836 research outputs found
Normal mode analysis of macromolecular systems with the Mobile Block Hessian method
Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3Na 3Na matrix with Na the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each.
Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible – but not necessarily optimized – geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian.
In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example
An efficient approach for the calculation of frequencies in macromolecules
I. INTRODUCTION. Conformational changes of macromolecules are essential in the understanding of e.g. proteins and drug design. The theoretical prediction is far from trivial, especially for large molecules. In many cases, collective motions are present which occur on a timescale (~ms) that is too long to be accessible through molecular dynamics simulations. Normal mode analysis (NMA) has been proven succesful in exploring the potential energy surface (PES) within the harmonic oscillator approximation.
The lowest frequency modes contribute the most to a conformational change. This paper presents a computationally attractive method that selects modes from the lower spectrum
Center-of-mass effects on the quasi-hole spectroscopic factors in the 16O(e,e'p) reaction
The spectroscopic factors for the low-lying quasi-hole states observed in the
16O(e,e'p)15N reaction are reinvestigated with a variational Monte Carlo
calculation for the structure of the initial and final nucleus. A computational
error in a previous report is rectified. It is shown that a proper treatment of
center-of-mass motion does not lead to a reduction of the spectroscopic factor
for -shell quasi-hole states, but rather to a 7% enhancement. This is in
agreement with analytical results obtained in the harmonic oscillator model.
The center-of-mass effect worsens the discrepancy between present theoretical
models and the experimentally observed single-particle strength. We discuss the
present status of this problem, including some other mechanisms that may be
relevant in this respect.Comment: 14 pages, no figures, uses Revtex, to be published in Phys. Rev. C 58
(1998
Correlation effects in single-particle overlap functions and one-nucleon removal reactions
Single-particle overlap functions and spectroscopic factors are calculated on
the basis of the one-body density matrices (ODM) obtained for the nucleus
employing different approaches to account for the effects of
correlations. The calculations use the relationship between the overlap
functions related to bound states of the (A-1)-particle system and the ODM for
the ground state of the A-particle system. The resulting bound-state overlap
functions are compared and tested in the description of the experimental data
from (p,d) reactions for which the shape of the overlap function is important.Comment: 11 pages, 4 figures include
Two-proton overlap functions in the Jastrow correlation method and cross section of the OC reaction
Using the relationship between the two-particle overlap functions (TOF's) and
the two-body density matrix (TDM), the TOF's for the
OC reaction are calculated on the
basis of a TDM obtained within the Jastrow correlation method. The main
contributions of the removal of and pairs from O
are considered in the calculation of the cross section of the
OC reaction using the Jastrow TOF's
which include short-range correlations (SRC). The results are compared with the
cross sections calculated with different theoretical treatments of the TOF's.Comment: 10 pages, 8 figures, ReVTeX
Projected seniority-two orbital optimization of the Antisymmetric Product of one-reference orbital Geminal
We present a new, non-variational orbital-optimization scheme for the
Antisymmetric Product of one-reference orbital Geminal wave function. Our
approach is motivated by the observation that an orbital-optimized
seniority-zero configuration interaction (CI) expansion yields similar results
to an orbital-optimized seniority-zero-plus-two CI expansion [J. Chem. Phys.,
135, 044119 (2011)]. A numerical analysis is performed for the C, LiF and
CH molecules as well as for the symmetric stretching of hypothetical
(linear) hydrogen chains. For these test cases, the proposed
orbital-optimization protocol yields similar results to its variational orbital
optimization counterpart, but prevents symmetry-breaking of molecular orbitals
in most cases.Comment: 7 pages, 2 figure
Polynomial scaling approximations and dynamic correlation corrections to doubly occupied configuration interaction wave functions
A class of polynomial scaling methods that approximate Doubly Occupied Configuration Interaction (DOCI) wave functions and improve the description of dynamic correlation is introduced. The accuracy of the resulting wave functions is analysed by comparing energies and studying the overlap between the newly developed methods and full configuration interaction wave functions, showing that a low energy does not necessarily entail a good approximation of the exact wave function. Due to the dependence of DOCI wave functions on the single-particle basis chosen, several orbital optimisation algorithms are introduced. An energy-based algorithm using the simulated annealing method is used as a benchmark. As a computationally more affordable alternative, a seniority number minimising algorithm is developed and compared to the energy based one revealing that the seniority minimising orbital set performs well. Given a well-chosen orbital basis, it is shown that the newly developed DOCI based wave functions are especially suitable for the computationally efficient description of static correlation and to lesser extent dynamic correlation.Fil: Van Raemdonck, Mario. Ghent University; BĂ©lgicaFil: Alcoba, Diego Ricardo. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de FĂsica de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de FĂsica de Buenos Aires; ArgentinaFil: Poelmans, Ward. Ghent University; BĂ©lgicaFil: De Baerdemacker, Stijn. Ghent University; BĂ©lgicaFil: Torre, Alicia. Universidad del PaĂs Vasco; EspañaFil: Lain, Luis. Universidad del PaĂs Vasco; EspañaFil: Massaccesi, Gustavo Ernesto. Universidad de Barcelona. Facultad de FĂsica. Departamento de FĂsica Fomental; EspañaFil: Van Neck, D.. Ghent University; BĂ©lgicaFil: Bultinck, P.. Ghent University; BĂ©lgic
One Body Density Matrix, Natural Orbits and Quasi Hole States in 16O and 40Ca
The one body density matrix, momentum distribution, natural orbits and quasi
hole states of 16O and 40Ca are analyzed in the framework of the correlated
basis function theory using state dependent correlations with central and
tensor components. Fermi hypernetted chain integral equations and single
operator chain approximation are employed to sum cluster diagrams at all
orders. The optimal trial wave function is determined by means of the
variational principle and the realistic Argonne v8' two-nucleon and Urbana IX
three-nucleon interactions. The correlated momentum distributions are in good
agreement with the available variational Monte Carlo results and show the well
known enhancement at large momentum values with respect to the independent
particle model. Diagonalization of the density matrix provides the natural
orbits and their occupation numbers. Correlations deplete the occupation number
of the first natural orbitals by more than 10%. The first following ones result
instead occupied by a few percent. Jastrow correlations lower the spectroscopic
factors of the valence states by a few percent (~1-3%) and an additional ~8-12%
depletion is provided by tensor correlations. It is confirmed that short range
correlations do not explain the spectroscopic factors extracted from (e,e'p)
experiments. 2h-1p perturbative corrections in the correlated basis are
expected to provide most of the remaining strength, as in nuclear matter.Comment: 25 pages, 9 figures. Submitted to Phys.Rev.
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