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 $p$-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 $^{16}O$ 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 16^{16}O(e,e′pp)14(e,e^{\prime}pp)^{14}Cg.s._{\rm g.s.} reaction

Using the relationship between the two-particle overlap functions (TOF's) and the two-body density matrix (TDM), the TOF's for the $^{16}$O$(e,e^{\prime}pp)^{14}$C$_{\rm g.s.}$ reaction are calculated on the basis of a TDM obtained within the Jastrow correlation method. The main contributions of the removal of $^1S_0$ and $^3P_1$ $pp$ pairs from $^{16}$O are considered in the calculation of the cross section of the $^{16}$O$(e,e^{\prime}pp)^{14}$C$_{\rm g.s.}$ 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$_2$, LiF and CH$_2$ 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; BélgicaFil: Alcoba, Diego Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Poelmans, Ward. Ghent University; BélgicaFil: De Baerdemacker, Stijn. Ghent University; BélgicaFil: Torre, Alicia. Universidad del País Vasco; EspañaFil: Lain, Luis. Universidad del País Vasco; EspañaFil: Massaccesi, Gustavo Ernesto. Universidad de Barcelona. Facultad de Física. Departamento de Física Fomental; EspañaFil: Van Neck, D.. Ghent University; BélgicaFil: Bultinck, P.. Ghent University; Bélgic

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.