Quantum control implemented as combinatorial optimization

Optimal control theory provides a general means for designing controls to manipulate quantum phenomena. Traditional implementation requires solving coupled nonlinear equations to obtain the optimal control solution, whereas this work introduces a combinatorial quantum control (CQC) algorithm to avoid this complexity. The CQC technique uses a predetermined toolkit of small time step propagators in conjunction with combinatorial optimization to identify a proper sequence for the toolkit members. Results indicate that the CQC technique exhibits invariance of search effort to the number of system states and very favorable scaling upon comparison to a standard gradient algorithm, taking into consideration that CQC is easily parallelizable. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Simulation and experimental study of an indigenously designed and constructed THGEM-based microdosimeter for dose-equivalent measurement

Most of the GEM/THGEM-based microdosimetric detectors presented in the literature simulate 2 μm of tissue which results in a flat neutron dose-equivalent response in the MeV region. The objective of this work was to introduce a neutron microdosimeter with a more extended flat response. In this regard, a THGEM-based microdosimeter with plexiglas walls, simulating 1 μm of tissue was designed and constructed. Its performance was investigated by both simulation and experimentation to determine the microdosimetric quantity of “lineal energy”.In the simulation study, lineal energy distribution, mean quality factor and dose-equivalent response of the microdosimeter for eleven neutron energies from 10 keV to 14 MeV, along with the energy spectrum of ²⁴¹Am-Be neutrons, were calculated by the Geant4 simulation toolkit. Obtained lineal energy distributions were compatible with the distributions determined by a Rossi counter. Also, the mean quality factors agreed well with the values reported by the ICRU report 40 which confirmed tissue equivalent behavior of the microdosimeter. They were different from the effective quality factor values within 15% between 20 keV and 14 MeV. This led to a flat dose-equivalent response with 20% difference from a median value of 0.82 in the above energy range which was an improvement compared with other THGEM-based detectors, simulating 2 μm of tissue. In spite of the satisfactory determination of the dose-equivalent, the microdosimeter had low detection sensitivity.In the experimental study, the measured lineal energy distribution of ²⁴¹Am-Be neutrons was in agreement with the simulated distribution. Further, the measured mean quality factor and dose-equivalent differed by 1.5% and 3.5%, respectively, from the calculated values. Finally, it could be concluded that the investigated microdosimeter reliably determined the desired dose-equivalent value of each neutron field with every energy spectrum lying between 20 keV and 14 MeV.     

Parametrization of macrolide antibiotics using the force field toolkit

Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMM‐compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given. © 2015 Wiley Periodicals, Inc.     

基于LabVIEW的自由活塞式斯特林制冷机性能测试系统开发

制冷机的自动性能测试、实验处理系统可大幅降低工作量,并保证测试的准确性。针对中国电子科技集团公司第十六研究所新研制开发的自由活塞式斯特林制冷机,开发了一种新的基于虚拟仪器的性能测试系统,该系统通过硬件和软件相结合,自动采集制冷机性能测试中的相关参数,并实现数据的实时显示、存储和图形化显示等功能。该测试系统测试制冷机性能以判定是否满足使用要求。该系统的开发应用将极大方便的提高测试的工作效率,加速合格制冷机的筛选工作。     

Internet resources for agent-based modelling

The use of agent-based models (ABMs) is steadily increasing in all the disciplines including environmental chemistry and toxicology. This growth is mainly driven by their ability to address problems that conventional modelling techniques cannot, such as the change of scale or the emergence of unanticipated phenomena resulting from interactions between their constitutive goal-directed agents. After a brief introduction on the basic principles of agent-based modelling and the presentation of selected case studies, the main software resources available on the Internet are presented. An attempt is made to estimate the complexity of these tools versus their potentialities and flexibility.     

A k-mean-directions Algorithm for Fast Clustering of Data on the Sphere

A k-means-type algorithm is proposed for efficiently clustering data constrained to lie on the surface of a p-dimensional unit sphere, or data that are mean-zero-unit-variance standardized observations such as those that occur when using Euclidean distance to cluster time series gene expression data using a correlation metric. We also provide methodology to initialize the algorithm and to estimate the number of clusters in the dataset. Results from a detailed series of experiments show excellent performance, even with very large datasets. The methodology is applied to the analysis of the mitotic cell division cycle of budding yeast dataset of Cho et al. [Molecular Cell (1998), 2, 65–73]. The entire dataset has not been analyzed previously, so our analysis provides an understanding for the complete set of genes acting in concert and differentially. We also use our methodology on the submitted abstracts of oral presentations made at the 2008 Joint Statistical Meetings (JSM) to identify similar topics. Our identified groups are both interpretable and distinct and the methodology provides a possible automated tool for efficient parallel scheduling of presentations at professional meetings.

The supplemental materials described in the article are available in the online supplements.     

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation

To assess the chemical reactivity, toxicity, and mobility of pollutants in the environment, knowledge of their species distributions is critical. Because their direct measurement is often infeasible, speciation modeling is widely adopted. Mercury (Hg) is a representative pollutant for which study of its speciation benefits from modeling. However, Hg speciation modeling is often hindered by a lack of reliable thermodynamic constants. Although computational chemistry (e.g., density functional theory [DFT]) can generate these constants, methods for directly coupling DFT and speciation modeling are not available. Here, we combine computational chemistry and continuum-scale modeling with curated online databases to ameliorate the problem of unreliable inputs to Hg speciation modeling. Our AQUA-MER databases and web server ( https://aquamer.ornl.gov ) provides direct speciation results by combining web-based interfaces to a speciation calculator, databases of thermodynamic constants, and a computational chemistry toolkit to estimate missing constants. Although Hg is presented as a concrete use case, AQUA-MER can also be readily applied to other elements. © 2019 Wiley Periodicals, Inc.     

Synthesis of β-Diamine Building Blocks by Photocatalytic Hydroamination of Enecarbamates with Amines,Ammonia and N−H Heterocycles

3-Amino-substituted saturated nitrogen heterocycles are an important subclass of β-diamines, appearing in a number of clinical agents. Herein, we report a unified approach to these products based upon the regioselective photoredox-mediated hydroamination of enecarbamates. The amine coupling partner can encompass diverse amine types under a single set of reaction conditions, including primary alkyl amines, ammonia, aryl and heteroaryl amines, and N−H heterocycles. The method enables the synthesis of a wide range of pharmaceutically relevant building blocks.     

Monte Carlo simulations of an innovative molecular breast imaging system for the small breast cancer diagnosis using GATE

ABSTRACT

This paper draws attention to the study of performance of a new Molecular Breast Imaging (MBI) device, whose purpose is the early diagnosis of breast cancer, using Monte Carlo simulations. MBI provides functional and specific information that are more appropriated to dense breasts. Two asymmetric heads with different types of collimators, facing each other in anti-parallel viewing direction, characterize the system. Detectors and phantoms, together with the data taking procedure, are shortly reported. Monte Carlo simulations using the GATE (GEANT4 Application for Tomographic Emission) simulation toolkit have been implemented to evaluate the optimal detector configuration, in terms of sensitivity and spatial resolution, and also to reproduce the real experimental data. The device can be used both in spot compression and in Limited Angle Tomography (LAT); in the latter configuration one detector head with pinhole collimator is able to rotate around the breast in order to diagnose and localized the small tumors.