Berechnung des Hochfrequenzverhaltens komplexer Strukturen mit der Methode gekoppelter Streuparameter – CSC

Es wird eine Methode zur Berechnung der Hochfrequenz-Eigenschaften komplexer Strukturen vorgestellt. Das Verfahren beruht auf der Zerlegung der Gesamtstruktur in einzelne einfachere Segmente, deren breitbandige S-Matrizen mit kommerziellen Programmen berechnet werden. Das Gesamtsystem kann von beliebiger Topologie sein, und die Zahl der die Segmente verkoppelnden Hohlleiter- Moden ist nicht begrenzt. Als Ergebnis steht bei offenen Strukturen deren vollständige S-Matrix, bei abgeschlossenen deren Resonanzeigenschaften zur Verfügung. Die theoretischen Grundlagen werden beschrieben und die Anwendung mit Beispielen aus dem Gebiet der Teilchenbeschleuniger und zu Eigenschaften schwach elliptisch geformter Resonatoren illustriert.</p><p style=&quot;line-height: 20px;&quot;> A method called Coupled S-Parameter Calculation – CSC is described which is used to calculate the rf properties of complex structures, i.e. either their scattering (devices with ports) or their resonance properties. The method is based on the segmentation of the entire system into sections being less complex, the external calculation of the section’s broadband S-matrices, and a combination scheme, which is applicable to any topology and number of modes. The method’s principle is described. Examples from the field of particle accelerator cavities and about the properties of weakly elliptical resonators are given

Optimal self-assembly of finite shapes at temperature 1 in 3D

Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for an arbitrary finite, connected shape $X \subset \mathbb{Z}^2$, there is a tile set that uniquely self-assembles into a 3D representation of a scaled-up version of $X$ at temperature 1 in 3D with optimal program-size complexity (the "program-size complexity", also known as "tile complexity", of a shape is the minimum number of tile types required to uniquely self-assemble it). Moreover, our construction is "just barely" 3D in the sense that it only places tiles in the $z = 0$ and $z = 1$ planes. Our result is essentially a just-barely 3D temperature 1 simulation of a similar 2D temperature 2 result by Soloveichik and Winfree (SICOMP 2007)

Modulating the Fibrillization of Parathyroid-Hormone (PTH) Peptides: Azo-Switches as Reversible and Catalytic Entities

We here report a novel strategy to control the bioavailability of the fibrillizing parathyroid hormone (PTH)-derived peptides, where the concentration of the bioactive form is controlled by an reversible, photoswitchable peptide. PTH1–84, a human hormone secreted by the parathyroid glands, is important for the maintenance of extracellular fluid calcium and phosphorus homeostasis. Controlling fibrillization of PTH1–84 represents an important approach for in vivo applications, in view of the pharmaceutical applications for this protein. We embed the azobenzene derivate 3-{[(4- aminomethyl)phenyl]diazenyl}benzoic acid (3,40-AMPB) into the PTH-derived peptide PTH25–37 to generate the artificial peptide AzoPTH25–37 via solid-phase synthesis. AzoPTH25–37 shows excellent photostability (more than 20 h in the dark) and can be reversibly photoswitched between its cis/trans forms. As investigated by ThT-monitored fibrillization assays, the trans-form of AzoPTH25–37 fibrillizes similar to PTH25–37, while the cis-form of AzoPTH25–37 generates only amorphous aggregates. Additionally, cis-AzoPTH25–37 catalytically inhibits the fibrillization of PTH25–37 in ratios of up to one-fifth. The approach reported here is designed to control the concentration of PTH-peptides, where the bioactive form can be catalytically controlled by an added photoswitchable peptide

Self-assembly, modularity and physical complexity

We present a quantitative measure of physical complexity, based on the amount of information required to build a given physical structure through self-assembly. Our procedure can be adapted to any given geometry, and thus to any given type of physical system. We illustrate our approach using self-assembling polyominoes, and demonstrate the breadth of its potential applications by quantifying the physical complexity of molecules and protein complexes. This measure is particularly well suited for the detection of symmetry and modularity in the underlying structure, and allows for a quantitative definition of structural modularity. Furthermore we use our approach to show that symmetric and modular structures are favoured in biological self-assembly, for example of protein complexes. Lastly, we also introduce the notions of joint, mutual and conditional complexity, which provide a useful distance measure between physical structures.Comment: 9 pages, submitted for publicatio

Self-replication and evolution of DNA crystals

Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required

One Tile to Rule Them All: Simulating Any Tile Assembly System with a Single Universal Tile

In the classical model of tile self-assembly, unit square tiles translate in the plane and attach edgewise to form large crystalline structures. This model of self-assembly has been shown to be capable of asymptotically optimal assembly of arbitrary shapes and, via information-theoretic arguments, increasingly complex shapes necessarily require increasing numbers of distinct types of tiles. We explore the possibility of complex and efficient assembly using systems consisting of a single tile. Our main result shows that any system of square tiles can be simulated using a system with a single tile that is permitted to flip and rotate. We also show that systems of single tiles restricted to translation only can simulate cellular automata for a limited number of steps given an appropriate seed assembly, and that any longer-running simulation must induce infinite assembly

Binary pattern tile set synthesis is NP-hard

In the field of algorithmic self-assembly, a long-standing unproven conjecture has been that of the NP-hardness of binary pattern tile set synthesis (2-PATS). The $k$-PATS problem is that of designing a tile assembly system with the smallest number of tile types which will self-assemble an input pattern of $k$ colors. Of both theoretical and practical significance, $k$-PATS has been studied in a series of papers which have shown $k$-PATS to be NP-hard for $k = 60$, $k = 29$, and then $k = 11$. In this paper, we close the fundamental conjecture that 2-PATS is NP-hard, concluding this line of study. While most of our proof relies on standard mathematical proof techniques, one crucial lemma makes use of a computer-assisted proof, which is a relatively novel but increasingly utilized paradigm for deriving proofs for complex mathematical problems. This tool is especially powerful for attacking combinatorial problems, as exemplified by the proof of the four color theorem by Appel and Haken (simplified later by Robertson, Sanders, Seymour, and Thomas) or the recent important advance on the Erd\H{o}s discrepancy problem by Konev and Lisitsa using computer programs. We utilize a massively parallel algorithm and thus turn an otherwise intractable portion of our proof into a program which requires approximately a year of computation time, bringing the use of computer-assisted proofs to a new scale. We fully detail the algorithm employed by our code, and make the code freely available online

Optimization of supply diversity for the self-assembly of simple objects in two and three dimensions

The field of algorithmic self-assembly is concerned with the design and analysis of self-assembly systems from a computational perspective, that is, from the perspective of mathematical problems whose study may give insight into the natural processes through which elementary objects self-assemble into more complex ones. One of the main problems of algorithmic self-assembly is the minimum tile set problem (MTSP), which asks for a collection of types of elementary objects (called tiles) to be found for the self-assembly of an object having a pre-established shape. Such a collection is to be as concise as possible, thus minimizing supply diversity, while satisfying a set of stringent constraints having to do with the termination and other properties of the self-assembly process from its tile types. We present a study of what we think is the first practical approach to MTSP. Our study starts with the introduction of an evolutionary heuristic to tackle MTSP and includes results from extensive experimentation with the heuristic on the self-assembly of simple objects in two and three dimensions. The heuristic we introduce combines classic elements from the field of evolutionary computation with a problem-specific variant of Pareto dominance into a multi-objective approach to MTSP.Comment: Minor typos correcte

The Power of Duples (in Self-Assembly): It's Not So Hip To Be Square

In this paper we define the Dupled abstract Tile Assembly Model (DaTAM), which is a slight extension to the abstract Tile Assembly Model (aTAM) that allows for not only the standard square tiles, but also "duple" tiles which are rectangles pre-formed by the joining of two square tiles. We show that the addition of duples allows for powerful behaviors of self-assembling systems at temperature 1, meaning systems which exclude the requirement of cooperative binding by tiles (i.e., the requirement that a tile must be able to bind to at least 2 tiles in an existing assembly if it is to attach). Cooperative binding is conjectured to be required in the standard aTAM for Turing universal computation and the efficient self-assembly of shapes, but we show that in the DaTAM these behaviors can in fact be exhibited at temperature 1. We then show that the DaTAM doesn't provide asymptotic improvements over the aTAM in its ability to efficiently build thin rectangles. Finally, we present a series of results which prove that the temperature-2 aTAM and temperature-1 DaTAM have mutually exclusive powers. That is, each is able to self-assemble shapes that the other can't, and each has systems which cannot be simulated by the other. Beyond being of purely theoretical interest, these results have practical motivation as duples have already proven to be useful in laboratory implementations of DNA-based tiles

GP-9s Are Ubiquitous Proteins Unlikely Involved in Olfactory Mediation of Social Organization in the Red Imported Fire Ant, Solenopsis invicta

The red imported fire ant (RIFA), Solenopsis invicta, is an invasive species, accidentally introduced in the United States that can cause painful (sometimes life-threatening) stings to human, pets, and livestock. Their colonies have two social forms: monogyne and polygyne that have a single and multiple functional queens, respectively. A major gene (Gp-9), identified as a putative pheromone-binding protein on the basis of a modest amino acid sequence identity, has been suggested to influence the expression of colony social organization. Monogyne queens are reported to possess only the GP-9B alleles, whereas polygyne queens possess both GP-9B and GP-9b. Thus, both social forms are reported to express GP-9B, with GP-9b being a marker expressed in polygynes but it is absent in monogynes. Here, we report two types of polygyne colonies, one that does not express GP-9b (monogyne-like) and the other expressing both proteins, GP-9B and GP-9b. Given their expression pattern, GP-9s are hemolymph proteins, which are more likely to be involved in the transport of lipids and small ligands within the homocoel. GP-9B existed in two forms, one of them is phosphorylated. The helical-rich content of the protein resembles the secondary structures of a beetle hemolymph protein and moth pheromone-binding proteins. An olfactory role is unlikely given the lack of specific expression in the sensillar lymph. In marked contrast to GP-9s, a chemosensory protein, SinvCSP, is demonstrated to be specifically expressed in the antennae. Within the antennae, expression of SinvCSP is restricted to the last two segments, which are known to house olfactory sensilla