XtalOpt: An open-source evolutionary algorithm for crystal structure prediction

The implementation and testing of XtalOpt, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XtalOpt are optimized using a novel benchmarking scheme. XtalOpt is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface.

Program summary

Program title:XtalOptCatalogue identifier: AEGX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 36 849No. of bytes in distributed program, including test data, etc.: 1 149 399Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: LinuxClassification: 7.7External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7].Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available to the scientific community for use and collaboration under the GNU Public License.Running time: User dependent. The program runs until stopped by the user.References:

• [1] 

  http://www.gnu.org/licenses/gpl.html.

• [2] 

  http://www.trolltech.com/.

• [3] 

  http://openbabel.org/.

• [4] 

  http://avogadro.openmolecules.net.

• [5] 

  http://cms.mpi.univie.ac.at/vasp.

• [6] 

  http://www.quantum-espresso.org.

• [7] 

  https://www.ivec.org/gulp.

• [8] 

  http://spglib.sourceforge.net.

     

Developing an Automated Enzyme Immunoassay for High-Throughput Screening of Bovine Serum Antibodies to Neospora Caninum

An enzyme-linked immunosorbent assay (ELISA) for Neospora caninum antibodies was automated with a robotic workstation, the Beckman Coulter Biomek 2000, to screen 200 bovine sera. Comparing these results with manually run ELISA data, a 95.92% agreement (K = 0.9592) between the two assays was obtained. The automated assay was specific and sensitive with excellent positive and negative predictive values. The results were repeatable and reproducible. The automation flexibility was high and the operation complexity was minimal. High-throughput screening (HTS) for bovine antibodies to Neospora caninum was achieved. The assay was developed according to the internationally recognized ISO17025 standard requirements.     

Semantics-driven annotation of patient-specific 3D data: a step to assist diagnosis and treatment of rheumatoid arthritis

In the digital era, patient-specific 3D models (3D-PSMs) are becoming increasingly relevant in computer-assisted diagnosis, surgery training on digital models, or implant design. While advanced imaging and reconstruction techniques can create accurate and detailed 3D models of patients’ anatomy, software tools that are able to fully exploit the potential of 3D-PSMs are still far from being satisfactory. In particular, there is still a lack of integrated approaches for extracting, coding, sharing and retrieving medically relevant information from 3D-PSMs and use it concretely as a support to diagnosis and treatment. In this article, we propose the SemAnatomy3D framework, which demonstrates how the ontology-driven annotation of 3D-PSMs and of their anatomically relevant features (parts of relevance) can assist clinicians to document more effectively pathologies and their evolution. We exemplify the idea in the context of the diagnosis of rheumatoid arthritis of the hand district, and show how feature extraction tools and semantic 3D annotation can provide a rich characterization of anatomical landmarks (e.g., articular facets, prominent features, ligament attachments) and pathological markers (erosions, bone loss). The core contributions are an ontology-driven part-based annotation method for the 3D-PSMs and a novel automatic localization of erosion and quantification of the OMERACT RAMRIS erosion score. Finally, our results have been compared against a medical ground truth.     

A new removable resist for high aspect ratio applications

A variety of different photo resists are used for fabrication of MEMS. Presently good results were reported for SU-8, a chemically amplified negative tone photoresist. But SU-8 has a disadvantage for some applications in LIGA technique, especially in the X-ray mask fabrication. After processing the finished resist pattern are hardly soluble from the substrate. This paper will briefly describe the current status of the development of the new negative tone photoresist CAR 44 whose big advantage is the easy removableness of the cross linked pattern. This work widely uses the contents of the presentation “A New Removable Resist for High Aspect Ratio Applications” to the High Aspect Ratio Micro Structure Technology workshop HARMST 2005 held in Gyeongyu (Republic of Korea), June 10–13, 2005.     

Functional characterization of protein stabilized emulsions: Emulsifying behaviour of proteins in a valve homogenizer

Protein stabilised emulsions have been prepared in a valve homogeniser incorporated into a recirculating emulsification system, where the power input and number of passes have been varied. The food proteins studied were a soy-bean protein isolate, a whey protein concentrate (WPC) and a sodium caseinate. The emulsions obtained were characterized in terms of particle size distribution and amount of protein adsorbed on to the fat surface (protein load). Generally, the final fat surface area of the emulsions obtained increases more as a function of power input than as a function of number of passes. Distribution width, c_s, decreases mostly with increasing power supply and number of passes, but at the highest power input c_s increases. The protein load on the fat globules is largely determined by the fat surface area and by the type of protein adsorbed. The soy proteins give a high protein load and the caseinates give a low protein adsorption at small fat surface areas created. This relation is reversed at large surface areas of the fat globules. The relation between percentage protein adsorbed from bulk as a function of surface area suggests that the caseinates mainly cover the newly created interface by adsorption from the bulk, whereas the soy proteins fulfil this task mostly by spreading at the interface. Salt addition to 0.2M-NaCl enhances protein adsorption at the fat globule interface in the case of soy protein and caseinate, but for the whey proteins protein load is higher in distilled water.     

Mobilizing Company Members' Full Innovative Potential

Most of the literature on innovation management highlights the fundamental role played by people in the innovation process and the need to fully develop the creative and innovative potential of organizations' members. This article offers the result of extensive research carried out among some of the most innovative companies in the Basque Country, a highly innovative region located in the north of Spain. It draws interesting conclusions about how these innovative companies combine strong leadership, human resource practices, and an organizational culture that enhances innovation capabilities among the company's employees. More specifically, it answers questions such as the following: Are human resources policies, leadership, and innovation culture implemented equally in Basque innovative companies? Do companies make the same effort in deploying these elements or routines and practices related to them? Can we see a pattern in the use of these elements among innovative firms? © 2012 Wiley Periodicals, Inc.     

Reviews: A text for all reasons

J. Wellington. (2000). Teaching and learning secondary science: Contemporary issues and practical approaches. London: Routledge. ISBN 0–4152–1403–3     

Persistent excitation condition within the dual control framework

Model Predictive Control framework is currently used in many different fields of expertise. The inherent part and very often also the main bottleneck is the model of a process used for the computation of predictions.Due to many reasons e.g. ageing, from time to time there exists a need to adjust/re-identify (if there was already some kind of a model-based controller) or to construct a brand new model (in other cases). Frequently, the process generating the data is under some kind of control, imposing thus problems when classical open loop identification methods are considered. The need for models identified from the data gathered in a closed-loop fashion and a request for possible re-identification of the model parameters lead to the emerge of dual control where the problems of control and system identification are addressed simultaneously.In this paper, we present a new algorithm based on the persistent excitation condition when the minimal eigenvalue of the information matrix is maximized in order to have sufficiently exciting optimal control signal satisfying the control requirements.     

FMAP: Distributed cooperative multi-agent planning

This paper proposes FMAP (Forward Multi-Agent Planning), a fully-distributed multi-agent planning method that integrates planning and coordination. Although FMAP is specifically aimed at solving problems that require cooperation among agents, the flexibility of the domain-independent planning model allows FMAP to tackle multi-agent planning tasks of any type. In FMAP, agents jointly explore the plan space by building up refinement plans through a complete and flexible forward-chaining partial-order planner. The search is guided by h _{D T G} , a novel heuristic function that is based on the concepts of Domain Transition Graph and frontier state and is optimized to evaluate plans in distributed environments. Agents in FMAP apply an advanced privacy model that allows them to adequately keep private information while communicating only the data of the refinement plans that is relevant to each of the participating agents. Experimental results show that FMAP is a general-purpose approach that efficiently solves tightly-coupled domains that have specialized agents and cooperative goals as well as loosely-coupled problems. Specifically, the empirical evaluation shows that FMAP outperforms current MAP systems at solving complex planning tasks that are adapted from the International Planning Competition benchmarks.     

Estimation of Basins of Attraction for Uncertain Systems with Affine and Lipschitz Dynamics

This paper is devoted to estimation and numerical approximation of basins of attraction for a class of uncertain systems. We consider systems described by a differential equation depending of a disturbance known by its bounds. By using viability theory tools, we derive basins of attraction lower and upper estimates. We present numerical simulation results of the viability kernel algorithm to basin of attraction approximation problems.