LabelHash: A Flexible and Extensible Method for Matching Structural Motifs

There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Below, we will briefly describe LabelHash, a new method for partial structure comparison. In partial structure comparison, the goal is to find the best geometric and chemical similarity between a set of 3D points called a _motif_ and a subset of a set of 3D points called the _target_. Both the motif and targets are represented as sets of labeled 3D points. A motif is ideally composed of the functionally most-relevant residues in a binding site. The labels denote the type of residue. Motif points can have multiple labels to denote that substitutions are allowed. Any subset of the target that has labels that are compatible with the motif’s labels is called a _match_. The aim is to find statistically significant matches to a structural motif. Our method preprocesses a background database of targets such as a non-redundant subset of the Protein Data Bank in such a way that we can look up in constant time partial matches to a motif. Using a variant of the previously described match augmentation algorithm (1), we obtain complete matches to our motif. The nonparametric statistical model developed by (2,3) corrects for any bias introduced by our algorithm. This bias is introduced by excluding matches that do not satisfy certain geometric constraints for efficiency reasons

The Equilibrium Shape of Quantum Dots

The formation of dislocation-free three-dimensional islands during the heteroepitaxial growth of lattice-mismatched materials has been observed experimentally for several material systems. The equilibrium shape of the islands is governed by the competition between the surface energy and the elastic relaxation energy of the islands as compared to the uniform strained film. As an exemplification we consider the experimentally intensively investigated growth of InAs quantum dots on a GaAs(001) substrate, deriving the equilibrium shape as a function of island volume. For this purpose InAs surface energies have been calculated within density-functional theory, and a continuum approach has been applied to compute the elastic relaxation energies.Comment: 10 pages, 4 figures. Submitted to Nuovo Cimento (November 27, 1996)

An Extensible Benchmarking Infrastructure for Motion Planning Algorithms

Sampling-based planning algorithms are the most common probabilistically complete algorithms and are widely used on many robot platforms. Within this class of algorithms, many variants have been proposed over the last 20 years, yet there is still no characterization of which algorithms are well-suited for which classes of problems. This has motivated us to develop a benchmarking infrastructure for motion planning algorithms. It consists of three main components. First, we have created an extensive benchmarking software framework that is included with the Open Motion Planning Library (OMPL), a C++ library that contains implementations of many sampling-based algorithms. Second, we have defined extensible formats for storing benchmark results. The formats are fairly straightforward so that other planning libraries could easily produce compatible output. Finally, we have created an interactive, versatile visualization tool for compact presentation of collected benchmark data. The tool and underlying database facilitate the analysis of performance across benchmark problems and planners.Comment: Submitted to IEEE Robotics & Automation Magazine (Special Issue on Replicable and Measurable Robotics Research), 201

A map on the space of rational functions

We describe dynamical properties of a map $\mathfrak{F}$ defined on the space of rational functions. The fixed points of $\mathfrak{F}$ are classified and the long time behavior of a subclass is described in terms of Eulerian polynomials

Development of a scanning electron mirror microscope

Scanning electron mirrors microscope design and developmen

Optimized stray-field-induced enhancement of the electron spin precession by buried Fe gates

The magnetic stray field from Fe gates is used to modify the spin precession frequency of InGaAs/GaAs quantum-well electrons in an external magnetic field. By using an etching process to position the gates directly in the plane of the quantum well, the stray-field influence on the spin precession increases significantly compared with results from previous studies with top-gated structures. In line with numerical simulations, the stray-field-induced precession frequency increases as the gap between the ferromagnetic gates is reduced. The inhomogeneous stray field leads to additional spin dephasing.Comment: 4 pages, 2 figure