680 research outputs found
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
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