Search results for "Energy minimization"
showing 10 items of 38 documents
Improving Docking Performance Using Negative Image-Based Rescoring
2017
Despite the large computational costs of molecular docking, the default scoring functions are often unable to recognize the active hits from the inactive molecules in large-scale virtual screening experiments. Thus, even though a correct binding pose might be sampled during the docking, the active compound or its biologically relevant pose is not necessarily given high enough score to arouse the attention. Various rescoring and post-processing approaches have emerged for improving the docking performance. Here, it is shown that the very early enrichment (number of actives scored higher than 1% of the highest ranked decoys) can be improved on average 2.5-fold or even 8.7-fold by comparing th…
Adaptive Bias Field Correction: Application on Abdominal MR Images
2017
Segmentation of medical images is one of the most important phases for disease diagnosis. Accuracy, robustness and stability of the results obtained by image segmentation is a major concern. Many segmentation methods rely on absolute values of intensity level, which are affected by a bias term due to in-homogeneous field in magnetic resonance images. The main objective of this paper is two folded: (1) To show efficiency of an energy minimization based approach, which uses intrinsic component optimization, on abdominal magnetic resonance images. (2) To propose an adaptive method to stop the optimization automatically. The proposed method can control the value of the energy functional and sto…
Adversarial reverse mapping of equilibrated condensed-phase molecular structures
2020
A tight and consistent link between resolutions is crucial to further expand the impact of multiscale modeling for complex materials. We herein tackle the generation of condensed molecular structures as a refinement -- backmapping -- of a coarse-grained structure. Traditional schemes start from a rough coarse-to-fine mapping and perform further energy minimization and molecular dynamics simulations to equilibrate the system. In this study we introduce DeepBackmap: A deep neural network based approach to directly predict equilibrated molecular structures for condensed-phase systems. We use generative adversarial networks to learn the Boltzmann distribution from training data and realize reve…
Theoretical study on hydration of symmetrically different diazanaphthalenes
2005
Abstract Quinazoline (symmetrical) and quinoxaline (unsymmetrical), 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 diprotonated cations and hydrated products have been carried out at three levels of theory. Geometry optimizations were performed at HF, DFT/B3LYP levels of theory using 6-311G* basis set and single point energies were calculated at the MP2 level of theory using the same basis set. In agreement with experimental results, calculations predict a two steps mechanism resulting in a hydrated cation in which the OH…
A theoretical study of the electronic spectrum of styrene
1999
Abstract The electronic spectrum of styrene has been studied by using multiconfigurational second-order perturbation theory (CASPT2). The study includes geometry optimization of the ground state, the lowest triplet state, and the lowest singlet excited state. The covalent 2 1 A ′ state placed vertically at 4.34 eV is assigned to the first band. The 1 1 A ′→3 1 A ′ transition located at 4.97 eV is responsible for the second band. The most intense feature involves the 5 1 A ′ state, which is calculated to lie 6.19 eV above the ground state. The lowest singlet–singlet Rydberg transition (3s) is predicted to occur at 5.85 eV.
ChemInform Abstract: Spectroscopic and Theoretical Studies on the Internal Rotational Barrier of 1-Acetylcyclohexene
1987
Abstract MINDO-3 molecular orbital calculations with full geometry optimization have been carried out on 1-acetylcyclohexene (ACH) in order to estimate the rotational barrier for the acetyl group, and to localize the less energetic conformation. MNDO calculations have also been carried out for comparative purposes. Both methods point to the non-delocalized structure with the two π-clouds perpendicular to the less energetic conformation. A decomposition of the barrier energy by means of Fourier analysis is made in order to characterize the contributions to the barrier. The UV spectrum of ACH has been recorded both in vapor phase and in hexane solution. These spectra are related to the one ca…
The Dialectics of Free Energy Minimization
2019
Karl Friston’s free energy minimization has been received with great enthusiasm. With good reason: it not only makes the bold claim to a unifying theory of the brain, but it is presented as an a priori principle applicable to living systems in general. In this article, we set out to show how the breadth of scope of Friston’s framework converges with the dialectics of Georg Hegel. Through an appeal to the work of Catherine Malabou, we aim to demonstrate how Friston not only reinvigorates Hegelian dialectics from the perspective of neuroscience, but that the implicit alignment with Hegel necessitates a reading of free energy minimization from the perspective of Hegel’s speculative philosophy.…
Fuzzy Logic based model for self-optimizing energy consumption in IoT environment
2021
Energy optimization is essential in IoT environments due to energy constraints for some IoT components. In fact, energy consumption has a direct impact on IoT system lifetime, which represents an important Quality of Service (QoS) parameter for IoT environments. In order to extend the IoT system lifetime, energy consumption optimization should be considered in several IoT components. In this paper, we specify an energy self-optimizing mechanism allowing to minimize data transmission energy consumption of IoT objects. This mechanism enables selecting specific objects to send the desired data while minimizing the energy consumed for the corresponding communication. Our proposal is made of a M…
High-spin states in tetrahedral X4 clusters (X = H, Li, Na, K)
2010
The high-spin electronic states for lithium, sodium, and potassium four-atom clusters were studied. In particular, we performed coupled cluster geometry optimization of the quintet state in tetrahedral geometry. The quintet state of these systems is characterized by having all the valence electron Unpaired, giving rise to the so-called no-pair bonding. Single-point full configuration interaction computations on the equilibrium geometries for the various Clusters are also presented. The analysis of the valence orbitals in a localized representation confirms the importance of the p atomic orbitals to explain this unusual type of bond. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 110: 8…
Graph cut-based method for segmenting the left ventricle from MRI or echocardiographic images
2017
International audience; In this paper, we present a fast and interactive graph cut method for 3D segmentation of the endocardial wall of the left ventricle (LV) adapted to work on two of the most widely used modalities: magnetic resonance imaging (MRI) and echocardiography. Our method accounts for the fundamentally different nature of both modalities: 3D echocardiographic images have a low contrast, a poor signal-to-noise ratio and frequent signal drop, while MR images are more detailed but also cluttered and contain highly anisotropic voxels. The main characteristic of our method is to work in a 3D Bezier coordinate system instead of the original Euclidean space. This comes with several ad…