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2015


Enzymatically active biomimetic micropropellers for the penetration of mucin gels
Enzymatically active biomimetic micropropellers for the penetration of mucin gels

Walker (Schamel), D., Käsdorf, B. T., Jeong, H. H., Lieleg, O., Fischer, P.

Science Advances, 1(11):e1500501, December 2015 (article)

Abstract
In the body, mucus provides an important defense mechanism by limiting the penetration of pathogens. It is therefore also a major obstacle for the efficient delivery of particle-based drug carriers. The acidic stomach lining in particular is difficult to overcome because mucin glycoproteins form viscoelastic gels under acidic conditions. The bacterium Helicobacter pylori has developed a strategy to overcome the mucus barrier by producing the enzyme urease, which locally raises the pH and consequently liquefies the mucus. This allows the bacteria to swim through mucus and to reach the epithelial surface. We present an artificial system of reactive magnetic micropropellers that mimic this strategy to move through gastric mucin gels by making use of surface-immobilized urease. The results demonstrate the validity of this biomimetic approach to penetrate biological gels, and show that externally propelled microstructures can actively and reversibly manipulate the physical state of their surroundings, suggesting that such particles could potentially penetrate native mucus.

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link (url) DOI [BibTex]

2015


link (url) DOI [BibTex]


The EChemPen: A Guiding Hand To Learn Electrochemical Surface Modifications
The EChemPen: A Guiding Hand To Learn Electrochemical Surface Modifications

Valetaud, M., Loget, G., Roche, J., Hueken, N., Fattah, Z., Badets, V., Fontaine, O., Zigah, D.

J. of Chem. Ed., 92(10):1700-1704, September 2015 (article)

Abstract
The Electrochemical Pen (EChemPen) was developed as an attractive tool for learning electrochemistry. The fabrication, principle, and operation of the EChemPen are simple and can be easily performed by students in practical classes. It is based on a regular fountain pen principle, where the electrolytic solution is dispensed at a tip to locally modify a conductive surface by triggering a localized electrochemical reaction. Three simple model reactions were chosen to demonstrate the versatility of the EChemPen for teaching various electrochemical processes. We describe first the reversible writing/erasing of metal letters, then the electrodeposition of a black conducting polymer "ink", and finally the colorful writings that can be generated by titanium anodization and that can be controlled by the applied potential. These entertaining and didactic experiments are adapted for teaching undergraduate students that start to study electrochemistry by means of surface modification reactions.

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DOI [BibTex]

DOI [BibTex]


Optimal Length of Low Reynolds Number Nanopropellers
Optimal Length of Low Reynolds Number Nanopropellers

Walker (Schamel), D., Kuebler, M., Morozov, K. I., Fischer, P., Leshansky, A. M.

Nano Letters, 15(7):4412-4416, June 2015 (article)

Abstract
Locomotion in fluids at the nanoscale is dominated by viscous drag. One efficient propulsion scheme is to use a weak rotating magnetic field that drives a chiral object. Froth bacterial flagella to artificial drills, the corkscrew is a universally useful chiral shape for propulsion in viscous environments. Externally powered magnetic micro- and nanomotors have been recently developed that allow for precise fuel-free propulsion in complex media. Here, we combine analytical and numerical theory with experiments on nanostructured screw-propellers to show that the optimal length is surprisingly short only about one helical turn, which is shorter than most of the structures in use to date. The results have important implications for the design of artificial actuated nano- and micropropellers and can dramatically reduce fabrication times, while ensuring optimal performance.

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DOI [BibTex]

DOI [BibTex]


A theoretical study of potentially observable chirality-sensitive NMR effects in molecules
A theoretical study of potentially observable chirality-sensitive NMR effects in molecules

Garbacz, P., Cukras, J., Jaszunski, M.

Phys. Chem. Chem. Phys., 17(35):22642-22651, May 2015 (article)

Abstract
Two recently predicted nuclear magnetic resonance effects, the chirality-induced rotating electric polarization and the oscillating magnetization, are examined for several experimentally available chiral molecules. We discuss in detail the requirements for experimental detection of chirality-sensitive NMR effects of the studied molecules. These requirements are related to two parameters: the shielding polarizability and the antisymmetric part of the nuclear magnetic shielding tensor. The dominant second contribution has been computed for small molecules at the coupled cluster and density functional theory levels. It was found that DFT calculations using the KT2 functional and the aug-cc-pCVTZ basis set adequately reproduce the CCSD(T) values obtained with the same basis set. The largest values of parameters, thus most promising from the experimental point of view, were obtained for the fluorine nuclei in 1,3-difluorocyclopropene and 1,3-diphenyl-2-fluoro-3-trifluoromethylcyclopropene.

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DOI [BibTex]

DOI [BibTex]


Dynamic Inclusion Complexes of Metal Nanoparticles Inside Nanocups
Dynamic Inclusion Complexes of Metal Nanoparticles Inside Nanocups

Alarcon-Correa, M., Lee, T. C., Fischer, P.

Angew. Chem. Int. Ed., 54(23):6730-6734, May 2015, Featured cover article. (article)

Abstract
Host-guest inclusion complexes are abundant in molecular systems and of fundamental importance in living organisms. Realizing a colloidal analogue of a molecular dynamic inclusion complex is challenging because inorganic nanoparticles (NPs) with a well-defined cavity and portal are difficult to synthesize in high yield and with good structural fidelity. Herein, a generic strategy towards the fabrication of dynamic 1: 1 inclusion complexes of metal nanoparticles inside oxide nanocups with high yield (> 70%) and regiospecificity (> 90%) by means of a reactive double Janus nanoparticle intermediate is reported. Experimental evidence confirms that the inclusion complexes are formed by a kinetically controlled mechanism involving a delicate interplay between bipolar galvanic corrosion and alloying-dealloying oxidation. Release of the NP guest from the nanocups can be efficiently triggered by an external stimulus. Featured cover article.

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DOI [BibTex]

DOI [BibTex]


Surface roughness-induced speed increase for active Janus micromotors
Surface roughness-induced speed increase for active Janus micromotors

Choudhury, U., Soler, L., Gibbs, J. G., Sanchez, S., Fischer, P.

Chem. Comm., 51(41):8660-8663, April 2015 (article)

Abstract
We demonstrate a simple physical fabrication method to control surface roughness of Janus micromotors and fabricate self-propelled active Janus microparticles with rough catalytic platinum surfaces that show a four-fold increase in their propulsion speed compared to conventional Janus particles coated with a smooth Pt layer.

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DOI [BibTex]

DOI [BibTex]


Active colloidal microdrills
Active colloidal microdrills

Gibbs, J. G., Fischer, P.

Chem. Comm., 51(20):4192-4195, Febuary 2015 (article)

Abstract
We demonstrate a chemically driven, autonomous catalytic microdrill. An asymmetric distribution of catalyst causes the helical swimmer to twist while it undergoes directed propulsion. A driving torque and hydrodynamic coupling between translation and rotation at low Reynolds number leads to drill-like swimming behaviour.

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DOI [BibTex]

DOI [BibTex]


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Probabilistic Interpretation of Linear Solvers

Hennig, P.

SIAM Journal on Optimization, 25(1):234-260, 2015 (article)

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Web PDF link (url) DOI [BibTex]

Web PDF link (url) DOI [BibTex]


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Active Reward Learning with a Novel Acquisition Function

Daniel, C., Kroemer, O., Viering, M., Metz, J., Peters, J.

Autonomous Robots, 39(3):389-405, 2015 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


Selectable Nanopattern Arrays for Nanolithographic Imprint and Etch-Mask Applications
Selectable Nanopattern Arrays for Nanolithographic Imprint and Etch-Mask Applications

Jeong, H. H., Mark, A. G., Lee, T., Son, K., Chen, W., Alarcon-Correa, M., Kim, I., Schütz, G., Fischer, P.

Adv. Science, 2(7):1500016, 2015, Featured cover article. (article)

Abstract
A parallel nanolithographic patterning method is presented that can be used to obtain arrays of multifunctional nanoparticles. These patterns can simply be converted into a variety of secondary nanopatterns that are useful for nanolithographic imprint, plasmonic, and etch-mask applications.

pf

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Learning Movement Primitive Attractor Goals and Sequential Skills from Kinesthetic Demonstrations

Manschitz, S., Kober, J., Gienger, M., Peters, J.

Robotics and Autonomous Systems, 74, Part A, pages: 97-107, 2015 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Bayesian Optimization for Learning Gaits under Uncertainty

Calandra, R., Seyfarth, A., Peters, J., Deisenroth, M.

Annals of Mathematics and Artificial Intelligence, pages: 1-19, 2015 (article)

am ei

DOI [BibTex]

DOI [BibTex]


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Probabilistic numerics and uncertainty in computations

Hennig, P., Osborne, M. A., Girolami, M.

Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, 471(2179), 2015 (article)

Abstract
We deliver a call to arms for probabilistic numerical methods: algorithms for numerical tasks, including linear algebra, integration, optimization and solving differential equations, that return uncertainties in their calculations. Such uncertainties, arising from the loss of precision induced by numerical calculation with limited time or hardware, are important for much contemporary science and industry. Within applications such as climate science and astrophysics, the need to make decisions on the basis of computations with large and complex data have led to a renewed focus on the management of numerical uncertainty. We describe how several seminal classic numerical methods can be interpreted naturally as probabilistic inference. We then show that the probabilistic view suggests new algorithms that can flexibly be adapted to suit application specifics, while delivering improved empirical performance. We provide concrete illustrations of the benefits of probabilistic numeric algorithms on real scientific problems from astrometry and astronomical imaging, while highlighting open problems with these new algorithms. Finally, we describe how probabilistic numerical methods provide a coherent framework for identifying the uncertainty in calculations performed with a combination of numerical algorithms (e.g. both numerical optimizers and differential equation solvers), potentially allowing the diagnosis (and control) of error sources in computations.

ei pn

PDF DOI [BibTex]

PDF DOI [BibTex]


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Kinematic and gait similarities between crawling human infants and other quadruped mammals

Righetti, L., Nylen, A., Rosander, K., Ijspeert, A.

Frontiers in Neurology, 6(17), February 2015 (article)

Abstract
Crawling on hands and knees is an early pattern of human infant locomotion, which offers an interesting way of studying quadrupedalism in one of its simplest form. We investigate how crawling human infants compare to other quadruped mammals, especially primates. We present quantitative data on both the gait and kinematics of seven 10-month-old crawling infants. Body movements were measured with an optoelectronic system giving precise data on 3-dimensional limb movements. Crawling on hands and knees is very similar to the locomotion of non-human primates in terms of the quite protracted arm at touch-down, the coordination between the spine movements in the lateral plane and the limbs, the relatively extended limbs during locomotion and the strong correlation between stance duration and speed of locomotion. However, there are important differences compared to primates, such as the choice of a lateral-sequence walking gait, which is similar to most non-primate mammals and the relatively stiff elbows during stance as opposed to the quite compliant gaits of primates. These finding raise the question of the role of both the mechanical structure of the body and neural control on the determination of these characteristics.

mg

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Novel plasticity rule can explain the development of sensorimotor intelligence

Der, R., Martius, G.

Proceedings of the National Academy of Sciences, 112(45):E6224-E6232, 2015 (article)

Abstract
Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no system-specific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking, which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.

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link (url) DOI Project Page [BibTex]

link (url) DOI Project Page [BibTex]


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Quantifying Emergent Behavior of Autonomous Robots

Martius, G., Olbrich, E.

Entropy, 17(10):7266, 2015 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]

2001


Isotropic second-order nonlinear optical susceptibilities
Isotropic second-order nonlinear optical susceptibilities

Fischer, P., Buckingham, A., Albrecht, A.

PHYSICAL REVIEW A, 64(5), 2001 (article)

Abstract
The second-order nonlinear optical susceptibility, in the electric dipole approximation, is only nonvanishing for materials that are noncentrosymmetric. Should the medium be isotropic, then only a chiral system. such as an optically active liquid, satisfies this symmetry requirement. We derive the quantum-mechanical form of the isotropic component of the sum- and difference-frequency susceptibility and discuss its unusual spectral properties. We show that any coherent second-order nonlinear optical process in a system of randomly oriented molecules requires the medium to be chiral. and the incident frequencies to be different and nonzero. Furthermore, a minimum of two nondegenerate excited molecular states are needed for the isotropic part of the susceptibility to be nonvanishing. The rotationally invariant susceptibility is zero in the static field limit and shows exceptionally sensitive resonance and dephasing effects that are particular to chiral centers.

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DOI [BibTex]

2001


DOI [BibTex]


Reply to ``Comment on `Phenomenological damping in optical response tensors'{''}
Reply to “Comment on ‘Phenomenological damping in optical response tensors’”

Buckingham, A., Fischer, P.

PHYSICAL REVIEW A, 63(4), 2001 (article)

Abstract
We show that damping factors must not be incorporated in the perturbation of the ground state by a static electric field. If they are included, as in the theory of Stedman et al. {[}preceding Comment. Phys. Rev. A 63, 047801 (2001)], then there would be an electric dipole in the y direction induced in a hydrogen atom in the M-s = + 1/2 state by a static electric field in the x direction. Such a dipole is excluded by symmetry.

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DOI [BibTex]


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Synchronized robot drumming by neural oscillator

Kotosaka, S., Schaal, S.

Journal of the Robotics Society of Japan, 19(1):116-123, 2001, clmc (article)

Abstract
Sensory-motor integration is one of the key issues in robotics. In this paper, we propose an approach to rhythmic arm movement control that is synchronized with an external signal based on exploiting a simple neural oscillator network. Trajectory generation by the neural oscillator is a biologically inspired method that can allow us to generate a smooth and continuous trajectory. The parameter tuning of the oscillators is used to generate a synchronized movement with wide intervals. We adopted the method for the drumming task as an example task. By using this method, the robot can realize synchronized drumming with wide drumming intervals in real time. The paper also shows the experimental results of drumming by a humanoid robot.

am

[BibTex]

[BibTex]


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Origins and violations of the 2/3 power law in rhythmic 3D movements

Schaal, S., Sternad, D.

Experimental Brain Research, 136, pages: 60-72, 2001, clmc (article)

Abstract
The 2/3 power law, the nonlinear relationship between tangential velocity and radius of curvature of the endeffector trajectory, has been suggested as a fundamental constraint of the central nervous system in the formation of rhythmic endpoint trajectories. However, studies on the 2/3 power law have largely been confined to planar drawing patterns of relatively small size. With the hypothesis that this strategy overlooks nonlinear effects that are constitutive in movement generation, the present experiments tested the validity of the power law in elliptical patterns which were not confined to a planar surface and which were performed by the unconstrained 7-DOF arm with significant variations in pattern size and workspace orientation. Data were recorded from five human subjects where the seven joint angles and the endpoint trajectories were analyzed. Additionally, an anthropomorphic 7-DOF robot arm served as a "control subject" whose endpoint trajectories were generated on the basis of the human joint angle data, modeled as simple harmonic oscillations. Analyses of the endpoint trajectories demonstrate that the power law is systematically violated with increasing pattern size, in both exponent and the goodness of fit. The origins of these violations can be explained analytically based on smooth rhythmic trajectory formation and the kinematic structure of the human arm. We conclude that in unconstrained rhythmic movements, the power law seems to be a by-product of a movement system that favors smooth trajectories, and that it is unlikely to serve as a primary movement generating principle. Our data rather suggests that subjects employed smooth oscillatory pattern generators in joint space to realize the required movement patterns.

am

link (url) [BibTex]

link (url) [BibTex]


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Graph-matching vs. entropy-based methods for object detection
Neural Networks, 14(3):345-354, 2001, clmc (article)

Abstract
Labeled Graph Matching (LGM) has been shown successful in numerous ob-ject vision tasks. This method is the basis for arguably the best face recognition system in the world. We present an algorithm for visual pattern recognition that is an extension of LGM ("LGM+"). We compare the performance of LGM and LGM+ algorithms with a state of the art statistical method based on Mutual Information Maximization (MIM). We present an adaptation of the MIM method for multi-dimensional Gabor wavelet features. The three pattern recognition methods were evaluated on an object detection task, using a set of stimuli on which none of the methods had been tested previously. The results indicate that while the performance of the MIM method operating upon Gabor wavelets is superior to the same method operating on pixels and to LGM, it is surpassed by LGM+. LGM+ offers a significant improvement in performance over LGM without losing LGMâ??s virtues of simplicity, biological plausibility, and a computational cost that is 2-3 orders of magnitude lower than that of the MIM algorithm. 

am

link (url) [BibTex]

link (url) [BibTex]


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Biomimetic gaze stabilization based on feedback-error learning with nonparametric regression networks

Shibata, T., Schaal, S.

Neural Networks, 14(2):201-216, 2001, clmc (article)

Abstract
Oculomotor control in a humanoid robot faces similar problems as biological oculomotor systems, i.e. the stabilization of gaze in face of unknown perturbations of the body, selective attention, stereo vision, and dealing with large information processing delays. Given the nonlinearities of the geometry of binocular vision as well as the possible nonlinearities of the oculomotor plant, it is desirable to accomplish accurate control of these behaviors through learning approaches. This paper develops a learning control system for the phylogenetically oldest behaviors of oculomotor control, the stabilization reflexes of gaze. In a step-wise procedure, we demonstrate how control theoretic reasonable choices of control components result in an oculomotor control system that resembles the known functional anatomy of the primate oculomotor system. The core of the learning system is derived from the biologically inspired principle of feedback-error learning combined with a state-of-the-art non-parametric statistical learning network. With this circuitry, we demonstrate that our humanoid robot is able to acquire high performance visual stabilization reflexes after about 40 s of learning despite significant nonlinearities and processing delays in the system.

am

link (url) [BibTex]


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Fast learning of biomimetic oculomotor control with nonparametric regression networks (in Japanese)

Shibata, T., Schaal, S.

Journal of the Robotics Society of Japan, 19(4):468-479, 2001, clmc (article)

am

[BibTex]

[BibTex]


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Bouncing a ball: Tuning into dynamic stability

Sternad, D., Duarte, M., Katsumata, H., Schaal, S.

Journal of Experimental Psychology: Human Perception and Performance, 27(5):1163-1184, 2001, clmc (article)

Abstract
Rhythmically bouncing a ball with a racket was investigated and modeled with a nonlinear map. Model analyses provided a variable defining a dynamically stable solution that obviates computationally expensive corrections. Three experiments evaluated whether dynamic stability is optimized and what perceptual support is necessary for stable behavior. Two hypotheses were tested: (a) Performance is stable if racket acceleration is negative at impact, and (b) variability is lowest at an impact acceleration between -4 and -1 m/s2. In Experiment 1 participants performed the task, eyes open or closed, bouncing a ball confined to a 1-dimensional trajectory. Experiment 2 eliminated constraints on racket and ball trajectory. Experiment 3 excluded visual or haptic information. Movements were performed with negative racket accelerations in the range of highest stability. Performance with eyes closed was more variable, leaving acceleration unaffected. With haptic information, performance was more stable than with visual information alone.

am

[BibTex]

[BibTex]


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Biomimetic oculomotor control

Shibata, T., Vijayakumar, S., Conradt, J., Schaal, S.

Adaptive Behavior, 9(3/4):189-207, 2001, clmc (article)

Abstract
Oculomotor control in a humanoid robot faces similar problems as biological oculomotor systems, i.e., capturing targets accurately on a very narrow fovea, dealing with large delays in the control system, the stabilization of gaze in face of unknown perturbations of the body, selective attention, and the complexity of stereo vision. In this paper, we suggest control circuits to realize three of the most basic oculomotor behaviors and their integration - the vestibulo-ocular and optokinetic reflex (VOR-OKR) for gaze stabilization, smooth pursuit for tracking moving objects, and saccades for overt visual attention. Each of these behaviors and the mechanism for their integration was derived with inspiration from computational theories as well as behavioral and physiological data in neuroscience. Our implementations on a humanoid robot demonstrate good performance of the oculomotor behaviors, which proves to be a viable strategy to explore novel control mechanisms for humanoid robotics. Conversely, insights gained from our models have been able to directly influence views and provide new directions for computational neuroscience research.

am

link (url) [BibTex]

link (url) [BibTex]

1998


Surface second-order nonlinear optical activity
Surface second-order nonlinear optical activity

Fischer, P., Buckingham, A.

JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, 15(12):2951-2957, 1998 (article)

Abstract
Following the recent observation of a large second-harmonic intensity difference from a monolayer of chiral molecules with left and right circularly polarized light, the scattering theory is generalized and extended to predict linear and circular intensity differences for the more Versatile sum-frequency spectroscopy. Estimates indicate that intensity differences should be detectable for a typical experimental arrangement. The second-order nonlinear surface susceptibility tensor is given for different surface point groups in the electric dipole approximation; it is shown that nonlinear optical activity phenomena unambiguously probe molecular chirality only for molecular monolayers that are symmetric about the normal. Other surface symmetries can give rise to intensity differences from monolayers composed of achiral molecules. A water surface is predicted to show Linear and nonlinear optical activity in the presence of an electric field parallel to the surface. (C) 1998 Optical Society of America {[}S0740-3224(98)01311-3] OCIS codes: 190.0190, 190.4350, 240.6490.

pf

DOI [BibTex]

1998


DOI [BibTex]


Linear electro-optic effect in optically active liquids
Linear electro-optic effect in optically active liquids

Buckingham, A., Fischer, P.

CHEMICAL PHYSICS LETTERS, 297(3-4):239-246, 1998 (article)

Abstract
A linear effect of an electrostatic field F on the intensity of sum- and difference-frequency generation in a chiral liquid is predicted. It arises in the electric dipole approximation. The effect changes sign with the enantiomer and on reversing the direction of the electrostatic field. The sum-frequency generator chi(alpha beta gamma)((2)) (-omega(3);omega(1),omega(2)), where omega(3) = omega(1) + omega(2), and the electric field-induced sum-frequency generator chi(alpha beta gamma delta)((3))(-omega(3);omega(1),omega(2),0)F-delta interfere and their contributions to the scattering power can be distinguished. Encouraging predictions are given for a typical experimental arrangement. (C) 1998 Elsevier Science B.V. All rights reserved.

pf

DOI [BibTex]

DOI [BibTex]


Monolayers of hexadecyltrimethylammonium p-tosylate at the air-water interface. 1. Sum-frequency spectroscopy
Monolayers of hexadecyltrimethylammonium p-tosylate at the air-water interface. 1. Sum-frequency spectroscopy

Bell, G., Li, Z., Bain, C., Fischer, P., Duffy, D.

JOURNAL OF PHYSICAL CHEMISTRY B, 102(47):9461-9472, 1998 (article)

Abstract
Sum-frequency vibrational spectroscopy has been used to determine the structure of monolayers of the cationic surfactant, hexadecyltrimethylammonium p-tosylate (C(16)TA(+)Ts(-)), at the surface of water. Selective deuteration of the cation or the anion allowed the separate detection of sum-frequency spectra of the surfactant and of counterions that are bound to the monolayer. The p-tosylate ions an oriented with their methyl groups pointing away from the aqueous subphase and with the C-2 axis tilted, on average, by 30-40 degrees from the surface normal. The vibrational spectra of C(16)TA(+) indicate that the number of gauche defects in the monolayer does not change dramatically when bromide counterions are replaced by p-tosylate. The ends of the hydrocarbon chains of C16TA+ are, however, tilted much further from the surface normal in the presence of p-tosylate than in the presence of bromide. A quantitative analysis of the sum-frequency spectra requires a knowledge of the molecular hyperpolarizability tensor: the role of ab initio calculations and Raman spectroscopy in determining the components of this tensor is discussed.

pf

DOI [BibTex]

DOI [BibTex]


Ultraviolet resonance Raman study of drug binding in dihydrofolate reductase, gyrase, and catechol O-methyltransferase
Ultraviolet resonance Raman study of drug binding in dihydrofolate reductase, gyrase, and catechol O-methyltransferase

Couling, V., Fischer, P., Klenerman, D., Huber, W.

BIOPHYSICAL JOURNAL, 75(2):1097-1106, 1998 (article)

Abstract
This paper presents a study of the use of ultraviolet resonance Raman (UVRR) spectroscopic methods as a means of elucidating aspects of drug-protein interactions. Some of the RR vibrational bands of the aromatic amino acids tyrosine and tryptophan are sensitive to the microenvironment, and the use of UV excitation radiation allows selective enhancement of the spectral features of the aromatic amino acids, enabling observation specifically of their change in microenvironment upon drug binding. The three drug-protein systems investigated in this study are dihydrofolate reductase with its inhibitor trimethoprim, gyrase with novobiocin, and catechol O-methyltransferase with dinitrocatechol. It is demonstrated that UVRR spectroscopy has adequate sensitivity to be a useful means of detecting drug-protein interactions in those systems for which the electronic absorption of the aromatic amino acids changes because of hydrogen bonding and/or possible dipole-dipole and dipole-polarizability interactions with the ligand.

pf

DOI [BibTex]

DOI [BibTex]


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Constructive incremental learning from only local information

Schaal, S., Atkeson, C. G.

Neural Computation, 10(8):2047-2084, 1998, clmc (article)

Abstract
We introduce a constructive, incremental learning system for regression problems that models data by means of spatially localized linear models. In contrast to other approaches, the size and shape of the receptive field of each locally linear model as well as the parameters of the locally linear model itself are learned independently, i.e., without the need for competition or any other kind of communication. Independent learning is accomplished by incrementally minimizing a weighted local cross validation error. As a result, we obtain a learning system that can allocate resources as needed while dealing with the bias-variance dilemma in a principled way. The spatial localization of the linear models increases robustness towards negative interference. Our learning system can be interpreted as a nonparametric adaptive bandwidth smoother, as a mixture of experts where the experts are trained in isolation, and as a learning system which profits from combining independent expert knowledge on the same problem. This paper illustrates the potential learning capabilities of purely local learning and offers an interesting and powerful approach to learning with receptive fields. 

am

link (url) [BibTex]

link (url) [BibTex]


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Local adaptive subspace regression

Vijayakumar, S., Schaal, S.

Neural Processing Letters, 7(3):139-149, 1998, clmc (article)

Abstract
Incremental learning of sensorimotor transformations in high dimensional spaces is one of the basic prerequisites for the success of autonomous robot devices as well as biological movement systems. So far, due to sparsity of data in high dimensional spaces, learning in such settings requires a significant amount of prior knowledge about the learning task, usually provided by a human expert. In this paper we suggest a partial revision of the view. Based on empirical studies, we observed that, despite being globally high dimensional and sparse, data distributions from physical movement systems are locally low dimensional and dense. Under this assumption, we derive a learning algorithm, Locally Adaptive Subspace Regression, that exploits this property by combining a dynamically growing local dimensionality reduction technique  as a preprocessing step with a nonparametric learning technique, locally weighted regression, that also learns the region of validity of the regression. The usefulness of the algorithm and the validity of its assumptions are illustrated for a synthetic data set, and for data of the inverse dynamics of human arm movements and an actual 7 degree-of-freedom anthropomorphic robot arm. 

am

link (url) [BibTex]

link (url) [BibTex]