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The UDKM1DSIM toolbox is a collection of MATLAB (MathWorks Inc.) classes and routines to simulate the structural dynamics and the according X-ray diffraction response in one-dimensional crystalline sample structures upon an arbitrary time-dependent external stimulus, e.g. an ultrashort laser pulse. The toolbox provides the capabilities to define arbitrary layered structures on the atomic level including a rich database of corresponding element-specific physical properties. The excitation of ultrafast dynamics is represented by an N-temperature model which is commonly applied for ultrafast optical excitations. Structural dynamics due to thermal stress are calculated by a linear-chain model of masses and springs. The resulting X-ray diffraction response is computed by dynamical X-ray theory. The UDKM1DSIM toolbox is highly modular and allows for introducing user-defined results at any step in the simulation procedure.
Program summary
Program title: udkm1Dsim
Catalogue identifier: AERH_v1_0
Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERH_v1_0.html
Licensing provisions: BSD
No. of lines in distributed program, including test data, etc.: 130221
No. of bytes in distributed program, including test data, etc.: 2746036
Distribution format: tar.gz
Programming language: Matlab (MathWorks Inc.).
Computer: PC/Workstation.
Operating system: Running Matlab installation required (tested on MS Win XP -7, Ubuntu Linux 11.04-13.04).
Has the code been vectorized or parallelized?: Parallelization for dynamical XRD computations. Number of processors used: 1-12 for Matlab Parallel Computing Toolbox; 1 - infinity for Matlab Distributed Computing Toolbox
External routines:
Optional: Matlab Parallel Computing Toolbox, Matlab Distributed Computing Toolbox Required (included in the package): mtimesx Fast Matrix Multiply for Matlab by James Tursa, xml io tools by Jaroslaw Tuszynski, textprogressbar by Paul Proteus
Nature of problem:
Simulate the lattice dynamics of 1D crystalline sample structures due to an ultrafast excitation including thermal transport and compute the corresponding transient X-ray diffraction pattern.
Solution method:
Restrictions:
The program is restricted to 1D sample structures and is further limited to longitudinal acoustic phonon modes and symmetrical X-ray diffraction geometries.
Unusual features: The program is highly modular and allows the inclusion of user-defined inputs at any time of the simulation procedure.
Running time: The running time is highly dependent on the number of unit cells in the sample structure and other simulation parameters such as time span or angular grid for X-ray diffraction computations. However, the example files are computed in approx. 1-5 min each on a 8 Core Processor with 16 GB RAM available.
Stripe rust (Pst) is a major disease of wheat crops leading untreated to severe yield losses. The use of fungicides is often essential to control Pst when sudden outbreaks are imminent. Sensors capable of detecting Pst in wheat crops could optimize the use of fungicides and improve disease monitoring in high-throughput field phenotyping. Now, deep learning provides new tools for image recognition and may pave the way for new camera based sensors that can identify symptoms in early stages of a disease outbreak within the field. The aim of this study was to teach an image classifier to detect Pst symptoms in winter wheat canopies based on a deep residual neural network (ResNet). For this purpose, a large annotation database was created from images taken by a standard RGB camera that was mounted on a platform at a height of 2 m. Images were acquired while the platform was moved over a randomized field experiment with Pst-inoculated and Pst-free plots of winter wheat. The image classifier was trained with 224 x 224 px patches tiled from the original, unprocessed camera images. The image classifier was tested on different stages of the disease outbreak. At patch level the image classifier reached a total accuracy of 90%. To test the image classifier on image level, the image classifier was evaluated with a sliding window using a large striding length of 224 px allowing for fast test performance. At image level, the image classifier reached a total accuracy of 77%. Even in a stage with very low disease spreading (0.5%) at the very beginning of the Pst outbreak, a detection accuracy of 57% was obtained. Still in the initial phase of the Pst outbreak with 2 to 4% of Pst disease spreading, detection accuracy with 76% could be attained. With further optimizations, the image classifier could be implemented in embedded systems and deployed on drones, vehicles or scanning systems for fast mapping of Pst outbreaks.
Design Issues in the Implementation of MPI2 One Sided Communication in Ethernet based Networks
(2007)
In current research, one sided communication of the MPI2 standard is pushed as a promising technique [6, 7, 10, 18]. But measurements of applications and MPI2 primitives show a different picture [17]. In this paper we analyze de sign issues of MPI2 one sided communication and its im plementations. We focus on asynchronous communication for parallel applications in Ethernet cluster environments. Further, one sided communication is compared to two sided communication. This paper will prove that the key problem to performance is not only the implementation of MPI2 one sided communication - it is the design.
Emotions are a central element of human experience. They occur with high frequency in everyday life and play an important role in decision making. However, currently there is no consensus among researchers on what constitutes an emotion and on how emotions should be investigated. This dissertation identifies three problems of current emotion research: the problem of ground truth, the problem of incomplete constructs and the problem of optimal representation. I argue for a focus on the detailed measurement of emotion manifestations with computer-aided methods to solve these problems. This approach is demonstrated in three research projects, which describe the development of methods specific to these problems as well as their application to concrete research questions.
The problem of ground truth describes the practice to presuppose a certain structure of emotions as the a priori ground truth. This determines the range of emotion descriptions and sets a standard for the correct assignment of these descriptions. The first project illustrates how this problem can be circumvented with a multidimensional emotion perception paradigm which stands in contrast to the emotion recognition paradigm typically employed in emotion research. This paradigm allows to calculate an objective difficulty measure and to collect subjective difficulty ratings for the perception of emotional stimuli. Moreover, it enables the use of an arbitrary number of emotion stimuli categories as compared to the commonly used six basic emotion categories. Accordingly, we collected data from 441 participants using dynamic facial expression stimuli from 40 emotion categories. Our findings suggest an increase in emotion perception difficulty with increasing actor age and provide evidence to suggest that young adults, the elderly and men underestimate their emotion perception difficulty. While these effects were predicted from the literature, we also found unexpected and novel results. In particular, the increased difficulty on the objective difficulty measure for female actors and observers stood in contrast to reported findings. Exploratory analyses revealed low relevance of person-specific variables for the prediction of emotion perception difficulty, but highlighted the importance of a general pleasure dimension for the ease of emotion perception.
The second project targets the problem of incomplete constructs which relates to vaguely defined psychological constructs on emotion with insufficient ties to tangible manifestations. The project exemplifies how a modern data collection method such as face tracking data can be used to sharpen these constructs on the example of arousal, a long-standing but fuzzy construct in emotion research. It describes how measures of distance, speed and magnitude of acceleration can be computed from face tracking data and investigates their intercorrelations. We find moderate to strong correlations among all measures of static information on one hand and all measures of dynamic information on the other. The project then investigates how self-rated arousal is tied to these measures in 401 neurotypical individuals and 19 individuals with autism. Distance to the neutral face was predictive of arousal ratings in both groups. Lower mean arousal ratings were found for the autistic group, but no difference in correlation of the measures and arousal ratings could be found between groups. Results were replicated in a high autistic traits group consisting of 41 participants. The findings suggest a qualitatively similar perception of arousal for individuals with and without autism. No correlations between valence ratings and any of the measures could be found which emphasizes the specificity of our tested measures for the construct of arousal.
The problem of optimal representation refers to the search for the best representation of emotions and the assumption that there is a one-fits-all solution. In the third project we introduce partial least squares analysis as a general method to find an optimal representation to relate two high-dimensional data sets to each other. The project demonstrates its applicability to emotion research on the question of emotion perception differences between men and women. The method was used with emotion rating data from 441 participants and face tracking data computed on 306 videos. We found quantitative as well as qualitative differences in the perception of emotional facial expressions between these groups. We showed that women’s emotional perception systematically captured more of the variance in facial expressions. Additionally, we could show that significant differences exist in the way that women and men perceive some facial expressions which could be visualized as concrete facial expression sequences. These expressions suggest differing perceptions of masked and ambiguous facial expressions between the sexes. In order to facilitate use of the developed method by the research community, a package for the statistical environment R was written. Furthermore, to call attention to the method and its usefulness for emotion research, a website was designed that allows users to explore a model of emotion ratings and facial expression data in an interactive fashion.
Arousal is one of the dimensions of core affect and frequently used to describe experienced or observed emotional states. While arousal ratings of facial expressions are collected in many studies it is not well understood how arousal is displayed in or interpreted from facial expressions. In the context of socioemotional disorders such as Autism Spectrum Disorder, this poses the question of a differential use of facial information for arousal perception. In this study, we demonstrate how automated face-tracking tools can be used to extract predictors of arousal judgments. We find moderate to strong correlations among all measures of static information on one hand and all measures of dynamic information on the other. Based on these results, we tested two measures, average distance to the neutral face and average facial movement speed, within and between neurotypical individuals (N = 401) and individuals with autism (N = 19). Distance to the neutral face was predictive of arousal in both groups. Lower mean arousal ratings were found for the autistic group, but no difference in correlation of the measures and arousal ratings could be found between groups. Results were replicated in an high autistic traits group. The findings suggest a qualitatively similar perception of arousal for individuals with and without autism. No correlations between valence ratings and any of the measures could be found, emphasizing the specificity of our tested measures. Distance and speed predictors share variability and thus speed should not be discarded as a predictor of arousal ratings.
Cloud-RAID
(2014)
Seminarband: Sensornetze
(2004)
Advances in biotechnologies rapidly increase the number of molecules of a cell which can be observed simultaneously. This includes expression levels of thousands or ten-thousands of genes as well as concentration levels of metabolites or proteins. Such Profile data, observed at different times or at different experimental conditions (e.g., heat or dry stress), show how the biological experiment is reflected on the molecular level. This information is helpful to understand the molecular behaviour and to identify molecules or combination of molecules that characterise specific biological condition (e.g., disease). This work shows the potentials of component extraction algorithms to identify the major factors which influenced the observed data. This can be the expected experimental factors such as the time or temperature as well as unexpected factors such as technical artefacts or even unknown biological behaviour. Extracting components means to reduce the very high-dimensional data to a small set of new variables termed components. Each component is a combination of all original variables. The classical approach for that purpose is the principal component analysis (PCA). It is shown that, in contrast to PCA which maximises the variance only, modern approaches such as independent component analysis (ICA) are more suitable for analysing molecular data. The condition of independence between components of ICA fits more naturally our assumption of individual (independent) factors which influence the data. This higher potential of ICA is demonstrated by a crossing experiment of the model plant Arabidopsis thaliana (Thale Cress). The experimental factors could be well identified and, in addition, ICA could even detect a technical artefact. However, in continuously observations such as in time experiments, the data show, in general, a nonlinear distribution. To analyse such nonlinear data, a nonlinear extension of PCA is used. This nonlinear PCA (NLPCA) is based on a neural network algorithm. The algorithm is adapted to be applicable to incomplete molecular data sets. Thus, it provides also the ability to estimate the missing data. The potential of nonlinear PCA to identify nonlinear factors is demonstrated by a cold stress experiment of Arabidopsis thaliana. The results of component analysis can be used to build a molecular network model. Since it includes functional dependencies it is termed functional network. Applied to the cold stress data, it is shown that functional networks are appropriate to visualise biological processes and thereby reveals molecular dynamics.
Motivation: Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values. Results: Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while optimizing the model, but can be estimated afterwards. Results are shown for both artificial and experimental datasets. In contrast to linear methods, non-linear methods were able to give better missing value estimations for non-linear structured data. Application: We applied this technique to a time course of metabolite data from a cold stress experiment on the model plant Arabidopsis thaliana, and could approximate the mapping function from any time point to the metabolite responses. Thus, the inverse NLPCA provides greatly improved information for better understanding the complex response to cold stress
Reliable and robust data processing is one of the hardest requirements for systems in fields such as medicine, security, automotive, aviation, and space, to prevent critical system failures caused by changes in operating or environmental conditions. In particular, Signal Integrity (SI) effects such as crosstalk may distort the signal information in sensitive mixed-signal designs. A challenge for hardware systems used in the space are radiation effects. Namely, Single Event Effects (SEEs) induced by high-energy particle hits may lead to faulty computation, corrupted configuration settings, undesired system behavior, or even total malfunction.
Since these applications require an extra effort in design and implementation, it is beneficial to master the standard cell design process and corresponding design flow methodologies optimized for such challenges. Especially for reliable, low-noise differential signaling logic such as Current Mode Logic (CML), a digital design flow is an orthogonal approach compared to traditional manual design. As a consequence, mandatory preliminary considerations need to be addressed in more detail. First of all, standard cell library concepts with suitable cell extensions for reliable systems and robust space applications have to be elaborated. Resulting design concepts at the cell level should enable the logical synthesis for differential logic design or improve the radiation-hardness. In parallel, the main objectives of the proposed cell architectures are to reduce the occupied area, power, and delay overhead. Second, a special setup for standard cell characterization is additionally required for a proper and accurate logic gate modeling. Last but not least, design methodologies for mandatory design flow stages such as logic synthesis and place and route need to be developed for the respective hardware systems to keep the reliability or the radiation-hardness at an acceptable level.
This Thesis proposes and investigates standard cell-based design methodologies and techniques for reliable and robust hardware systems implemented in a conventional semi-conductor technology. The focus of this work is on reliable differential logic design and robust radiation-hardening-by-design circuits. The synergistic connections of the digital design flow stages are systematically addressed for these two types of hardware systems. In more detail, a library for differential logic is extended with single-ended pseudo-gates for intermediate design steps to support the logic synthesis and layout generation with commercial Computer-Aided Design (CAD) tools. Special cell layouts are proposed to relax signal routing. A library set for space applications is similarly extended by novel Radiation-Hardening-by-Design (RHBD) Triple Modular Redundancy (TMR) cells, enabling a one fault correction. Therein, additional optimized architectures for glitch filter cells, robust scannable and self-correcting flip-flops, and clock-gates are proposed. The circuit concepts and the physical layout representation views of the differential logic gates and the RHBD cells are discussed. However, the quality of results of designs depends implicitly on the accuracy of the standard cell characterization which is examined for both types therefore. The entire design flow is elaborated from the hardware design description to the layout representations. A 2-Phase routing approach together with an intermediate design conversion step is proposed after the initial place and route stage for reliable, pure differential designs, whereas a special constraining for RHBD applications in a standard technology is presented.
The digital design flow for differential logic design is successfully demonstrated on a reliable differential bipolar CML application. A balanced routing result of its differential signal pairs is obtained by the proposed 2-Phase-routing approach. Moreover, the elaborated standard cell concepts and design methodology for RHBD circuits are applied to the digital part of a 7.5-15.5 MSPS 14-bit Analog-to-Digital Converter (ADC) and a complex microcontroller architecture. The ADC is implemented in an unhardened standard semiconductor technology and successfully verified by electrical measurements. The overhead of the proposed hardening approach is additionally evaluated by design exploration of the microcontroller application. Furthermore, the first obtained related measurement results of novel RHBD-∆TMR flip-flops show a radiation-tolerance up to a threshold Linear Energy Transfer (LET) of 46.1, 52.0, and 62.5 MeV cm2 mg-1 and savings in silicon area of 25-50 % for selected TMR standard cell candidates.
As a conclusion, the presented design concepts at the cell and library levels, as well as the design flow modifications are adaptable and transferable to other technology nodes. In particular, the design of hybrid solutions with integrated reliable differential logic modules together with robust radiation-tolerant circuit parts is enabled by the standard cell concepts and design methods proposed in this work.
Use of a standard non-rad-hard digital cell library in the rad-hard design can be a cost-effective solution for space applications. In this paper we demonstrate how a standard non-rad-hard flip-flop, as one of the most vulnerable digital cells, can be converted into a rad-hard flip-flop without modifying its internal structure. We present five variants of a Triple Modular Redundancy (TMR) flip-flop: baseline TMR flip-flop, latch-based TMR flip-flop, True-Single Phase Clock (TSPC) TMR flip-flop, scannable TMR flip-flop and self-correcting TMR flipflop. For all variants, the multi-bit upsets have been addressed by applying special placement constraints, while the Single Event Transient (SET) mitigation was achieved through the usage of customized SET filters and selection of optimal inverter sizes for the clock and reset trees. The proposed flip-flop variants feature differing performance, thus enabling to choose the optimal solution for every sensitive node in the circuit, according to the predefined design constraints. Several flip-flop designs have been validated on IHP's 130nm BiCMOS process, by irradiation of custom-designed shift registers. It has been shown that the proposed TMR flip-flops are robust to soft errors with a threshold Linear Energy Transfer (LET) from (32.4 MeV.cm(2)/mg) to (62.5 MeV.cm(2)/mg), depending on the variant.