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2015


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Scalable Robust Principal Component Analysis using Grassmann Averages

Hauberg, S., Feragen, A., Enficiaud, R., Black, M.

IEEE Trans. Pattern Analysis and Machine Intelligence (PAMI), December 2015 (article)

Abstract
In large datasets, manual data verification is impossible, and we must expect the number of outliers to increase with data size. While principal component analysis (PCA) can reduce data size, and scalable solutions exist, it is well-known that outliers can arbitrarily corrupt the results. Unfortunately, state-of-the-art approaches for robust PCA are not scalable. We note that in a zero-mean dataset, each observation spans a one-dimensional subspace, giving a point on the Grassmann manifold. We show that the average subspace corresponds to the leading principal component for Gaussian data. We provide a simple algorithm for computing this Grassmann Average (GA), and show that the subspace estimate is less sensitive to outliers than PCA for general distributions. Because averages can be efficiently computed, we immediately gain scalability. We exploit robust averaging to formulate the Robust Grassmann Average (RGA) as a form of robust PCA. The resulting Trimmed Grassmann Average (TGA) is appropriate for computer vision because it is robust to pixel outliers. The algorithm has linear computational complexity and minimal memory requirements. We demonstrate TGA for background modeling, video restoration, and shadow removal. We show scalability by performing robust PCA on the entire Star Wars IV movie; a task beyond any current method. Source code is available online.

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preprint pdf from publisher supplemental Project Page [BibTex]

2015


preprint pdf from publisher supplemental Project Page [BibTex]


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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]

link (url) DOI [BibTex]


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SMPL: A Skinned Multi-Person Linear Model

Loper, M., Mahmood, N., Romero, J., Pons-Moll, G., Black, M. J.

ACM Trans. Graphics (Proc. SIGGRAPH Asia), 34(6):248:1-248:16, ACM, New York, NY, October 2015 (article)

Abstract
We present a learned model of human body shape and pose-dependent shape variation that is more accurate than previous models and is compatible with existing graphics pipelines. Our Skinned Multi-Person Linear model (SMPL) is a skinned vertex-based model that accurately represents a wide variety of body shapes in natural human poses. The parameters of the model are learned from data including the rest pose template, blend weights, pose-dependent blend shapes, identity-dependent blend shapes, and a regressor from vertices to joint locations. Unlike previous models, the pose-dependent blend shapes are a linear function of the elements of the pose rotation matrices. This simple formulation enables training the entire model from a relatively large number of aligned 3D meshes of different people in different poses. We quantitatively evaluate variants of SMPL using linear or dual-quaternion blend skinning and show that both are more accurate than a Blend-SCAPE model trained on the same data. We also extend SMPL to realistically model dynamic soft-tissue deformations. Because it is based on blend skinning, SMPL is compatible with existing rendering engines and we make it available for research purposes.

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pdf video code/model errata DOI Project Page Project Page [BibTex]

pdf video code/model errata DOI Project Page Project Page [BibTex]


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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]


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Dyna: A Model of Dynamic Human Shape in Motion

Pons-Moll, G., Romero, J., Mahmood, N., Black, M. J.

ACM Transactions on Graphics, (Proc. SIGGRAPH), 34(4):120:1-120:14, ACM, August 2015 (article)

Abstract
To look human, digital full-body avatars need to have soft tissue deformations like those of real people. We learn a model of soft-tissue deformations from examples using a high-resolution 4D capture system and a method that accurately registers a template mesh to sequences of 3D scans. Using over 40,000 scans of ten subjects, we learn how soft tissue motion causes mesh triangles to deform relative to a base 3D body model. Our Dyna model uses a low-dimensional linear subspace to approximate soft-tissue deformation and relates the subspace coefficients to the changing pose of the body. Dyna uses a second-order auto-regressive model that predicts soft-tissue deformations based on previous deformations, the velocity and acceleration of the body, and the angular velocities and accelerations of the limbs. Dyna also models how deformations vary with a person’s body mass index (BMI), producing different deformations for people with different shapes. Dyna realistically represents the dynamics of soft tissue for previously unseen subjects and motions. We provide tools for animators to modify the deformations and apply them to new stylized characters.

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pdf preprint video data DOI Project Page Project Page [BibTex]

pdf preprint video data DOI Project Page Project Page [BibTex]


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Linking Objects to Actions: Encoding of Target Object and Grasping Strategy in Primate Ventral Premotor Cortex

Vargas-Irwin, C. E., Franquemont, L., Black, M. J., Donoghue, J. P.

Journal of Neuroscience, 35(30):10888-10897, July 2015 (article)

Abstract
Neural activity in ventral premotor cortex (PMv) has been associated with the process of matching perceived objects with the motor commands needed to grasp them. It remains unclear how PMv networks can flexibly link percepts of objects affording multiple grasp options into a final desired hand action. Here, we use a relational encoding approach to track the functional state of PMv neuronal ensembles in macaque monkeys through the process of passive viewing, grip planning, and grasping movement execution. We used objects affording multiple possible grip strategies. The task included separate instructed delay periods for object presentation and grip instruction. This approach allowed us to distinguish responses elicited by the visual presentation of the objects from those associated with selecting a given motor plan for grasping. We show that PMv continuously incorporates information related to object shape and grip strategy as it becomes available, revealing a transition from a set of ensemble states initially most closely related to objects, to a new set of ensemble patterns reflecting unique object-grip combinations. These results suggest that PMv dynamically combines percepts, gradually navigating toward activity patterns associated with specific volitional actions, rather than directly mapping perceptual object properties onto categorical grip representations. Our results support the idea that PMv is part of a network that dynamically computes motor plans from perceptual information. Significance Statement: The present work demonstrates that the activity of groups of neurons in primate ventral premotor cortex reflects information related to visually presented objects, as well as the motor strategy used to grasp them, linking individual objects to multiple possible grips. PMv could provide useful control signals for neuroprosthetic assistive devices designed to interact with objects in a flexible way.

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publisher link DOI Project Page [BibTex]

publisher link DOI Project Page [BibTex]


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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]


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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]


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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]


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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]


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Multi-view and 3D Deformable Part Models

Pepik, B., Stark, M., Gehler, P., Schiele, B.

Pattern Analysis and Machine Intelligence, 37(11):14, IEEE, March 2015 (article)

Abstract
As objects are inherently 3-dimensional, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2], 3D object classes [3], Pascal3D+ [4], Pascal VOC 2007 [5], EPFL multi-view cars [6]).

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DOI Project Page [BibTex]

DOI Project Page [BibTex]


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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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Spike train SIMilarity Space (SSIMS): A framework for single neuron and ensemble data analysis

Vargas-Irwin, C. E., Brandman, D. M., Zimmermann, J. B., Donoghue, J. P., Black, M. J.

Neural Computation, 27(1):1-31, MIT Press, January 2015 (article)

Abstract
We present a method to evaluate the relative similarity of neural spiking patterns by combining spike train distance metrics with dimensionality reduction. Spike train distance metrics provide an estimate of similarity between activity patterns at multiple temporal resolutions. Vectors of pair-wise distances are used to represent the intrinsic relationships between multiple activity patterns at the level of single units or neuronal ensembles. Dimensionality reduction is then used to project the data into concise representations suitable for clustering analysis as well as exploratory visualization. Algorithm performance and robustness are evaluated using multielectrode ensemble activity data recorded in behaving primates. We demonstrate how Spike train SIMilarity Space (SSIMS) analysis captures the relationship between goal directions for an 8-directional reaching task and successfully segregates grasp types in a 3D grasping task in the absence of kinematic information. The algorithm enables exploration of virtually any type of neural spiking (time series) data, providing similarity-based clustering of neural activity states with minimal assumptions about potential information encoding models.

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pdf: publisher site pdf: author's proof DOI Project Page [BibTex]

pdf: publisher site pdf: author's proof DOI Project Page [BibTex]


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Metric Regression Forests for Correspondence Estimation

Pons-Moll, G., Taylor, J., Shotton, J., Hertzmann, A., Fitzgibbon, A.

International Journal of Computer Vision, pages: 1-13, 2015 (article)

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springer PDF Project Page [BibTex]

springer PDF Project Page [BibTex]


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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.

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link (url) DOI [BibTex]

link (url) DOI [BibTex]

2014


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MoSh: Motion and Shape Capture from Sparse Markers

Loper, M. M., Mahmood, N., Black, M. J.

ACM Transactions on Graphics, (Proc. SIGGRAPH Asia), 33(6):220:1-220:13, ACM, New York, NY, USA, November 2014 (article)

Abstract
Marker-based motion capture (mocap) is widely criticized as producing lifeless animations. We argue that important information about body surface motion is present in standard marker sets but is lost in extracting a skeleton. We demonstrate a new approach called MoSh (Motion and Shape capture), that automatically extracts this detail from mocap data. MoSh estimates body shape and pose together using sparse marker data by exploiting a parametric model of the human body. In contrast to previous work, MoSh solves for the marker locations relative to the body and estimates accurate body shape directly from the markers without the use of 3D scans; this effectively turns a mocap system into an approximate body scanner. MoSh is able to capture soft tissue motions directly from markers by allowing body shape to vary over time. We evaluate the effect of different marker sets on pose and shape accuracy and propose a new sparse marker set for capturing soft-tissue motion. We illustrate MoSh by recovering body shape, pose, and soft-tissue motion from archival mocap data and using this to produce animations with subtlety and realism. We also show soft-tissue motion retargeting to new characters and show how to magnify the 3D deformations of soft tissue to create animations with appealing exaggerations.

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pdf video data pdf from publisher link (url) DOI Project Page Project Page Project Page [BibTex]

2014


pdf video data pdf from publisher link (url) DOI Project Page Project Page Project Page [BibTex]


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Can I recognize my body’s weight? The influence of shape and texture on the perception of self

Piryankova, I., Stefanucci, J., Romero, J., de la Rosa, S., Black, M., Mohler, B.

ACM Transactions on Applied Perception for the Symposium on Applied Perception, 11(3):13:1-13:18, September 2014 (article)

Abstract
The goal of this research was to investigate women’s sensitivity to changes in their perceived weight by altering the body mass index (BMI) of the participants’ personalized avatars displayed on a large-screen immersive display. We created the personalized avatars with a full-body 3D scanner that records both the participants’ body geometry and texture. We altered the weight of the personalized avatars to produce changes in BMI while keeping height, arm length and inseam fixed and exploited the correlation between body geometry and anthropometric measurements encapsulated in a statistical body shape model created from thousands of body scans. In a 2x2 psychophysical experiment, we investigated the relative importance of visual cues, namely shape (own shape vs. an average female body shape with equivalent height and BMI to the participant) and texture (own photo-realistic texture or checkerboard pattern texture) on the ability to accurately perceive own current body weight (by asking them ‘Is the avatar the same weight as you?’). Our results indicate that shape (where height and BMI are fixed) had little effect on the perception of body weight. Interestingly, the participants perceived their body weight veridically when they saw their own photo-realistic texture and significantly underestimated their body weight when the avatar had a checkerboard patterned texture. The range that the participants accepted as their own current weight was approximately a 0.83 to −6.05 BMI% change tolerance range around their perceived weight. Both the shape and the texture had an effect on the reported similarity of the body parts and the whole avatar to the participant’s body. This work has implications for new measures for patients with body image disorders, as well as researchers interested in creating personalized avatars for games, training applications or virtual reality.

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pdf DOI Project Page Project Page [BibTex]

pdf DOI Project Page Project Page [BibTex]


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Breathing Life into Shape: Capturing, Modeling and Animating 3D Human Breathing

Tsoli, A., Mahmood, N., Black, M. J.

ACM Transactions on Graphics, (Proc. SIGGRAPH), 33(4):52:1-52:11, ACM, New York, NY, July 2014 (article)

Abstract
Modeling how the human body deforms during breathing is important for the realistic animation of lifelike 3D avatars. We learn a model of body shape deformations due to breathing for different breathing types and provide simple animation controls to render lifelike breathing regardless of body shape. We capture and align high-resolution 3D scans of 58 human subjects. We compute deviations from each subject’s mean shape during breathing, and study the statistics of such shape changes for different genders, body shapes, and breathing types. We use the volume of the registered scans as a proxy for lung volume and learn a novel non-linear model relating volume and breathing type to 3D shape deformations and pose changes. We then augment a SCAPE body model so that body shape is determined by identity, pose, and the parameters of the breathing model. These parameters provide an intuitive interface with which animators can synthesize 3D human avatars with realistic breathing motions. We also develop a novel interface for animating breathing using a spirometer, which measures the changes in breathing volume of a “breath actor.”

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pdf video link (url) DOI Project Page Project Page Project Page [BibTex]


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Nanopropellers and Their Actuation in Complex Viscoelastic Media

Schamel, D., Mark, A. G., Gibbs, J. G., Miksch, C., Morozov, K. I., Leshansky, A. M., Fischer, P.

ACS Nano, 8(9):8794-8801, June 2014, Featured cover article. (article)

Abstract
Tissue and biological fluids are complex viscoelastic media with a nanoporous macromolecular structure. Here, we demonstrate that helical nanopropellers can be controllably steered through such a biological gel. The screw-propellers have a filament diameter of about 70 nm and are smaller than previously reported nanopropellers as well as any swimming microorganism. We show that the nanoscrews will move through high-viscosity solutions with comparable velocities to that of larger micropropellers, even though they are so small that Brownian forces suppress their actuation in pure water. When actuated in viscoelastic hyaluronan gels, the nanopropellers appear to have a significant advantage, as they are of the same size range as the gel’s mesh size. Whereas larger helices will show very low or negligible propulsion in hyaluronan solutions, the nanoscrews actually display significantly enhanced propulsion velocities that exceed the highest measured speeds in Newtonian fluids. The nanopropellers are not only promising for applications in the extracellular environment but small enough to be taken up by cells.

Featured cover article.

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Video - Helical Micro and Nanopropellers for Applications in Biological Fluidic Environments link (url) DOI [BibTex]


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3D Traffic Scene Understanding from Movable Platforms

Geiger, A., Lauer, M., Wojek, C., Stiller, C., Urtasun, R.

IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 36(5):1012-1025, published, IEEE, Los Alamitos, CA, May 2014 (article)

Abstract
In this paper, we present a novel probabilistic generative model for multi-object traffic scene understanding from movable platforms which reasons jointly about the 3D scene layout as well as the location and orientation of objects in the scene. In particular, the scene topology, geometry and traffic activities are inferred from short video sequences. Inspired by the impressive driving capabilities of humans, our model does not rely on GPS, lidar or map knowledge. Instead, it takes advantage of a diverse set of visual cues in the form of vehicle tracklets, vanishing points, semantic scene labels, scene flow and occupancy grids. For each of these cues we propose likelihood functions that are integrated into a probabilistic generative model. We learn all model parameters from training data using contrastive divergence. Experiments conducted on videos of 113 representative intersections show that our approach successfully infers the correct layout in a variety of very challenging scenarios. To evaluate the importance of each feature cue, experiments using different feature combinations are conducted. Furthermore, we show how by employing context derived from the proposed method we are able to improve over the state-of-the-art in terms of object detection and object orientation estimation in challenging and cluttered urban environments.

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pdf link (url) [BibTex]

pdf link (url) [BibTex]


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Adaptive Offset Correction for Intracortical Brain Computer Interfaces

Homer, M. L., Perge, J. A., Black, M. J., Harrison, M. T., Cash, S. S., Hochberg, L. R.

IEEE Transactions on Neural Systems and Rehabilitation Engineering, 22(2):239-248, March 2014 (article)

Abstract
Intracortical brain computer interfaces (iBCIs) decode intended movement from neural activity for the control of external devices such as a robotic arm. Standard approaches include a calibration phase to estimate decoding parameters. During iBCI operation, the statistical properties of the neural activity can depart from those observed during calibration, sometimes hindering a user’s ability to control the iBCI. To address this problem, we adaptively correct the offset terms within a Kalman filter decoder via penalized maximum likelihood estimation. The approach can handle rapid shifts in neural signal behavior (on the order of seconds) and requires no knowledge of the intended movement. The algorithm, called MOCA, was tested using simulated neural activity and evaluated retrospectively using data collected from two people with tetraplegia operating an iBCI. In 19 clinical research test cases, where a nonadaptive Kalman filter yielded relatively high decoding errors, MOCA significantly reduced these errors (10.6 ± 10.1\%; p < 0.05, pairwise t-test). MOCA did not significantly change the error in the remaining 23 cases where a nonadaptive Kalman filter already performed well. These results suggest that MOCA provides more robust decoding than the standard Kalman filter for iBCIs.

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pdf DOI Project Page [BibTex]

pdf DOI Project Page [BibTex]


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Circular polarization interferometry: circularly polarized modes of cholesteric liquid crystals

Sanchez-Castillo, A., Eslami, S., Giesselmann, F., Fischer, P.

OPTICS EXPRESS, 22(25):31227-31236, 2014 (article)

Abstract
We describe a novel polarization interferometer which permits the determination of the refractive indices for circularly-polarized light. It is based on a Jamin-Lebedeff interferometer, modified with waveplates, and permits us to experimentally determine the refractive indices n(L) and n(R) of the respectively left- and right-circularly polarized modes in a cholesteric liquid crystal. Whereas optical rotation measurements only determine the circular birefringence, i.e. the difference (n(L) - n(R)), the interferometer also permits the determination of their absolute values. We report refractive indices of a cholesteric liquid crystal in the region of selective (Bragg) reflection as a function of temperature. (C) 2014 Optical Society of America

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DOI [BibTex]

DOI [BibTex]


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Self-Propelling Nanomotors in the Presence of Strong Brownian Forces

Lee, T., Alarcon-Correa, M., Miksch, C., Hahn, K., Gibbs, J. G., Fischer, P.

NANO LETTERS, 14(5):2407-2412, 2014 (article)

Abstract
Motility in living systems is due to an array of complex molecular nanomotors that are essential for the function and survival of cells. These protein nanomotors operate not only despite of but also because of stochastic forces. Artificial means of realizing motility rely on local concentration or temperature gradients that are established across a particle, resulting in slip velocities at the particle surface and thus motion of the particle relative to the fluid. However, it remains unclear if these artificial motors can function at the smallest of scales, where Brownian motion dominates and no actively propelled living organisms can be found. Recently, the first reports have appeared suggesting that the swimming mechanisms of artificial structures may also apply to enzymes that are catalytically active. Here we report a scheme to realize artificial Janus nanoparticles (JNPs) with an overall size that is comparable to that of some enzymes similar to 30 nm. Our JNPs can catalyze the decomposition of hydrogen peroxide to water and oxygen and thus actively move by self-electrophoresis. Geometric anisotropy of the Pt-Au Janus nanoparticles permits the simultaneous observation of their translational and rotational motion by dynamic light scattering. While their dynamics is strongly influenced by Brownian rotation, the artificial Janus nanomotors show bursts of linear ballistic motion resulting in enhanced diffusion.

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DOI [BibTex]


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Shape control in wafer-based aperiodic 3D nanostructures

Hyeon-Ho, J., Mark, A. G., Gibbs, J. G., Reindl, T., Waizmann, U., Weis, J., Fischer, P.

NANOTECHNOLOGY, 25(23), 2014, Cover article. (article)

Abstract
Controlled local fabrication of three-dimensional (3D) nanostructures is important to explore and enhance the function of single nanodevices, but is experimentally challenging. We present a scheme based on e-beam lithography (EBL) written seeds, and glancing angle deposition (GLAD) grown structures to create nanoscale objects with defined shapes but in aperiodic arrangements. By using a continuous sacrificial corral surrounding the features of interest we grow isolated 3D nanostructures that have complex cross-sections and sidewall morphology that are surrounded by zones of clean substrate.

Cover article.

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DOI [BibTex]

DOI [BibTex]


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A freely-moving monkey treadmill model

Foster, J., Nuyujukian, P., Freifeld, O., Gao, H., Walker, R., Ryu, S., Meng, T., Murmann, B., Black, M., Shenoy, K.

J. of Neural Engineering, 11(4):046020, 2014 (article)

Abstract
Objective: Motor neuroscience and brain-machine interface (BMI) design is based on examining how the brain controls voluntary movement, typically by recording neural activity and behavior from animal models. Recording technologies used with these animal models have traditionally limited the range of behaviors that can be studied, and thus the generality of science and engineering research. We aim to design a freely-moving animal model using neural and behavioral recording technologies that do not constrain movement. Approach: We have established a freely-moving rhesus monkey model employing technology that transmits neural activity from an intracortical array using a head-mounted device and records behavior through computer vision using markerless motion capture. We demonstrate the excitability and utility of this new monkey model, including the fi rst recordings from motor cortex while rhesus monkeys walk quadrupedally on a treadmill. Main results: Using this monkey model, we show that multi-unit threshold-crossing neural activity encodes the phase of walking and that the average ring rate of the threshold crossings covaries with the speed of individual steps. On a population level, we find that neural state-space trajectories of walking at diff erent speeds have similar rotational dynamics in some dimensions that evolve at the step rate of walking, yet robustly separate by speed in other state-space dimensions. Significance: Freely-moving animal models may allow neuroscientists to examine a wider range of behaviors and can provide a flexible experimental paradigm for examining the neural mechanisms that underlie movement generation across behaviors and environments. For BMIs, freely-moving animal models have the potential to aid prosthetic design by examining how neural encoding changes with posture, environment, and other real-world context changes. Understanding this new realm of behavior in more naturalistic settings is essential for overall progress of basic motor neuroscience and for the successful translation of BMIs to people with paralysis.

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pdf Supplementary DOI Project Page [BibTex]

pdf Supplementary DOI Project Page [BibTex]


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Swimming by reciprocal motion at low Reynolds number

Qiu, T., Lee, T., Mark, A. G., Morozov, K. I., Muenster, R., Mierka, O., Turek, S., Leshansky, A. M., Fischer, P.

NATURE COMMUNICATIONS, 5, 2014, Max Planck Press Release. (article)

Abstract
Biological microorganisms swim with flagella and cilia that execute nonreciprocal motions for low Reynolds number (Re) propulsion in viscous fluids. This symmetry requirement is a consequence of Purcell's scallop theorem, which complicates the actuation scheme needed by microswimmers. However, most biomedically important fluids are non-Newtonian where the scallop theorem no longer holds. It should therefore be possible to realize a microswimmer that moves with reciprocal periodic body-shape changes in non-Newtonian fluids. Here we report a symmetric `micro-scallop', a single-hinge microswimmer that can propel in shear thickening and shear thinning (non-Newtonian) fluids by reciprocal motion at low Re. Excellent agreement between our measurements and both numerical and analytical theoretical predictions indicates that the net propulsion is caused by modulation of the fluid viscosity upon varying the shear rate. This reciprocal swimming mechanism opens new possibilities in designing biomedical microdevices that can propel by a simple actuation scheme in non-Newtonian biological fluids.

Max Planck Press Release.

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Video - A Swimming Micro-Scallop Video - Winner of the Micro-robotic Design Challenge in Hamlyn Symposium on Medical Robotics DOI [BibTex]

Video - A Swimming Micro-Scallop Video - Winner of the Micro-robotic Design Challenge in Hamlyn Symposium on Medical Robotics DOI [BibTex]


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Nanohelices by shadow growth

Gibbs, J. G., Mark, A. G., Lee, T., Eslami, S., Schamel, D., Fischer, P.

NANOSCALE, 6(16):9457-9466, 2014 (article)

Abstract
The helix has remarkable qualities and is prevalent in many fields including mathematics, physics, chemistry, and biology. This shape, which is chiral by nature, is ubiquitous in biology with perhaps the most famous example being DNA. Other naturally occurring helices are common at the nanoscale in the form of protein secondary structures and in various macromolecules. Nanoscale helices exhibit a wide range of interesting mechanical, optical, and electrical properties which can be intentionally engineered into the structure by choosing the correct morphology and material. As technology advances, these fabrication parameters can be fine-tuned and matched to the application of interest. Herein, we focus on the fabrication and properties of nanohelices grown by a dynamic shadowing growth method combined with fast wafer-scale substrate patterning which has a number of distinct advantages. We review the fabrication methodology and provide several examples that illustrate the generality and utility of nanohelices shadow-grown on nanopatterns.

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Video - Fabrication of Designer Nanostructures DOI [BibTex]


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Chiral Nanomagnets

Eslami, S., Gibbs, J. G., Rechkemmer, Y., van Slageren, J., Alarcon-Correa, M., Lee, T., Mark, A. G., Rikken, G. L. J. A., Fischer, P.

ACS PHOTONICS, 1(11):1231-1236, 2014 (article)

Abstract
We report on the enhanced optical properties of chiral magnetic nanohelices with critical dimensions comparable to the ferromagnetic domain size. They are shown to be ferromagnetic at room temperature, have defined chirality, and exhibit large optical activity in the visible as verified by electron microscopy, superconducting quantum interference device (SQUID) magnetometry, natural circular dichroism (NCD), and magnetic circular dichroism (MCD) measurements. The structures exhibit magneto-chiral dichroism (MChD), which directly demonstrates coupling between their structural chirality and magnetism. A chiral nickel (Ni) film consisting of an array of nanohelices similar to 100 nm in length exhibits an MChD anisotropy factor g(MChD) approximate to 10(-4) T-1 at room temperature in a saturation field of similar to 0.2 T, permitting polarization-independent control of the film's absorption properties through magnetic field modulation. This is also the first report of MChD in a material with structural chirality on the order of the wavelength of light, and therefore the Ni nanohelix array is a metamaterial with magnetochiral properties that can be tailored through a dynamic deposition process.

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DOI [BibTex]

DOI [BibTex]


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Wireless powering of e-swimmers

Roche, J., Carrara, S., Sanchez, J., Lannelongue, J., Loget, G., Bouffier, L., Fischer, P., Kuhn, A.

SCIENTIFIC REPORTS, 4, 2014 (article)

Abstract
Miniaturized structures that can move in a controlled way in solution and integrate various functionalities are attracting considerable attention due to the potential applications in fields ranging from autonomous micromotors to roving sensors. Here we introduce a concept which allows, depending on their specific design, the controlled directional motion of objects in water, combined with electronic functionalities such as the emission of light, sensing, signal conversion, treatment and transmission. The approach is based on electric field-induced polarization, which triggers different chemical reactions at the surface of the object and thereby its propulsion. This results in a localized electric current that can power in a wireless way electronic devices in water, leading to a new class of electronic swimmers (e-swimmers).

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DOI [BibTex]

DOI [BibTex]


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Swelling and shrinking behaviour of photoresponsive phosphonium-based ionogel microstructures

Czugala, M., O’Connell, C., Blin, C., Fischer, P., Fraser, K. J., Benito-Lopez, F., Diamond, D.

SENSORS AND ACTUATORS B-CHEMICAL, 194, pages: 105-113, 2014 (article)

Abstract
Photoresponsive N-isopropylacrylamide ionogel microstructures are presented in this study. These ionogels are synthesised using phosphonium based room temperature ionic liquids, together with the photochromic compound benzospiropyran. The microstructures can be actuated using light irradiation, facilitating non-contact and non-invasive operation. For the first time, the characterisation of the swelling and shrinking behaviour of several photopatterned ionogel microstructures is presented and the influence of surface-area-to-volume ratio on the swelling kinetics is evaluated. It was found that the swelling and shrinking behaviour of the ionogels is strongly dependent on the nature of the ionic liquid. In particular, the {[}P-6,P-6,P-6,P-14]{[}NTf2] ionogel exhibits the greatest degree of swelling, reaching up to 180\% of its initial size, and the fastest shrinkage rate (k(sh) = 29 +/- 4 x 10(-2) s(-1)). (C) 2014 Elsevier B. V. All rights reserved.

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DOI [BibTex]

DOI [BibTex]


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A Quantitative Analysis of Current Practices in Optical Flow Estimation and the Principles behind Them

Sun, D., Roth, S., Black, M. J.

International Journal of Computer Vision (IJCV), 106(2):115-137, 2014 (article)

Abstract
The accuracy of optical flow estimation algorithms has been improving steadily as evidenced by results on the Middlebury optical flow benchmark. The typical formulation, however, has changed little since the work of Horn and Schunck. We attempt to uncover what has made recent advances possible through a thorough analysis of how the objective function, the optimization method, and modern implementation practices influence accuracy. We discover that "classical'' flow formulations perform surprisingly well when combined with modern optimization and implementation techniques. One key implementation detail is the median filtering of intermediate flow fields during optimization. While this improves the robustness of classical methods it actually leads to higher energy solutions, meaning that these methods are not optimizing the original objective function. To understand the principles behind this phenomenon, we derive a new objective function that formalizes the median filtering heuristic. This objective function includes a non-local smoothness term that robustly integrates flow estimates over large spatial neighborhoods. By modifying this new term to include information about flow and image boundaries we develop a method that can better preserve motion details. To take advantage of the trend towards video in wide-screen format, we further introduce an asymmetric pyramid downsampling scheme that enables the estimation of longer range horizontal motions. The methods are evaluated on Middlebury, MPI Sintel, and KITTI datasets using the same parameter settings.

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pdf full text code [BibTex]

pdf full text code [BibTex]

2009


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Full phase and amplitude control in computer-generated holography

Fratz, M., Fischer, P., Giel, D. M.

OPTICS LETTERS, 34(23):3659-3661, 2009 (article)

Abstract
We report what we believe to be the first realization of a computer-generated complex-valued hologram recorded in a single film of photoactive polymer. Complex-valued holograms give rise to a diffracted optical field with control over its amplitude and phase. The holograms are generated by a one-step direct laser writing process in which a spatial light modulator (SLM) is imaged onto a polymer film. Temporal modulation of the SLM during exposure controls both the strength of the induced birefringence and the orientation of the fast axis. We demonstrate that complex holograms can be used to impart arbitrary amplitude and phase profiles onto a beam and thereby open new possibilities in the control of optical beams. (C) 2009 Optical Society of America

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[BibTex]

2009


[BibTex]


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Digital polarization holograms with defined magnitude and orientation of each pixel’s birefringence

Fratz, M., Giel, D. M., Fischer, P.

OPTICS LETTERS, 34(8):1270-1272, 2009 (article)

Abstract
A new form of digital polarization holography is demonstrated that permits both the amplitude and the phase of a diffracted beam to be independently controlled. This permits two independent intensity images to be stored in the same hologram. To fabricate the holograms, a birefringence with defined retardance and orientation of the fast axis is recorded into a photopolymer film. The holograms are selectively read out by choosing the polarization state of the read beam. Polarization holograms of this kind increase the data density in holographic data storage and allow higher quality diffractive optical elements to be written. (C) 2009 Optical Society of America

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[BibTex]


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Controlled Propulsion of Artificial Magnetic Nanostructured Propellers

Ghosh, A., Fischer, P.

NANO LETTERS, 9(6):2243-2245, 2009, Featured highlight ‘Nanotechnology: The helix that delivers’ Nature 459, 13 (2009). (article)

Abstract
For biomedical applications, such as targeted drug delivery and microsurgery, it is essential to develop a system of swimmers that can be propelled wirelessly in fluidic environments with good control. Here, we report the construction and operation of chiral colloidal propellers that can be navigated in water with micrometer-level precision using homogeneous magnetic fields. The propellers are made via nanostructured surfaces and can be produced in large numbers. The nanopropellers can carry chemicals, push loads, and act as local probes in rheological measurements.

Featured highlight ‘Nanotechnology: The helix that delivers’ Nature 459, 13 (2009).

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Video - Nanospropellers DOI [BibTex]

Video - Nanospropellers DOI [BibTex]


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Absolute Asymmetric Reduction Based on the Relative Orientation of Achiral Reactants

Kuhn, A., Fischer, P.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 48(37):6857-6860, 2009 (article)

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DOI [BibTex]

DOI [BibTex]