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1.
J Chem Phys ; 155(5): 054102, 2021 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-34364321

RESUMO

Markov state models (MSMs) have become one of the preferred methods for the analysis and interpretation of molecular dynamics (MD) simulations of conformational transitions in biopolymers. While there is great variation in terms of implementation, a well-defined workflow involving multiple steps is often adopted. Typically, molecular coordinates are first subjected to dimensionality reduction and then clustered into small "microstates," which are subsequently lumped into "macrostates" using the information from the slowest eigenmodes. However, the microstate dynamics is often non-Markovian, and long lag times are required to converge the relevant slow dynamics in the MSM. Here, we propose a variation on this typical workflow, taking advantage of hierarchical density-based clustering. When applied to simulation data, this type of clustering separates high population regions of conformational space from others that are rarely visited. In this way, density-based clustering naturally implements assignment of the data based on transitions between metastable states, resulting in a core-set MSM. As a result, the state definition becomes more consistent with the assumption of Markovianity, and the timescales of the slow dynamics of the system are recovered more effectively. We present results of this simplified workflow for a model potential and MD simulations of the alanine dipeptide and the FiP35 WW domain.


Assuntos
Dipeptídeos/química , Cadeias de Markov , Simulação de Dinâmica Molecular/estatística & dados numéricos , Proteínas/química , Análise por Conglomerados , Conformação Proteica , Domínios WW
2.
J Chem Phys ; 153(4): 044101, 2020 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-32752719

RESUMO

Analytic energy gradients with respect to nuclear motion are derived for non-singlet compounds in the natural orbital functional theory. We exploit the formulation for multiplets in order to obtain a simple formula valid for any many-electron system in its ground mixed state with a total spin S and all possible spin projection Sz values. We demonstrate that the analytic gradients can be obtained without resorting to linear response theory or involving iterative procedures. A single evaluation is required, so integral derivatives can be computed on-the-fly along the calculation, thus improving the effectiveness of screening by the Schwarz inequality. The results for small- and medium-sized molecules with many spin multiplicities are shown. Our results are compared with the experimental data and accurate theoretical equilibrium geometries.

3.
J Chem Phys ; 152(6): 064108, 2020 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-32061239

RESUMO

This work deals with the problem of strongly correlated electrons in two-dimensions. We give a reduced density matrix (RDM) based tool through which the ground-state energy is given as a functional of the natural orbitals and their occupation numbers. Specifically, the Piris Natural Orbital Functional 7 (PNOF7) is used for studying the 2D Hubbard model and hydrogen square lattices. The singlet ground-state is studied, as well as the doublet mixed quantum state obtained by extracting an electron from the system. Our method satisfies two-index necessary N-representability conditions of the two-particle RDM (2RDM) and guarantees the conservation of the total spin. We show the ability of PNOF7 to describe strong correlation effects in two-dimensional (2D) systems by comparing our results with the exact diagonalization, density matrix renormalization group (DMRG), and auxiliary-field quantum Monte Carlo calculations. PNOF7 overcomes variational 2RDM methods with two- and three-index positivity N-representability conditions, reducing computational cost to mean-field scaling. Consistent results are obtained for small and large systems up to 144 electrons, weak and strong correlation regimes, and many filling situations. Unlike other methods, there is no dependence on dimensionality in the results obtained with PNOF7 and no particular difficulties have been observed to converge PNOF7 away from half-filling. Smooth double occupancy of sites is obtained, regardless of the filling. Symmetric dissociation of 2D hydrogen lattices shows that long-range nondynamic correlation dramatically affects electron detachment energies. PNOF7 compares well with DMRG along the dissociation curve.

4.
J Phys Condens Matter ; 32(17): 17LT01, 2020 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-31952058

RESUMO

The one-particle reduced density matrix functional theory in its natural orbital functional (NOF) version is used to study strongly correlated electrons. We show the ability of the Piris NOF 7 (PNOF7) to describe non-dynamic correlation effects in one-dimensional (1D) systems. An extensive study of 1D systems that includes Hydrogen (H) chains and the 1D Hubbard model with periodic boundary conditions is provided. Different filling situations and large sizes with up to 122 electrons are considered. Compared to quasi-exact results, PNOF7 is accurate in different correlation regimes for the 1D Hubbard model even away from the half-filling, and maintains its accuracy when the system size increases. The symmetric and asymmetric dissociations of the linear H chain composed of 50 atoms are described to remark the importance of long-range interactions in presence of strong correlation effects. Our results compare remarkably well with those obtained at the density-matrix renormalization group level of theory.

5.
J Phys Condens Matter ; 31(16): 165501, 2019 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-30673638

RESUMO

Natural orbital functional theory is considered for systems with one or more unpaired electrons. An extension of the Piris natural orbital functional (PNOF) based on electron pairing approach is presented, specifically, we extend the independent pair model, PNOF5, and the interactive pair model PNOF7 to describe spin-uncompensated systems. An explicit form for the two-electron cumulant of high-spin cases is only taken into account, so that singly occupied orbitals with the same spin are solely considered. The rest of the electron pairs with opposite spins remain paired. The reconstructed two-particle reduced density matrix fulfills certain N-representability necessary conditions, as well as guarantees the conservation of the total spin. The theory is applied to model systems with strong non-dynamic (static) electron correlation, namely, the one-dimensional Hubbard model with periodic boundary conditions and hydrogen rings. For the latter, PNOF7 compares well with exact diagonalization results so the model presented here is able to provide a correct description of the strong-correlation effects.

6.
J Chem Phys ; 151(24): 244121, 2019 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-31893894

RESUMO

An adiabatic connection (AC) is developed as an electron correlation correction for doubly occupied configuration interaction (DOCI) wave functions. Following the work of Pernal [Phys. Rev. Lett. 120, 013001 (2018)], the working equations of the approach, termed AC-DOCI, are rooted in the extended random phase approximation (ERPA) and require knowledge of only the ground-state two-electron reduced density matrix (2RDM) from the DOCI. As such, the AC is naturally suited to modeling electron correlation in variational 2RDM (v2RDM)-based approximations to the DOCI. The v2RDM-driven AC-DOCI is applied to the dissociation of molecular nitrogen and the double dissociation of water; the approach yields energies that are similar in quality to those from second-order multireference perturbation theory near equilibrium, but the quality of the AC-DOCI energy degrades at stretched geometries. The exact adiabatic connection path suggests the assumption that the one-electron reduced-density matrix is constant along the AC path is invalid at stretched geometries, but this deficiency alone cannot explain the observed behavior. Rather, it appears that the ERPA's single-particle-transition ansatz cannot, in general, provide good approximations to the 2RDM along the AC path. The AC-DOCI is also applied to a set of 45 reaction energies; for these systems, the approach has an average accuracy that is comparable to that of single-reference second-order many-body perturbation theory.

7.
Artigo em Inglês | MEDLINE | ID: mdl-29313829

RESUMO

There was an error when collecting the data in the results corresponding to PNOF7 for the homogeneous 4 sites square and 6 sites hexagone Hubbard models reported in the article. And also for MBB and CGA for the 10 sites Hubbard model including an Aubry-André potential.

8.
J Chem Phys ; 146(1): 014102, 2017 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-28063441

RESUMO

The analytic energy gradients with respect to nuclear motion are derived for the natural orbital functional (NOF) theory. The resulting equations do not require resorting to linear-response theory, so the computation of NOF energy gradients is analogous to gradient calculations at the Hartree-Fock level of theory. The structures of 15 spin-compensated systems, composed of first- and second-row atoms, are optimized employing the conjugate gradient algorithm. As functionals, two orbital-pairing approaches were used, namely, the fifth and sixth Piris NOFs (PNOF5 and PNOF6). For the latter, the obtained equilibrium geometries are compared with coupled cluster singles and doubles calculations and accurate empirical data.

9.
J Chem Phys ; 144(20): 204108, 2016 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-27250280

RESUMO

The molecular electric dipole, quadrupole, and octupole moments of a selected set of 21 spin-compensated molecules are determined employing the extended version of the Piris natural orbital functional 6 (PNOF6), using the triple-ζ Gaussian basis set with polarization functions developed by Sadlej, at the experimental geometries. The performance of the PNOF6 is established by carrying out a statistical analysis of the mean absolute errors with respect to the experiment. The calculated PNOF6 electric moments agree satisfactorily with the corresponding experimental data and are in good agreement with the values obtained by accurate ab initio methods, namely, the coupled-cluster single and doubles and multi-reference single and double excitation configuration interaction methods.

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