An off-lattice, self-learning kinetic Monte Carlo method using local environments

We present a method called local environment kinetic Monte Carlo (LE-KMC) method for efficiently performing off-lattice, self-learning kinetic Monte Carlo (KMC) simulations of activated processes in material systems. Like other off-lattice KMC schemes, new atomic processes can be found on-the-fly in LE-KMC. However, a unique feature of LE-KMC is that as long as the assumption that all processes and rates depend only on the local environment is satisfied, LE-KMC provides a general algorithm for (i) unambiguously describing a process in terms of its local atomic environments, (ii) storing new processes and environments in a catalog for later use with standard KMC, and (iii) updating the system based on the local information once a process has been selected for a KMC move. Search, classification, storage and retrieval steps needed while employing local environments and processes in the LE-KMC method are discussed. The advantages and computational cost of LE-KMC are discussed. We assess the performance of the LE-KMC algorithm by considering test systems involving diffusion in a submonolayer Ag and Ag-Cu alloy films on Ag(001) surface.     

Potential drugs and nondrugs: prediction and identification of important structural features

Using decision trees, a model to discriminate between potential drugs and nondrugs has been developed. Compounds from the Available Chemical Directory and the World Drug Index databases were used as training set; the molecular structures were represented using extended atom types. The error rate on an independent validation data set is 17.4%. The number of false negatives can be reduced by penalizing the misclassification of drugs so that 92 out of 100 potential drugs are correctly recognized. At the same time, 34 out of 100 nondrugs are classified as potential drugs. The predictions of the model can be used to guide the purchase or selection of compounds for biological screening or the design of combinatorial libraries. The visualization of the generated models in the form of colored trees allowed us to identify a few, surprisingly simple features that explain the most significant differences between drugs and nondrugs in the training set: Just by testing the presence of hydroxyl, tertiary or secondary amino, carboxyl, phenol, or enol groups, already three quarters of all drugs could be correctly recognized. The nondrugs, on the other hand, are characterized by their aromatic nature with a low content of functional groups besides halogens. The general applicability of the model is shown by the predictions made for several Organon databases.     

Integrated receiver architectures for board-to-board free-space optical interconnects

In many computer and server communications copper cables and wires are currently being used for data transmission and interconnects. However, due to significant shortcomings, such as long transmission time, high noise level, unstable electrical properties, and high power consumption for cooling, researchers are increasingly turning their research interests toward alternatives, such as fiber optic interconnects and free-space optical communication technologies. In this paper, we present design considerations for an integrated receiver for high-speed free-space line-of-sight optical interconnects for distortion-free data transmission in an environment with mechanical vibrations and air turbulences. The receiver consists of an array of high-speed photodiodes for data communication and an array of quadrant photodiodes for real-time beam tracking in order to compensate for the beam misalignment caused by vibrations in servers. Different configurations for spatially positioning the quadrant and data photodiodes are discussed for 4×4 and 9×9 multielement optical detector arrays. We also introduce a new beam tracking device, termed the strip quadrant photodiodes, in order to accurately track highly focused optical beams with very small beam diameter.     

Line-addressable digital-deflection programmable micromirror array

We report a novel digital-deflection programmable micromirror array driven by micromechanical digital-to-analog converters that eliminates the need for electrical digital-to-analog converters for analog displacement control, thus simplifying the driving circuitry and reducing the overall system cost. Furthermore, owing to the bistable and hysteretic characteristics of parallel-plate electrostatic actuators, an array of micromirrors can be controlled by means of row- and column-addressing lines, which drastically reduce the number of routing wires and allow array sizes to increase while they maintain high array quality.