a basis set for density functional pseudopotential calculations

Daubechies wavelets are a powerful systematic basis set for electronic structure calculations because they are orthogonal and localized both in real and Fourier space. We describe in detail how this basis set can be used to obtain a highly efficient and accurate method for density functional electronic structure calculations. An implementation of this method is available in the ABINIT free software package. This code shows high systematic convergence properties, very good performances and an excellent efficiency for parallel calculations.Comment: 15 pages, 11 figure

Size-consistent self-consistent configuration interaction from a complete active space : Excited states

The self-consistent size consistent on a complete active space singly and doubly configuration interaction (SC)2CAS-SDCI method is applied to excited states. The (SC)2 correction is performed on a closed shell state, and the excited states are obtained by diagonalization of the dressed matrix. A theoretical justification of the transferability of the improvement concerning the dressing state to all roots of the matrix is presented. The method is tested by three tests on the spectrum of small [email protected] ; [email protected]

Investigation of A1g phonons in YBa2Cu3O7 by means of LAPW atomic-force calculations

We report first-principles frozen-phonon calculations for the determination of the force-free geometry and the dynamical matrix of the five Raman-active A1g modes in YBa2Cu3O7. To establish the shape of the phonon potentials atomic forces are calculated within the LAPW method. Two different schemes - the local density approximation (LDA) and a generalized gradient approximation (GGA) - are employed for the treatment of electronic exchange and correlation effects. We find that in the case of LDA the resulting phonon frequencies show a deviation from experimental values of approximately -10%. Invoking GGA the frequency values are significantly improved and also the eigenvectors are in very good agreement with experimental findings.Comment: 15 page

Analytic Energy Gradients for Multiconfigurational Self-Consistent Field Second-Order Quasidegenerate Perturbation Theory (MC-QDPT)

An analytic energy gradient method for second-order quasidegenerate perturbation theory with multiconfigurational self-consistent field reference functions (MC-QDPT) is derived along the lines of the response function formalism (RFF). According to the RFF, the gradients are calculated without solving coupled perturbed equations. Instead, it is necessary to solve seven sets of linear equations in order to determine Lagrangian multipliers, corresponding to four sets of parameter constraining conditions and three sets of additional parameter defining conditions in the Lagrangian. Just one of these linear equations is a large scale linear equation; the others are reducible to just partial differentiations or simple equations solvable by straightforward subroutines

A Doubly Nudged Elastic Band Method for Finding Transition States

A modification of the nudged elastic band (NEB) method is presented that enables stable optimisations to be run using both the limited-memory quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet (SQVV) minimisers. The performance of this new `doubly nudged' DNEB method is analysed in conjunction with both minimisers and compared with previous NEB formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to two orders of magnitude. Applications to permutational rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an updated algorithm for constructing complicated multi-step pathways using successive DNEB runs.Comment: 13 pages, 8 figures, 2 table