Search results for "Energy minimization"
showing 10 items of 38 documents
Forecasting Techniques for Energy Optimization in Buildings
2014
Ab initio conformational study of 2,2′:5′,2″-terthiophene
1996
Abstract The conformers of 2,2′:5′,2″-terthiophene were determined through ab initio MO full geometry optimization with a 6-31G * basis set. Different minima were found corresponding to twisted anti, anti, syn, anti and syn, syn structures. An estimate of the interconversion rate between conformers was performed.
Improved AMYR program: an algorithm for the theoretical simulation of molecular associations, including geometrical and topological characterization …
1991
Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility of carrying out energy minimizations through variable metric methods, as well as the optional calculation of geometrical and topological indices. Program AMYR has been adapted also for high-performance computing and vectorization. An interactive version of the program carries out real-time molecular graphics showing simultaneously the energy prof…
Solution structure of aD,L-alternating oligonorleucine as a model of double-stranded antiparallel ?-helix
2002
Conformational characteristics of alternating D,L linear peptides are of particular interest because of their capacity to form transmembrane channels with different transport properties, as some natural antibiotics do. Single- and double-stranded beta-helical structures are common for alternating D,L peptides. The stability of the beta-helix depends on several structural factors, such as the backbone peptide length, type and position of side chains, and nature of terminal groups. The NMR and molecular dynamics solution conformation of a synthetic alternating D,L-oligopeptide with 15 norleucines (XVMe) has been used as a model to get insight in to the conformational features of double-strand…
Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results
2018
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
The energy minimization problem for two-level dissipative quantum systems
2010
In this article, we study the energy minimization problem of dissipative two-level quantum systems whose dynamics is governed by the Kossakowski–Lindblad equations. In the first part, we classify the extremal curve solutions of the Pontryagin maximum principle. The optimality properties are analyzed using the concept of conjugate points and the Hamilton–Jacobi–Bellman equation. This analysis completed by numerical simulations based on adapted algorithms allows a computation of the optimal control law whose robustness with respect to the initial conditions and dissipative parameters is also detailed. In the final section, an application in nuclear magnetic resonance is presented.
Multiframe image restoration in the presence of noisy blur kernel
2009
We wish to recover an original image u from several blurry-noisy versions f k , called frames. We assume a more severe degradation model, in which the image u has been blurred by a noisy (stochastic) point spread function. We consider the problem of restoring the degraded image in a variational framework. Since the recovery of u from one single frame f is a highly ill-posed problem, we formulate two minimization problems based on the multiframe approach proposed for image super-resolution by Marquina-Osher [13]. Several experimental results for image restoration are shown, illustrating that the proposed models give visually satisfactory results.
Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing…
1998
We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by "homology distance constraints," while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good …
Systematic conformational search analysis of the SRR and RRR epimers of 7-hydroxymatairesinol
2009
An extensive and systematic conformational search was performed on the two epimers of the natural lignan 7-hydroxymatairesinol (HMR), by means of a home-made Systematic Conformational Search Analysis (SCSA) code, designed to select more and more stable conformers through sequential geometry optimization of trial structures at increasing levels of calculation theory. In the present case, the starting molecular structures were selected by the semi-empirical AM1 method and filtered – i.e. decreased in number by choosing the more stable species – on the basis of their energy calculated by the HF method and the 6-31G(d) basis set. The geometries obtained were further refined by performing densit…