On bonded Indian and uniformly parallel insertion systems and their generative power

Insertion is an operation in formal language theory that generalizes the operation of concatenation of words, where its variants allow the operation in different ways. Parallel insertion is a variant of insertion that simultaneously adds words between all letters of a word and also at the right and left extremities. In previous research, restrictions on the applicability have been imposed leading to socalled bonded insertion systems with a sequential and a parallel variant. Motivated by the atomic behavior of chemical compounds in the process of chemical bonding, the generative power of bonded insertion systems has been investigated where a language hierarchy was obtained. In this paper, we introduce new variants of bonded parallel insertion systems, namely bonded Indian parallel insertion systems and bonded uniformly parallel insertion systems. We present some results regarding the generative power of these new systems and a language hierarchy

An optofluidic router in a low-cost (PDMS) platform for rapid parallel sample analysis

En col·laboració amb la Universitat de Barcelona (UB), la Universitat Autònoma de Barcelona (UAB) i l'Institut de Ciències Fotòniques (ICFO)Optofluidic system for (bio)chemical applications are becoming more demanding in terms of num- ber of control points, number of light sources and readout equipment. So far, most of these sys- tems require several light sources/detectors for suitable performance, increasing their complexity and cost. In this work, we present an easily integrated, fluidically controlled optical router that fa- cilitates coupling of several light sources or detectors. By using PDMS mirrors and phaseguides, the switching liquid is guided and pinned in desired angles, so that the incident light undergoes total internal reflection and can be reflected towards the output channels without any movable parts. The developed router presents ideal performance for lab on a chip applications, achieving switching frequencies between 0.07 ± 0.025 and 4 ± 2 Hz, depending on the flow rate of the switching liquid. The cross-talk levels are at 20 dB from channel output power to static noise level. With the use of parabolic mirrors, channel coupling efficiencies decrease just 2.38 dBm over four channels. The dynamic switching noise reduces the cross-talk levels by 2-5 dB, depending on the incorporation of ink-apertures. The insertion loss of these devices ranges from 17.34 to 25.42 dB. These results prove the viability of the fluidically controlled router in the low-cost PDMS platform. The intended goal of this work has been to simplify and speed up parallel sample analysis with the router integrated into a multiple path photonic component on a single chip. Development on this front is ongoing to rapidly measure methadone concentrations on chip

Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by biology's fantastic ability to assemble biomolecules that form systems with complicated structure and dynamics, from molecular motors that walk on rigid tracks and proteins that dynamically alter the structure of the cell during mitosis, to embryonic development where large-scale complicated organisms efficiently grow from a single cell. Using this active self-assembly model, we show how to efficiently self-assemble shapes and patterns from simple monomers. For example, we show how to grow a line of monomers in time and number of monomer states that is merely logarithmic in the length of the line. Our main results show how to grow arbitrary connected two-dimensional geometric shapes and patterns in expected time that is polylogarithmic in the size of the shape, plus roughly the time required to run a Turing machine deciding whether or not a given pixel is in the shape. We do this while keeping the number of monomer types logarithmic in shape size, plus those monomers required by the Kolmogorov complexity of the shape or pattern. This work thus highlights the efficiency advantages of active self-assembly over passive self-assembly and motivates experimental effort to construct general-purpose active molecular self-assembly systems

26. Theorietag Automaten und Formale Sprachen 23. Jahrestagung Logik in der Informatik: Tagungsband

Der Theorietag ist die Jahrestagung der Fachgruppe Automaten und Formale Sprachen der Gesellschaft für Informatik und fand erstmals 1991 in Magdeburg statt. Seit dem Jahr 1996 wird der Theorietag von einem eintägigen Workshop mit eingeladenen Vorträgen begleitet. Die Jahrestagung der Fachgruppe Logik in der Informatik der Gesellschaft für Informatik fand erstmals 1993 in Leipzig statt. Im Laufe beider Jahrestagungen finden auch die jährliche Fachgruppensitzungen statt. In diesem Jahr wird der Theorietag der Fachgruppe Automaten und Formale Sprachen erstmalig zusammen mit der Jahrestagung der Fachgruppe Logik in der Informatik abgehalten. Organisiert wurde die gemeinsame Veranstaltung von der Arbeitsgruppe Zuverlässige Systeme des Instituts für Informatik an der Christian-Albrechts-Universität Kiel vom 4. bis 7. Oktober im Tagungshotel Tannenfelde bei Neumünster. Während des Tre↵ens wird ein Workshop für alle Interessierten statt finden. In Tannenfelde werden • Christoph Löding (Aachen) • Tomás Masopust (Dresden) • Henning Schnoor (Kiel) • Nicole Schweikardt (Berlin) • Georg Zetzsche (Paris) eingeladene Vorträge zu ihrer aktuellen Arbeit halten. Darüber hinaus werden 26 Vorträge von Teilnehmern und Teilnehmerinnen gehalten, 17 auf dem Theorietag Automaten und formale Sprachen und neun auf der Jahrestagung Logik in der Informatik. Der vorliegende Band enthält Kurzfassungen aller Beiträge. Wir danken der Gesellschaft für Informatik, der Christian-Albrechts-Universität zu Kiel und dem Tagungshotel Tannenfelde für die Unterstützung dieses Theorietags. Ein besonderer Dank geht an das Organisationsteam: Maike Bradler, Philipp Sieweck, Joel Day. Kiel, Oktober 2016 Florin Manea, Dirk Nowotka und Thomas Wilk

Generating finite cyclic and dihedral groups using sequential insertion systems with interactions

The operation of insertion has been studied extensively throughout the years for its impact in many areas of theoretical computer science such as DNA computing. First introduced as a generalization of the concatenation operation, many variants of insertion have been introduced, each with their own computational properties. In this paper, we introduce a new variant that enables the generation of some special types of groups called sequential insertion systems with interactions. We show that these new systems are able to generate all finite cyclic and dihedral groups

Accelerated hardware video object segmentation: From foreground detection to connected components labelling

This is the preprint version of the Article - Copyright @ 2010 ElsevierThis paper demonstrates the use of a single-chip FPGA for the segmentation of moving objects in a video sequence. The system maintains highly accurate background models, and integrates the detection of foreground pixels with the labelling of objects using a connected components algorithm. The background models are based on 24-bit RGB values and 8-bit gray scale intensity values. A multimodal background differencing algorithm is presented, using a single FPGA chip and four blocks of RAM. The real-time connected component labelling algorithm, also designed for FPGA implementation, run-length encodes the output of the background subtraction, and performs connected component analysis on this representation. The run-length encoding, together with other parts of the algorithm, is performed in parallel; sequential operations are minimized as the number of run-lengths are typically less than the number of pixels. The two algorithms are pipelined together for maximum efficiency

Investigation of Antimicrobial Peptides in Lipid Membranes by Solid-State NMR

Solid-state NMR spectroscopy is an important tool for studying the chemical and three-dimensional structures of organic and inorganic solids because of its intrinsic atomic-level structural information, nonperturbing nature, and the large range of dynamic time scales. It is especially powerful in studying insoluble and noncrystalline membrane proteins, which are difficult to analyze by traditional X-ray crystallography or solution NMR techniques. In this thesis, various NMR techniques are used to study the structure and dynamics of membrane proteins within lipid bilayers. The main protein we are focusing on is human neutrophil peptide 1 (HNP-1). It is a small cysteine-rich cationic antimicrobial protein found in human neutrophils. It forms the first line of defense by the innate immune system of humans against pathogens. The antimicrobial activity of HNP-1 is believed to be caused by disruption of the microbial cell membrane and various models of HNP-membrane interaction have been proposed. However, none of these mechanistic models are based on structure information from the lipid bilayer. Therefore, understanding the peptide structure in the presence of membrane and its interaction with the lipids will shed light on the antimicrobial mechanism of HNP-1. As a first step, we have calculated the minimum-energy structures of uniformly 13C, 15N-labeled microcrystalline HNP-1 based on all NMR torsion angle and distance restraints determined by various 2D and 3D correlation techniques. The solid-state NMR structure has close similarity to the crystal structures of the HNP family. Then we reconstituted HNP-1 into DMPC/DMPG lipid bilayers. We confirmed that the protein is predominantly dimerized at high protein/lipid molar ratios by 19F spin diffusion experiments. Various methods under magic-angle spinning (MAS) such as 13C-31P REDOR, 1H spin diffusion and 13C DIPSHIFT have been utilized to study the interaction of HNP-1 with lipid bilayers. The experimental results strongly support a dimer pore topology of HNP-1 in which the polar top of the dimer lines an aqueous pore while the hydrophobic bottom faces the lipid chains. The second focus of this thesis is the oriented bicelle alignment , we have studied the alignment of bicelles with different lipids combinations, long- to short-chain lipid ratios, hydration levels and a phase diagram was generated. We also show that the orientation of a protein called HNP-1, which has 3 β-strands and dimerizes, can be simulated by predicting the correlation of the 15N anisotropic chemical shift and the N-H dipolar coupling