TY - JOUR A1 - Thon, Ingo A1 - Landwehr, Niels A1 - De Raedt, Luc T1 - Stochastic relational processes efficient inference and applications JF - Machine learning N2 - One of the goals of artificial intelligence is to develop agents that learn and act in complex environments. Realistic environments typically feature a variable number of objects, relations amongst them, and non-deterministic transition behavior. While standard probabilistic sequence models provide efficient inference and learning techniques for sequential data, they typically cannot fully capture the relational complexity. On the other hand, statistical relational learning techniques are often too inefficient to cope with complex sequential data. In this paper, we introduce a simple model that occupies an intermediate position in this expressiveness/efficiency trade-off. It is based on CP-logic (Causal Probabilistic Logic), an expressive probabilistic logic for modeling causality. However, by specializing CP-logic to represent a probability distribution over sequences of relational state descriptions and employing a Markov assumption, inference and learning become more tractable and effective. Specifically, we show how to solve part of the inference and learning problems directly at the first-order level, while transforming the remaining part into the problem of computing all satisfying assignments for a Boolean formula in a binary decision diagram. We experimentally validate that the resulting technique is able to handle probabilistic relational domains with a substantial number of objects and relations. KW - Statistical relational learning KW - Stochastic relational process KW - Markov processes KW - Time series KW - CP-Logic Y1 - 2011 U6 - https://doi.org/10.1007/s10994-010-5213-8 SN - 0885-6125 VL - 82 IS - 2 SP - 239 EP - 272 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Rabenalt, Thomas A1 - Goessel, Michael A1 - Leininger, Andreas T1 - Masking of X-Values by use of a hierarchically configurable register JF - Journal of electronic testing : theory and applications N2 - In this paper we consider masking of unknowns (X-values) for VLSI circuits. We present a new hierarchical method of X-masking which is a major improvement of the method proposed in [4], called WIDE1. By the method proposed, the number of observable scan cells is optimized and data volume for X-masking can be significantly reduced in comparison to WIDEL This is demonstrated for three industrial designs. In cases where all X-values have to be masked the novel approach is especially efficient. KW - Masking of X-values KW - Hierarchically configurable mask register Y1 - 2011 U6 - https://doi.org/10.1007/s10836-010-5179-2 SN - 0923-8174 VL - 27 IS - 1 SP - 31 EP - 41 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Zaupa, Alessandro A1 - Neffe, Axel T. A1 - Pierce, Benjamin F. A1 - Lendlein, Andreas A1 - Hofmann, Dieter T1 - A molecular dynamic analysis of gelatin as an amorphous material Prediction of mechanical properties of gelatin systems JF - The international journal of artificial organs N2 - Biomaterials are used in regenerative medicine for induced autoregeneration and tissue engineering. This is often challenging, however, due to difficulties in tailoring and controlling the respective material properties. Since functionalization is expected to offer better control, in this study gelatin chains were modified with physically interacting groups based on tyrosine with the aim of causing the formation of physical crosslinks. This method permits application-specific properties like swelling and better tailoring of mechanical properties. The design of the crosslink strategy was supported by molecular dynamic (MD) simulations of amorphous bulk models for gelatin and functionalized gelatins at different water contents (0.8 and 25 wt.-%). The results permitted predictions to be formulated about the expected crosslink density and its influence on equilibrium swelling behavior and on elastic material properties. The models of pure gelatin were used to validate the strategy by comparison between simulated and experimental data such as density, backbone conformation angle distribution, and X-ray scattering spectra. A key result of the simulations was the prediction that increasing the number of aromatic functions attached to the gelatin chain leads to an increase in the number of physical netpoints observed in the simulated bulk packing models. By comparison with the Flory-Rehner model, this suggested reduced equilibrium swelling of the functionalized materials in water, a prediction that was subsequently confirmed by our experimental work. The reduction and control of the equilibrium degree of swelling in water is a key criterion for the applicability of functionalized gelatins when used, for example, as matrices for induced autoregeneration of tissues. KW - Physical Network KW - Biopolymer material KW - Molecular modeling KW - Gelatin Y1 - 2011 U6 - https://doi.org/10.5301/IJAO.2010.6083 SN - 0391-3988 VL - 34 IS - 2 SP - 139 EP - 151 PB - Wichtig CY - Milano ER - TY - JOUR A1 - Reiche, Jürgen A1 - Kratz, Karl A1 - Hofmann, Dieter A1 - Lendlein, Andreas T1 - Current status of Langmuir monolayer degradation of polymeric biomaterials JF - The international journal of artificial organs N2 - Langmuir monolayer degradation (LMD) experiments with polymers possessing outstanding biomedical application potential yield information regarding the kinetics of their hydrolytic or enzymatic chain scission under well-defined and adjustable degradation conditions. A brief review is given of LMD investigations, including the author's own work on 2-dimensional (2D) polymer systems, providing chain scission data, which are not disturbed by simultaneously occurring transport phenomena, such as water penetration into the sample or transport of scission fragments out of the sample. A knowledge-based approach for the description and simulation of polymer hydrolytic and enzymatic degradation based on a combination of fast LMD experiments and computer simulation of the water penetration is briefly introduced. Finally, the advantages and disadvantages of this approach are discussed. KW - Monolayer KW - Hydrolytic degradation KW - Enzymatic degradation KW - Biomaterial KW - Degradable polymer Y1 - 2011 U6 - https://doi.org/10.5301/IJAO.2011.6401 SN - 0391-3988 VL - 34 IS - 2 SP - 123 EP - 128 PB - Wichtig CY - Milano ER - TY - JOUR A1 - Tran Thanh Tuan, A1 - Scherbaum, Frank A1 - Malischewsky, Peter G. T1 - On the relationship of peaks and troughs of the ellipticity (H/V) of Rayleigh waves and the transmission response of single layer over half-space models JF - Geophysical journal international N2 - One of the key challenges in the context of local site effect studies is the determination of frequencies where the shakeability of the ground is enhanced. In this context, the H/V technique has become increasingly popular and peak frequencies of H/V spectral ratio are sometimes interpreted as resonance frequencies of the transmission response. In the present study, assuming that Rayleigh surface wave is dominant in H/V spectral ratio, we analyse theoretically under which conditions this may be justified and when not. We focus on 'layer over half-space' models which, although seemingly simple, capture many aspects of local site effects in real sedimentary structures. Our starting point is the ellipticity of Rayleigh waves. We use the exact formula of the H/V-ratio presented by Malischewsky & Scherbaum (2004) to investigate the main characteristics of peak and trough frequencies. We present a simple formula illustrating if and where H/V-ratio curves have sharp peaks in dependence of model parameters. In addition, we have constructed a map, which demonstrates the relation between the H/V-peak frequency and the peak frequency of the transmission response in the domain of the layer's Poisson ratio and the impedance contrast. Finally, we have derived maps showing the relationship between the H/V-peak and trough frequency and key parameters of the model such as impedance contrast. These maps are seen as diagnostic tools, which can help to guide the interpretation of H/V spectral ratio diagrams in the context of site effect studies. KW - Site effects KW - Theoretical seismology KW - Wave propagation Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-246X.2010.04863.x SN - 0956-540X VL - 184 IS - 2 SP - 793 EP - 800 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Fanselow, Gisbert A1 - Lenertova, Denisa T1 - Left peripheral focus mismatches between syntax and information structure JF - Natural language & linguistic theory N2 - In Czech, German, and many other languages, part of the semantic focus of the utterance can be moved to the left periphery of the clause. The main generalization is that only the leftmost accented part of the semantic focus can be moved. We propose that movement to the left periphery is generally triggered by an unspecific edge feature of C (Chomsky 2008) and its restrictions can be attributed to requirements of cyclic linearization, modifying the theory of cyclic linearization developed by Fox and Pesetsky (2005). The crucial assumption is that structural accent is a direct consequence of being linearized at merge, thus it is indirectly relevant for (locality restrictions on) movement. The absence of structural accent correlates with givenness. Given elements may later receive (topic or contrastive) accents, which accounts for fronting in multiple focus/contrastive topic constructions. Without any additional assumptions, the model can account for movement of pragmatically unmarked elements to the left periphery ('formal fronting', Frey 2005). Crucially, the analysis makes no reference at all to concepts of information structure in the syntax, in line with the claim of Chomsky (2008) that UG specifies no direct link between syntax and information structure. KW - Czech KW - German KW - Focus KW - Topic KW - Information structure KW - Intervention effects KW - Cyclic linearization KW - A-bar-movement KW - Prosody-syntax interface KW - Accentuation Y1 - 2011 U6 - https://doi.org/10.1007/s11049-010-9109-x SN - 0167-806X VL - 29 IS - 1 SP - 169 EP - 209 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Hoban, Matty J. A1 - Campbell, Earl T. A1 - Loukopoulos, Klearchos A1 - Browne, Dan E. T1 - Non-adaptive measurement-based quantum computation and multi-party Bell inequalities JF - New journal of physics : the open-access journal for physics N2 - Quantum correlations exhibit behaviour that cannot be resolved with a local hidden variable picture of the world. In quantum information, they are also used as resources for information processing tasks, such as measurement-based quantum computation (MQC). In MQC, universal quantum computation can be achieved via adaptive measurements on a suitable entangled resource state. In this paper, we look at a version of MQC in which we remove the adaptivity of measurements and aim to understand what computational abilities remain in the resource. We show that there are explicit connections between this model of computation and the question of non-classicality in quantum correlations. We demonstrate this by focusing on deterministic computation of Boolean functions, in which natural generalizations of the Greenberger-Horne-Zeilinger paradox emerge; we then explore probabilistic computation via, which multipartite Bell inequalities can be defined. We use this correspondence to define families of multi-party Bell inequalities, which we show to have a number of interesting contrasting properties. Y1 - 2011 U6 - https://doi.org/10.1088/1367-2630/13/2/023014 SN - 1367-2630 VL - 13 IS - 1 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Havelius, Kajsa G. V. A1 - Reschke, Stefan A1 - Horn, Sebastian A1 - Doerlng, Alexander A1 - Niks, Dimitri A1 - Hille, Russ A1 - Schulzke, Carola A1 - Leimkühler, Silke A1 - Haumann, Michael T1 - Structure of the molybdenum site in YedY, a sulfite oxidase homologue from escherichia coli JF - Inorganic chemistry N2 - YedY from Escherichia coil is a new member of the sulfite oxidase family of molybdenum cofactor (Moco)-containing oxidoreductases. We investigated the atomic structure of the molybdenum site in YedY by X-ray absorption spectroscopy, in comparison to human sulfite oxidase (hSO) and to a Mo(IV) model complex. The K-edge energy was indicative of Mo(V) in YedY, in agreement with X- and Q-band electron paramagnetic resonance results, whereas the hSO protein contained Mo(VI). In YedY and hSO, molybdenum is coordinated by two sulfur ligands from the molybdopterin ligand of the Moco, one thiolate sulfur of a cysteine (average Mo-S bond length of similar to 2.4 angstrom), and one (axial) oxo ligand (Mo=O, similar to 1.7 angstrom). hSO contained a second oxo group at Mo as expected, but in YedY, two species in about a 1:1 ratio were found at the active site, corresponding to an equatorial Mo-OH bond (similar to 2.1 angstrom) or possibly to a shorter M-O(-) bond. Yet another oxygen (or nitrogen) at a similar to 2.6 angstrom distance to Mo in YedY was identified, which could originate from a water molecule in the substrate binding cavity or from an amino acid residue close to the molybdenum site, i.e., Glu104, that is replaced by a glycine in hSO, or Asn45. The addition of the poor substrate dimethyl sulfoxide to YedY left the molybdenum coordination unchanged at high pH. In contrast, we found indications that the better substrate trimethylamine N-oxide and the substrate analogue acetone were bound at a similar to 2.6 angstrom distance to the molybdenum, presumably replacing the equatorial oxygen ligand. These findings were used to interpret the recent crystal structure of YedY and bear implications for its catalytic mechanism. Y1 - 2011 U6 - https://doi.org/10.1021/ic101291j SN - 0020-1669 VL - 50 IS - 3 SP - 741 EP - 748 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Giewekemeyer, K. A1 - Krueger, S. P. A1 - Kalbfleisch, S. A1 - Bartels, Meike A1 - Beta, Carsten A1 - Salditt, T. T1 - X-ray propagation microscopy of biological cells using waveguides as a quasipoint source JF - Physical review : A, Atomic, molecular, and optical physics N2 - We have used x-ray waveguides as highly confining optical elements for nanoscale imaging of unstained biological cells using the simple geometry of in-line holography. The well-known twin-image problem is effectively circumvented by a simple and fast iterative reconstruction. The algorithm which combines elements of the classical Gerchberg-Saxton scheme and the hybrid-input-output algorithm is optimized for phase-contrast samples, well-justified for imaging of cells at multi-keV photon energies. The experimental scheme allows for a quantitative phase reconstruction from a single holographic image without detailed knowledge of the complex illumination function incident on the sample, as demonstrated for freeze-dried cells of the eukaryotic amoeba Dictyostelium discoideum. The accessible resolution range is explored by simulations, indicating that resolutions on the order of 20 nm are within reach applying illumination times on the order of minutes at present synchrotron sources. Y1 - 2011 U6 - https://doi.org/10.1103/PhysRevA.83.023804 SN - 1050-2947 VL - 83 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Huber, Christian A1 - Klamroth, Tillmann T1 - Explicitly time-dependent coupled cluster singles doubles calculations of laser-driven many-electron dynamics JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr N2 - We report explicitly time-dependent coupled cluster singles doubles (TD-CCSD) calculations, which simulate the laser-driven correlated many-electron dynamics in molecular systems. Small molecules, i.e., HF, H(2)O, NH(3), and CH(4), are treated mostly with polarized valence double zeta basis sets. We determine the coupled cluster ground states by imaginary time propagation for these molecules. Excited state energies are obtained from the Fourier transform of the time-dependent dipole moment after an ultrashort, broadband laser excitation. The time-dependent expectation values are calculated from the complex cluster amplitudes using the corresponding configuration interaction singles doubles wave functions. Also resonant laser excitations of these excited states are simulated, in order to explore the limits for the numerical stability of our current TD-CCSD implementation, which uses time-independent molecular orbitals to form excited configurations. Y1 - 2011 U6 - https://doi.org/10.1063/1.3530807 SN - 0021-9606 VL - 134 IS - 5 PB - American Institute of Physics CY - Melville ER -