Development Of Hybrid Method Research Articles

Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11.

ABSTRACTHybrid approaches combine computational methods with experimental data. The information contained in the experimental data can be leveraged to probe the structure of proteins otherwise elusive to computational methods. Compared with computational methods, the structures produced by hybrid methods exhibit some degree of experimental validation. In spite of these advantages, most hybrid methods have not yet been validated in blind tests, hampering their development. Here, we describe the first blind test of a specific cross‐link based hybrid method in CASP. This blind test was coordinated by the CASP organizers and utilized a novel, high‐density cross‐linking/mass‐spectrometry (CLMS) approach that is able to collect high‐density CLMS data in a matter of days. This experimental protocol was developed in the Rappsilber laboratory. This approach exploits the chemistry of a highly reactive, photoactivatable cross‐linker to produce an order of magnitude more cross‐links than homobifunctional cross‐linkers. The Rappsilber laboratory generated experimental CLMS data based on this protocol, submitted the data to the CASP organizers which then released this data to the CASP11 prediction groups in a separate, CLMS assisted modeling experiment. We did not observe a clear improvement of assisted models, presumably because the properties of the CLMS data—uncertainty in cross‐link identification and residue‐residue assignment, and uneven distribution over the protein—were largely unknown to the prediction groups and their approaches were not yet tailored to this kind of data. We also suggest modifications to the CLMS‐CASP experiment and discuss the importance of rigorous blind testing in the development of hybrid methods. Proteins 2016; 84(Suppl 1):152–163. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Estimating job cycle time in a wafer fabrication factory: A novel and effective approach based on post-classification

Estimating job cycle time is an important task for a semiconductor manufacturer as it helps to strengthen relationships with customers and is also conducive to the sustainable development of the manufacturer. The research trend in this field has moved toward the development of hybrid methods, especially those that are classification-based. Most existing methods use pre-classification; however, such methods have several drawbacks, such as incompatibility with the estimation method and unequal sizes of different job groups. In contrast, a post-classification approach has great potential, and therefore is used as a basis for the new approach in this study. In the proposed methodology, a systematic procedure is established to divide jobs into several groups according to their estimation errors. In this way, the classification and estimation stages can be combined seamlessly because they optimize the same objectives. A real case is used to evaluate the effectiveness of the proposed methodology and the experimental results support its superiority over several existing methods. The shortcomings of the existing methods based on pre-classification are also clearly illustrated.

Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method.

The increasing power and popularity of cryo-electron microscopy (cryo-EM) in structural biology brought about the development of so-called hybrid methods, which permit the interpretation of cryo-EM density maps beyond their nominal resolution in terms of atomic models. The Cryo-EM Modeling Challenge 2010 is the first community effort to bring together developers of hybrid methods as well as cryo-EM experimentalists. Participating in the challenge, the molecular dynamics flexible fitting (MDFF) method was applied to a number of cryo-EM density maps. The results are described here with special emphasis on the use of symmetry-based restraints to improve the quality of atomic models derived from density maps of symmetric complexes; on a comparison of the stereochemical quality of atomic models resulting from different hybrid methods; and on application of MDFF to electron crystallography data.

Development of Hybrid Method between Finite Element Method and Geometrical Theory for Propagation Simulation of Ultrasonic Waves

Development of Hybrid Method between Finite Element Method and Geometrical Theory for Propagation Simulation of Ultrasonic Waves

Multiscale overlap coupling for hybrid computations

A class of multiscale overlap coupling methods is proposed for hybrid computations which supplement partially-resolved simulations using low-frequency solutions. In this class of methods, the largest resolved scales of the partially-resolved simulation are forced to resemble low-frequency solutions in overlapping near-boundary regions. Simultaneously, the higher-frequency resolved scales are allowed to develop freely. The latter feature addresses a basic deficiency which has been encountered in the development of hybrid methods, that of poorly-excited high-wavenumber scales at interfaces between partially-resolved simulations and low-frequency solutions. The methods are embedded within the variational-multiscale framework and are elaborated for the case of a randomly-forced Burgers equation. Examples are given to illustrate their performance.

Analysis of combined conduction and radiation heat transfer in presence of participating medium by the development of hybrid method

The current study addresses the mathematical modeling aspects of coupled conductive and radiative heat transfer in the presence of absorbing, emitting and isotropic scattering gray medium within two-dimensional square enclosure. A blended method where the concepts of modified differential approximation employed by combining discrete ordinate method and spherical harmonics method, has been developed for modeling the radiative transport equation. The gray participating medium is bounded by isothermal walls of two-dimensional enclosure which are considered to be opaque, diffuse and gray. The effect of various influencing parameters i.e., radiation–conduction parameter, surface emissivity, single scattering albedo and optical thickness has been illustrated. The adaptability of the present method has also been addressed.

Three steps to ethnography: A discussion of interdisciplinary contributions

In this paper recent research involving interdisciplinary ethnography is presented as an exploration of its contribution to studies of people and technology in the workplace. Three main patterns of interaction between ethnography and ‘the others’ are examined. First, the influence of ethnography in promoting people-oriented perspectives of technology is discussed with reference to workplace studies in manufacturing. Second, ethnography contribution to the development of hybrid methods for the design and implementation of technology for use in the workplace is illustrated by several examples of such frameworks. Third, the influence of ethnographic research to providing a theoretical basis for computer-mediated communication is explored and documented by analyses of design teams working together as part of construction projects. From a practical point of view, this exploration has resulted in a brief discussion of the broad range of ‘users’ in the real-life workplace who benefit from ethnographic research. Future work in this area will rely on a reflexive stance on the part of the ethnographer in relation to both users of technology and users of ethnography.

An integrated software system for hybrid flight simulation: The boeing hybrid simulator

The Boeing Hybrid Simulator is a general-purpose hybrid computer designed to provide a laboratory for the development of hybrid methods of solving a variety of aero-space problems as well as to support large-scale simulations. The first such simulation is a Flight Simulation Program which provides both a three-degrees-of-freedom missile performance analysis tool and a six-degrees-of-freedom missile subsystem design analysis tool. The 3D simulation was implemented by placing the integrations of the translational equations on the analog, utilizing the digital for function generation, some algebraic manipulations, and basic bookkeeping. The 6D was implemented by placing the integrations of the rotational equations on the analog and the integrations of the translational equations on the digital. Phase control was supplied on the analog in both cases. A hybrid oriented execute-time monitor system supported the simulations by 1) providing a flexibile man-machine relationship, 2) providing an automatic and manual control capability, and 3) reducing digital and analog setup time. It enabled the man at the console to bring system packages into computer memory either to temporarily displace the simulations or to tie in with them in such a way that activities closely related to the execution of the simulations occur at the end of frame calculations.