Search results for "Energy minimization"
showing 10 items of 38 documents
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
1996
A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented i…
Ab initiosimulations on rutile-based titania nanowires
2012
The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the a…
[MoO2(SCPh2CO2)2]2− and [MoO(SCPh2CO2)2]− anion complexes. A theoretical structure characterization
1995
Abstract Geometry optimization of [MoO 2 (SCH 2 CO 2 ) 2 ] 2− and [MoO(SCH 2 CO 2 ) 2 ] − systems as models of [MoO 2 (SCPh 2 CO 2 ) 2 ] 2− and [MoO(SCPh 2 CO 2 ) 2 ] − anion complexes have been carried out at STO-3G, 3-21G, LANL1MB and LANL2DZ basis set levels. A comparison of the theoretical results and X-ray experimental data has been performed. STO-3G minimal basis set produces the best geometrical agreement, in particular the distances and orientations of the different ligands linked to molybdenum transition metal. A large structural overlap with STO-3G optimized geometry and X-ray data has been found for the [MoO 2 (SCPh 2 CO 2 ) 2 ] 2− and [MoO(SCPh 2 CO 2 ) 2 ] − anion complexes.
Theoretical study on hydration of two particular diazanaphthalenes
2005
Abstract Cinnoline (1) and Phthalazine (2), diazanaphthalenes involved in certain biological reactions, have been studied computational with the purpose of comparing their protonation and covalent hydration mechanisms. Geometry optimizations of neutral, mono- and di-protonated cations and hydrated products were performed at HF, DFT/B3LYP levels of theory using 6-311G* basis set and single points energies were calculated at the MP2 level of theory using the same basis set. In agreement with experimental results, calculations predict a two-step mechanism resulting in a hydrated cation in which the OH of the water is located depending on the position of both nitrogen in the diazanaphthalene mo…
Perturbative treatment of triple excitations in internally contracted multireference coupled cluster theory.
2012
Internally contracted multireference coupled cluster (ic-MRCC) methods with perturbative treatment of triple excitations are formulated based on Dyall's definition of a zeroth-order Hamiltonian. The iterative models ic-MRCCSDT-1, ic-MRCC3, and their variants ic-MRCCSD(T), ic-MRCC(3) which determine the energy correction from triples by a non-iterative step are consistent in the single-reference limit with CCSDT-1a, CC3, CCSD(T), and CC(3), respectively. Numerical tests on the potential energy surfaces of BeH(2), H(2)O, and N(2) as well as on the structure and harmonic vibrational frequencies of the ozone molecule show that these methods account very well for higher order correlation effects…
A worrisome failure of the CC2 coupled-cluster method when applied to ozone
2010
Abstract The approximate coupled-cluster singles and doubles model CC2 is widely used for calculations of excited states in large molecules. We demonstrate a surprising failure of the CC2 geometry optimization of ozone, whereby the CC2 method predicts a barrierless, exothermic, and symmetric dissociation to three oxygen atoms. This is particularly astonishing since both second-order Moller–Plesset perturbation theory and coupled-cluster singles and doubles give reasonable equilibrium structures. We find that [ [ H , T 1 ] , T 1 ] leads to an unbalanced treatment of T 1 and T 2 in the CC2 equations. Results presented here suggest that considerable caution should be exercised when applying th…
Joint User Association and Dynamic Beam Operation for High Latitude Muti-beam LEO Satellites
2021
In Low Earth Orbit (LEO) satellites, which run in polar orbit, the area of overlap among beams becomes wider as the latitude of satellites increases, which leads to intolerable interference and extra energy consumption. To minimize the onboard power with QoS requirements, we propose an energy optimization model with considering power allocation, user association and dynamic beam ON/OFF operation jointly. Moreover, the frequent beam ON/OFF operations lead to the large number of user handovers, so handover cost is also considered in the model. The original problem is decomposed into two levels due to the high coupling of variables and the successive convex approximation is employed. A low com…
AMYR 2: A new version of a computer program for pair potential calculation of molecular associations
1998
AMYR is a computer program for the calculation of molecular associations using Fraga's pairwise atom-atom potential. The interaction energy is evaluated through a 1R expansion. The electrostatic energy is calculated through either the one-centre-per atom or the three-centres-per atom model by Hunter and Sanders. A pairwise dispersion energy term is included in the potential and corrected by a damping function. The program carries out energy minimizations through variable metric methods. The new version allows for the stationary point analysis of the intermolecular potential by means of the Hessian eigenvalues. Although using low-gradient thresholds optimization procedures to avoid many stat…
Gradient-enhanced model and its micromorphic regularization for simulation of Lüders-like bands in shape memory alloys
2018
Abstract Shape memory alloys, notably NiTi, often exhibit softening pseudoelastic response that results in formation and propagation of Luders-like bands upon loading, for instance, in uniaxial tension. A common approach to modelling softening and strain localization is to resort to gradient-enhanced formulations that are capable of restoring well-posedness of the boundary-value problem. This approach is also followed in the present paper by introducing a gradient-enhancement into a simple one-dimensional model of pseudoelasticity. In order to facilitate computational treatment, a micromorphic-type regularization of the gradient-enhanced model is subsequently performed. The formulation empl…
Atomistic modeling of crystal structure of Ca1.67SiHx
2015
The atomic structure of calcium-silicate-hydrate (C-1.67-S-H-x) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three m…