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2008


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Causal Reasoning by Evaluating the Complexity of Conditional Densities with Kernel Methods

Sun, X., Janzing, D., Schölkopf, B.

Neurocomputing, 71(7-9):1248-1256, March 2008 (article)

Abstract
We propose a method to quantify the complexity of conditional probability measures by a Hilbert space seminorm of the logarithm of its density. The concept of reproducing kernel Hilbert spaces (RKHSs) is a flexible tool to define such a seminorm by choosing an appropriate kernel. We present several examples with artificial data sets where our kernel-based complexity measure is consistent with our intuitive understanding of complexity of densities. The intention behind the complexity measure is to provide a new approach to inferring causal directions. The idea is that the factorization of the joint probability measure P(effect, cause) into P(effect|cause)P(cause) leads typically to "simpler" and "smoother" terms than the factorization into P(cause|effect)P(effect). Since the conventional constraint-based approach of causal discovery is not able to determine the causal direction between only two variables, our inference principle can in particular be useful when combined with other existing methods. We provide several simple examples with real-world data where the true causal directions indeed lead to simpler (conditional) densities.

ei

Web DOI [BibTex]


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Natural Actor-Critic

Peters, J., Schaal, S.

Neurocomputing, 71(7-9):1180-1190, March 2008 (article)

Abstract
In this paper, we suggest a novel reinforcement learning architecture, the Natural Actor-Critic. The actor updates are achieved using stochastic policy gradients em- ploying Amari’s natural gradient approach, while the critic obtains both the natural policy gradient and additional parameters of a value function simultaneously by lin- ear regression. We show that actor improvements with natural policy gradients are particularly appealing as these are independent of coordinate frame of the chosen policy representation, and can be estimated more efficiently than regular policy gra- dients. The critic makes use of a special basis function parameterization motivated by the policy-gradient compatible function approximation. We show that several well-known reinforcement learning methods such as the original Actor-Critic and Bradtke’s Linear Quadratic Q-Learning are in fact Natural Actor-Critic algorithms. Empirical evaluations illustrate the effectiveness of our techniques in comparison to previous methods, and also demonstrate their applicability for learning control on an anthropomorphic robot arm.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Inferring Spike Trains From Local Field Potentials

Rasch, M., Gretton, A., Murayama, Y., Maass, W., Logothetis, N.

Journal of Neurophysiology, 99(3):1461-1476, March 2008 (article)

Abstract
We investigated whether it is possible to infer spike trains solely on the basis of the underlying local field potentials (LFPs). Using support vector machines and linear regression models, we found that in the primary visual cortex (V1) of monkeys, spikes can indeed be inferred from LFPs, at least with moderate success. Although there is a considerable degree of variation across electrodes, the low-frequency structure in spike trains (in the 100-ms range) can be inferred with reasonable accuracy, whereas exact spike positions are not reliably predicted. Two kinds of features of the LFP are exploited for prediction: the frequency power of bands in the high gamma-range (40–90 Hz) and information contained in lowfrequency oscillations ( 10 Hz), where both phase and power modulations are informative. Information analysis revealed that both features code (mainly) independent aspects of the spike-to-LFP relationship, with the low-frequency LFP phase coding for temporally clustered spiking activity. Although both features and prediction quality are similar during seminatural movie stimuli and spontaneous activity, prediction performance during spontaneous activity degrades much more slowly with increasing electrode distance. The general trend of data obtained with anesthetized animals is qualitatively mirrored in that of a more limited data set recorded in V1 of non-anesthetized monkeys. In contrast to the cortical field potentials, thalamic LFPs (e.g., LFPs derived from recordings in the dorsal lateral geniculate nucleus) hold no useful information for predicting spiking activity.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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ISD: A Software Package for Bayesian NMR Structure Calculation

Rieping, W., Nilges, M., Habeck, M.

Bioinformatics, 24(8):1104-1105, February 2008 (article)

Abstract
SUMMARY: The conventional approach to calculating biomolecular structures from nuclear magnetic resonance (NMR) data is often viewed as subjective due to its dependence on rules of thumb for deriving geometric constraints and suitable values for theory parameters from noisy experimental data. As a result, it can be difficult to judge the precision of an NMR structure in an objective manner. The Inferential Structure Determination (ISD) framework, which has been introduced recently, addresses this problem by using Bayesian inference to derive a probability distribution that represents both the unknown structure and its uncertainty. It also determines additional unknowns, such as theory parameters, that normally need be chosen empirically. Here we give an overview of the ISD software package, which implements this methodology. AVAILABILITY: The program is available at http://www.bioc.cam.ac.uk/isd

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Probabilistic Structure Calculation

Nilges, M., Habeck, M., Rieping, W.

Comptes Rendus Chimie, 11(4-5):356-369, February 2008 (article)

Abstract
Molecular structures are usually calculated from experimental data with some method of energy minimisation or non-linear optimisation. Key aims of a structure calculation are to estimate the coordinate uncertainty, and to provide a meaningful measure of the quality of the fit to the data. We discuss approaches to optimally combine prior information and experimental data and the connection to probability theory. We analyse the appropriate statistics for NOEs and NOE-derived distances, and the related question of restraint potentials. Finally, we will discuss approaches to determine the appropriate weight on the experimental evidence and to obtain in this way an estimate of the data quality from the structure calculation. Whereas objective estimates of coordinates and their uncertainties can only be obtained by a full Bayesian treatment of the problem, standard structure calculation methods continue to play an important role. To obtain the full benefit of these methods, they should be founded on a rigorous Baye sian analysis.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Fast Projection-based Methods for the Least Squares Nonnegative Matrix Approximation Problem

Kim, D., Sra, S., Dhillon, I.

Statistical Analysis and Data Mining, 1(1):38-51, February 2008 (article)

Abstract
Nonnegative matrix approximation (NNMA) is a popular matrix decomposition technique that has proven to be useful across a diverse variety of fields with applications ranging from document analysis and image processing to bioinformatics and signal processing. Over the years, several algorithms for NNMA have been proposed, e.g. Lee and Seung‘s multiplicative updates, alternating least squares (ALS), and gradient descent-based procedures. However, most of these procedures suffer from either slow convergence, numerical instability, or at worst, serious theoretical drawbacks. In this paper, we develop a new and improved algorithmic framework for the least-squares NNMA problem, which is not only theoretically well-founded, but also overcomes many deficiencies of other methods. Our framework readily admits powerful optimization techniques and as concrete realizations we present implementations based on the Newton, BFGS and conjugate gradient methods. Our algorithms provide numerical resu lts supe rior to both Lee and Seung‘s method as well as to the alternating least squares heuristic, which was reported to work well in some situations but has no theoretical guarantees[1]. Our approach extends naturally to include regularization and box-constraints without sacrificing convergence guarantees. We present experimental results on both synthetic and real-world datasets that demonstrate the superiority of our methods, both in terms of better approximations as well as computational efficiency.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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A Unifying Probabilistic Framework for Analyzing Residual Dipolar Couplings

Habeck, M., Nilges, M., Rieping, W.

Journal of Biomolecular NMR, 40(2):135-144, February 2008 (article)

Abstract
Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the analysis of dipolar coupling data. We present a probabilistic framework for analyzing residual dipolar couplings and demonstrate that it is possible to estimate the atomic coordinates, the complete molecular alignment tensor, and the error of the couplings simultaneously. As a by-product, we also obtain estimates of the uncertainty in the coordinates and the alignment tensor. We show that our approach encompasses existing methods for determining the alignment tensor as special cases, including least squares estimation, histogram fitting, and elimination of an explicit alignment tensor in the restraint energy.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Contour-propagation Algorithms for Semi-automated Reconstruction of Neural Processes

Macke, J., Maack, N., Gupta, R., Denk, W., Schölkopf, B., Borst, A.

Journal of Neuroscience Methods, 167(2):349-357, January 2008 (article)

Abstract
A new technique, ”Serial Block Face Scanning Electron Microscopy” (SBFSEM), allows for automatic sectioning and imaging of biological tissue with a scanning electron microscope. Image stacks generated with this technology have a resolution sufficient to distinguish different cellular compartments, including synaptic structures, which should make it possible to obtain detailed anatomical knowledge of complete neuronal circuits. Such an image stack contains several thousands of images and is recorded with a minimal voxel size of 10-20nm in the x and y- and 30nm in z-direction. Consequently, a tissue block of 1mm3 (the approximate volume of the Calliphora vicina brain) will produce several hundred terabytes of data. Therefore, highly automated 3D reconstruction algorithms are needed. As a first step in this direction we have developed semiautomated segmentation algorithms for a precise contour tracing of cell membranes. These algorithms were embedded into an easy-to-operate user interface, which allows direct 3D observation of the extracted objects during the segmentation of image stacks. Compared to purely manual tracing, processing time is greatly accelerated.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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A Quantum-Statistical-Mechanical Extension of Gaussian Mixture Model

Tanaka, K., Tsuda, K.

Journal of Physics: Conference Series, 95(012023):1-9, January 2008 (article)

Abstract
We propose an extension of Gaussian mixture models in the statistical-mechanical point of view. The conventional Gaussian mixture models are formulated to divide all points in given data to some kinds of classes. We introduce some quantum states constructed by superposing conventional classes in linear combinations. Our extension can provide a new algorithm in classifications of data by means of linear response formulas in the statistical mechanics.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Learning to control in operational space

Peters, J., Schaal, S.

International Journal of Robotics Research, 27, pages: 197-212, 2008, clmc (article)

Abstract
One of the most general frameworks for phrasing control problems for complex, redundant robots is operational space control. However, while this framework is of essential importance for robotics and well-understood from an analytical point of view, it can be prohibitively hard to achieve accurate control in face of modeling errors, which are inevitable in com- plex robots, e.g., humanoid robots. In this paper, we suggest a learning approach for opertional space control as a direct inverse model learning problem. A first important insight for this paper is that a physically cor- rect solution to the inverse problem with redundant degrees-of-freedom does exist when learning of the inverse map is performed in a suitable piecewise linear way. The second crucial component for our work is based on the insight that many operational space controllers can be understood in terms of a constrained optimal control problem. The cost function as- sociated with this optimal control problem allows us to formulate a learn- ing algorithm that automatically synthesizes a globally consistent desired resolution of redundancy while learning the operational space controller. From the machine learning point of view, this learning problem corre- sponds to a reinforcement learning problem that maximizes an immediate reward. We employ an expectation-maximization policy search algorithm in order to solve this problem. Evaluations on a three degrees of freedom robot arm are used to illustrate the suggested approach. The applica- tion to a physically realistic simulator of the anthropomorphic SARCOS Master arm demonstrates feasibility for complex high degree-of-freedom robots. We also show that the proposed method works in the setting of learning resolved motion rate control on real, physical Mitsubishi PA-10 medical robotics arm.

am ei

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Voltage-Controllable Magnetic Composite Based on Multifunctional Polyethylene Microparticles

Ghosh, A., Sheridon, N. K., Fischer, P.

SMALL, 4(11):1956-1958, 2008 (article)

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DOI [BibTex]


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ENHANCED ADHESION OF PDMS SURFACES FUNCTIONALIZED BY POLY (n-BUTYL ACRYLATE) BRUSHES INSPIRED BY GECKO FOOT HAIRS

Nese, A., Lee, H., Dong, H., Aksak, B., Cusick, B., Kowalewski, T., Matyjaszewski, K., Sitti, M.

Polymer Preprints, 49(2):107, 2008 (article)

pi

[BibTex]

[BibTex]


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Design and development of the lifting and propulsion mechanism for a biologically inspired water runner robot

Floyd, S., Sitti, M.

IEEE transactions on robotics, 24(3):698-709, IEEE, 2008 (article)

pi

[BibTex]

[BibTex]


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Control of Cell Behavior by Aligned Micro/Nanofibrous Biomaterial Scaffolds Fabricated by Spinneret-Based Tunable Engineered Parameters (STEP) Technique

Nain, A. S., Phillippi, J. A., Sitti, M., MacKrell, J., Campbell, P. G., Amon, C.

Small, 4(8):1153-1159, Wiley Online Library, 2008 (article)

pi

[BibTex]

[BibTex]


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Adaptation to a sub-optimal desired trajectory

M. Mistry, E. A. G. L. T. Y. S. S. M. K.

Advances in Computational Motor Control VII, Symposium at the Society for Neuroscience Meeting, Washington DC, 2008, 2008, clmc (article)

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PDF [BibTex]

PDF [BibTex]


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Texture, microstructure and mechanical properties of equiaxed ultrafine-grained Zr fabricated by accumulative roll bonding

Jiang, L., Perez-Prado, M. T., Gruber, P. A., Arzt, E., Ruano, O. A., Kassner, M. E.

{Acta Materialia}, 56(6):1228-1242, 2008 (article)

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[BibTex]

[BibTex]


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Theory of size mismatched alloy systems: many-body Kanzaki forces

Shchyglo, O., Diaz-Ortiz, A., Udyansky, A., Bugaev, V. N., Reichert, H., Dosch, H., Drautz, R.

{Journal of Physics: Condensed Matter}, 20, pages: 1-9, 2008 (article)

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[BibTex]

[BibTex]


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Pinning of domain walls in composite particles

Kronmüller, H., Goll, D.

{Physica B}, 403, pages: 237-241, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Chaotic vortex dynamics and low current phases in the remanent state of MgB2 thin films

Albrecht, J., Audehm, P., Djupmyr, M.

{Superconductor Science and Technology}, 21, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Continuous and discontinuous grain-boundary wetting in ZnxAl1-x

Straumal, B. B., Gornakova, A. S., Kogtenkova, O. A., Protasova, S. G., Sursaeva, V. G., Baretzky, B.

{Physical Review B}, 78, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Magnetic circular dichroism in two-photon absorption and depth-resolved magnetic microscopy

Seib, J., Fähnle, M.

{Physical Review B}, 77, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Heat of adsorption for hydrogen in microporous high-surface-area materials

Schmitz, B., Müller, U., Trukhan, N., Schubert, M., Férey, G., Hirscher, M.

{ChemPhysChem}, 9, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Untersuchungen der Desorption von Wasserstoff in metall-organischen Gerüsten

Panella, B., Hönes, K., Müller, U., Trukhan, N., Schubert, M., Pütter, H., Hirscher, M.

{Angewandte Chemie}, 120, pages: 2169-2173, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Influence of domain wall pinning on the dynamic behavior of magnetic vortex structures: Time-resolved scanning x-ray transmission microscopy in NiFe thin film structures

Vansteenkiste, A., De Baerdemaeker, J., Chou, K. W., Stoll, H., Curcic, M., Tyliszczak, T., Woltersdorf, G., Back, C. H., Schütz, G., Van Waeyenberge, B.

{Physical Review B}, 77, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Temperature dependence of mechanical properties in ultrathin Au films with and without passivation

Gruber, P. A., Olliges, S., Arzt, E., Spolenak, R.

{Journal of Materials Research}, 23(9):2406-2419, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Structure, phase composition, and microhardness of carbon steels after high-pressure torsion

Mazilkin, A. A., Straumal, B., Protasova, S. G., Dobatkin, S. V., Baretzky, B.

{Journal of Materials Science}, 43, pages: 3800-3805, 2008 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Rolling and spinning friction characterization of fine particles using lateral force microscopy based contact pushing

Sümer, B., Sitti, M.

Journal of Adhesion Science and Technology, 22(5-6):481-506, Taylor & Francis Group, 2008 (article)

pi

[BibTex]

[BibTex]


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Modeling the soft backing layer thickness effect on adhesion of elastic microfiber arrays

Long, R., Hui, C., Kim, S., Sitti, M.

Journal of Applied Physics, 104(4):044301, AIP, 2008 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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Cross-talk compensation in atomic force microscopy

Onal, C. D., Sümer, B., Sitti, M.

Review of scientific instruments, 79(10):103706, AIP, 2008 (article)

pi

[BibTex]

[BibTex]


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Operational space control: A theoretical and emprical comparison

Nakanishi, J., Cory, R., Mistry, M., Peters, J., Schaal, S.

International Journal of Robotics Research, 27(6):737-757, 2008, clmc (article)

Abstract
Dexterous manipulation with a highly redundant movement system is one of the hallmarks of hu- man motor skills. From numerous behavioral studies, there is strong evidence that humans employ compliant task space control, i.e., they focus control only on task variables while keeping redundant degrees-of-freedom as compliant as possible. This strategy is robust towards unknown disturbances and simultaneously safe for the operator and the environment. The theory of operational space con- trol in robotics aims to achieve similar performance properties. However, despite various compelling theoretical lines of research, advanced operational space control is hardly found in actual robotics imple- mentations, in particular new kinds of robots like humanoids and service robots, which would strongly profit from compliant dexterous manipulation. To analyze the pros and cons of different approaches to operational space control, this paper focuses on a theoretical and empirical evaluation of different methods that have been suggested in the literature, but also some new variants of operational space controllers. We address formulations at the velocity, acceleration and force levels. First, we formulate all controllers in a common notational framework, including quaternion-based orientation control, and discuss some of their theoretical properties. Second, we present experimental comparisons of these approaches on a seven-degree-of-freedom anthropomorphic robot arm with several benchmark tasks. As an aside, we also introduce a novel parameter estimation algorithm for rigid body dynamics, which ensures physical consistency, as this issue was crucial for our successful robot implementations. Our extensive empirical results demonstrate that one of the simplified acceleration-based approaches can be advantageous in terms of task performance, ease of parameter tuning, and general robustness and compliance in face of inevitable modeling errors.

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link (url) [BibTex]

link (url) [BibTex]


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Interfaces in driven Ising models: shear enhances confinement

Smith, T. H. R., Vasilyev, O., Abraham, D. B., Maciolek, A., Schmidt, M.

{Physical Review Letters}, 101(6), 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Planar high-Tc superconducting quantum interference device gradiometer for simultaneous measurements of two magnetic field gradients

Steppke, A., Becker, C., Grosse, V., Dörrer, L., Schmidl, F., Seidel, P., Djupmyr, M., Albrecht, J.

{Applied Physics Letters}, 92, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Terminal contact elements of insect attachment devices studied by transmission X-ray microscopy

Eimüller, T., Guttmann, P., Gorb, S. N.

{Journal of Experimental Biology}, 211, pages: 1958-1963, 2008 (article)

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[BibTex]

[BibTex]


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Increase of Co solubility with decreasing grain size in ZnO

Straumal, B. B., Mazilkin, A. A., Protasova, S. G., Myatiev, A. A., Straumal, P. B., Baretzky, B.

{Acta Materialia}, 56, pages: 6246-6256, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Uncompensated moments in the MnPd/Fe exchange bias system

Brück, S., Schütz, G., Goering, E., Ji, X., Krishnan, K. M.

{Physical Review Letters}, 101, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Aqueous deposition of ultraviolet luminescent columnar tin-doped indium hydroxide films

Qiu, Y., Bellina, P., Jeurgens, L. P. H., Leineweber, A., Welzel, U., Gerstel, P., Jiang, L., van Aken, P. A., Bill, J., Aldinger, F.

{Advanced Functional Materials}, 18, pages: 2572-2583, 2008 (article)

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[BibTex]

[BibTex]


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Unified theory of near-adiabatic magnetization dynamics for collinear and noncollinear magnetization

Steiauf, D., Seib, J., Fähnle, M.

{Physical Review B}, 78, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Hardmetals with nanograin reinforced binder: binder fine structure and hardness

Konyashin, I., Ries, B., Lachmann, F., Cooper, R., Mazilkin, A., Straumal, B., Aretz, A., Babaev, V.

{International Journal of Refractory Metals \& Hard Materials}, 26, pages: 583-588, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Adhesion of biologically inspired oil-coated polymer micropillars

Cheung, E., Sitti, M.

Journal of Adhesion Science and Technology, 22(5-6):569-589, Taylor & Francis Group, 2008 (article)

pi

[BibTex]

[BibTex]


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Vision-based feedback strategy for controlled pushing of microparticles

Lynch, N. A., Onal, C. D., Schuster, E., Sitti, M.

Journal of Micro-Nano Mechatronics, 4(1-2):73-83, Springer-Verlag, 2008 (article)

pi

[BibTex]

[BibTex]


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Effect of quantity and configuration of attached bacteria on bacterial propulsion of microbeads

Behkam, B., Sitti, M.

Applied Physics Letters, 93(22):223901, AIP, 2008 (article)

pi

[BibTex]

[BibTex]


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Interfaces in confined Ising models: Kawasaki, Glauber and sheared dynamics

Smith, T. H. R., Vasilyev, O., Abraham, D. B., Maciolek, A., Schmidt, M.

{Journal of Physics: Condensed Matter}, 20(49), 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Critical fields of an exchange coupled two-layer composite particle

Goll, D., Kronmüller, H.

{Physica B}, 403, pages: 1854-1859, 2008 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Coercivity and domain structure of nanograined Fe-C alloys after high-pressure torsion

Protasova, S. G., Straumal, B., Dobatkin, S. V., Goll, D., Schütz, G., Baretzky, B., Mazilkin, A. A., Nebrasov, A. N.

{Journal of Materials Science}, 43, pages: 3775-3781, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Epitaxial growth and properties of (001)-oriented TbBaCo2O6-αfilms

Kasper, N. V., Wochner, P., Vigliante, A., Dosch, H., Jakob, G., Carstanjen, H. D., Kremer, R. K.

{Journal of Applied Physics}, 103, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Magnetic properties of exchange-coupled L10-FePt/Fe composite elements

Goll, D., Breitling, A., Macke, S.

{IEEE Transactions on Magnetics}, 44(11):3472-3475, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Colloidal cobalt-doped ZnO nanorods: synthesis, structural, and magnetic properties

Büsgen, T., Hilgendorff, M., Irsen, S., Wilhelm, F., Rogalev, A., Goll, D., Giersig, M.

{Journal of Physical Chemistry C}, 112(7):2412-2417, 2008 (article)

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DOI [BibTex]

DOI [BibTex]


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Raman studies of hydrogen adsorbed on nanostructured porous materials

Panella, B., Hirscher, M.

{Physical Chemistry Chemical Physics}, 10, pages: 2910-2917, 2008 (article)

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DOI [BibTex]

DOI [BibTex]