From LTL to rLTL monitoring

Runtime monitoring is commonly used to detect the violation of desired properties in safety critical systems by observing run prefixes of the system. Bauer et al. introduced an influential framework for monitoring Linear Temporal Logic (LTL) properties, which is based on a three-valued semantics: the formula is already satisfied by the given prefix, it is already violated, or it is still undetermined, i.e., it can be satisfied and violated. However, a wide range of formulas are not monitorable under this approach, meaning that every prefix is undetermined. In particular, Bauer et al. report that 44% of the formulas they consider in their experiments fall into this category. Recently, robust semantics for LTL were introduced to capture degrees of violation of universal properties. Here, we define robust semantics for run prefixes and show its potential in monitoring: every formula considered by Bauer et al. is monitorable under our approach. Furthermore, we show that properties expressed with the robust semantics can be monitored by deterministic automata

Capturing and stabilizing folded proteins in lattices formed with branched oligonucleotide hybrids

The encapsulation of folded proteins in stabilizing matrices is one of the challenges of soft‐matter materials science. Capturing such fragile bio‐macromolecules from aqueous solution, and embedding them in a lattice that stabilizes them against denaturation and decomposition is difficult. Here, we report that tetrahedral oligonucleotide hybrids as branching elements, and connecting DNA duplexes with sticky ends can assemble into materials. The material‐forming property was used to capture DNA‐binding proteins selectively from aqueous protein mixtures. The three‐dimensional networks also encapsulate guest molecules in a size‐selective manner, accommodating proteins up to a molecular weight of approximately 159 kDa for the connecting duplex lengths tested. Exploratory experiments with green fluorescent protein showed that, when embedded in the DNA‐based matrix, the protein is more stable toward denaturation than in the free form, and retains its luminescent properties for at least 90 days in dry form. The noncrystalline biohybrid matrices presented herein may be used for capturing other proteins or for producing functional materials

Transitions in solvate crystals of a tetraaryladamantane

Obtaining high-resolution structures of liquid compounds can be difficult. Encapsulating them in the lattice of a larger organic molecule acting as crystallization chaperone is one option to overcome this difficulty. Tetraaryladamantane ethers can play the role of chaperones, accommodating a range of different guest molecules in their crystals. How well-ordered crystalline arrangements for molecules of different shape are achieved is not clear. Cases in which more than one structure is found may shed light on this phenomenon. Here, we report low-order cubic crystal structures of 1,3,5,7-tetrakis(2,4-dimethoxyphenyl)adamantane (TDA) encapsulating ortho-xylene or cyclohexane, together with better ordered structures obtained after warming the crystals to 60 °C. Evidence for cubic crystal systems was also found for limonene, hexachlorobutadiene and eucalyptol, with a transition to a triclinic system for the former two, but no transition up to 70 °C for the latter. These findings indicate that some solvate structures of TDA can readily undergo structural transitions to less solvated, better ordered systems. Crystals obtained by rapid thermal crystallization may be in kinetically trapped states, and the transition to a solvate-free crystal system appears to have a kinetic barrier that depends strongly on the structure of the liquid guest molecules encapsulated in the lattice.Deutsche ForschungsgemeinschaftProjekt DEA

Non-porous organic crystals and their interaction with guest molecules from the gas phase

Some organic molecules encapsulate solvents upon crystallization. One class of compounds that shows a high propensity to form such crystalline solvates are tetraaryladamantanes (TAAs). Recently, tetrakis(dialkoxyphenyl)-adamantanes have been shown to encapsulate a wide range of guest molecules in their crystals, and to stabilize the guest molecules against undesired reactions. The term ‘encapsulating organic crystals’ (EnOCs) has been coined for these species. In this work, we studied the behavior of three TAAs upon exposition to different guest molecules by means of sorption technique. We firstly measured the vapor adsorption/desorption isotherms with water, tetrahydrofuran and toluene, and secondly, we studied the uptake of methane on dry and wet TAAs. Uptake of methane beyond one molar equivalent was detected for wet crystals, even though the materials showed a lack of porosity. Thus far, such behavior, which we ascribe to methane hydrate formation, had been described for porous non-crystalline materials or crystals with detectable porosity, not for non-porous organic crystals. Our results show that TAA crystals have interesting properties beyond the formation of conventional solvates. Gas-containing organic crystals may find application as reservoirs for gases that are difficult to encapsulate or are slow to form crystalline hydrates in the absence of a host compound. Wet tetraaryladamantane crystals take up methane in form of methane hydrate structure I, even though they appear non-porous to argon.Deutsche ForschungsgemeinschaftUniversity of StuttgartProjekt DEA

Simulation of an oil film at the sea surface and its radiometric properties in the SWIR

The knowledge of the optical contrast of an oil layer on the sea under various surface roughness conditions is of great interest for oil slick monitoring techniques. This paper presents a 3D simulation of a dynamic sea surface contaminated by a floating oil film. The simulation considers the damping influence of oil on the ocean waves and its physical properties. It calculates the radiance contrast of the sea surface polluted by the oil film in relation to a clean sea surface for the SWIR spectral band. Our computer simulation combines the 3D simulation of a maritime scene (open clear sea/clear sky) with an oil film at the sea surface. The basic geometry of a clean sea surface is modeled by a composition of smooth wind driven gravity waves. Oil on the sea surface attenuates the capillary and short gravity waves modulating the wave power density spectrum of these waves. The radiance of the maritime scene is calculated in the SWIR spectral band with the emitted sea surface radiance and the specularly reflected sky radiance as components. Wave hiding and shadowing, especially occurring at low viewing angles, are considered. The specular reflection of the sky radiance at the clean sea surface is modeled by an analytical statistical bidirectional reflectance distribution function (BRDF) of the sea surface. For oil at the sea surface, a specific BRDF is used influenced by the reduced surface roughness, i.e., the modulated wave density spectrum. The radiance contrast of an oil film in relation to the clean sea surface is calculated for different viewing angles, wind speeds, and oil types characterized by their specific physical properties

From LTL to rLTL monitoring: improved monitorability through robust semantics

Runtime monitoring is commonly used to detect the violation of desired properties in safety critical cyber-physical systems by observing its executions. Bauer et al. introduced an influential framework for monitoring Linear Temporal Logic (LTL) properties based on a three-valued semantics for a finite execution: the formula is already satisfied by the given execution, it is already violated, or it is still undetermined, i.e., it can still be satisfied and violated by appropriate extensions of the given execution. However, a wide range of formulas are not monitorable under this approach, meaning that there are executions for which satisfaction and violation will always remain undetermined no matter how it is extended. In particular, Bauer et al. report that 44% of the formulas they consider in their experiments fall into this category. Recently, a robust semantics for LTL was introduced to capture different degrees by which a property can be violated. In this paper we introduce a robust semantics for finite strings and show its potential in monitoring: every formula considered by Bauer et al. is monitorable under our approach. Furthermore, we discuss which properties that come naturally in LTL monitoring-such as the realizability of all truth values-can be transferred to the robust setting. We show that LTL formulas with robust semantics can be monitored by deterministic automata, and provide tight bounds on the size of the constructed automaton. Lastly, we report on a prototype implementation and compare it to the LTL monitor of Bauer et al. on a sample of examples

From LTL to rLTL monitoring: improved monitorability through robust semantics

Runtime monitoring is commonly used to detect the violation of desired properties in safety critical cyber-physical systems by observing its executions. Bauer et al. introduced an influential framework for monitoring Linear Temporal Logic (LTL) properties based on a three-valued semantics for a finite execution: the formula is already satisfied by the given execution, it is already violated, or it is still undetermined, i.e., it can still be satisfied and violated by appropriate extensions of the given execution. However, a wide range of formulas are not monitorable under this approach, meaning that there are executions for which satisfaction and violation will always remain undetermined no matter how it is extended. In particular, Bauer et al. report that 44% of the formulas they consider in their experiments fall into this category. Recently, a robust semantics for LTL was introduced to capture different degrees by which a property can be violated. In this paper we introduce a robust semantics for finite strings and show its potential in monitoring: every formula considered by Bauer et al. is monitorable under our approach. Furthermore, we discuss which properties that come naturally in LTL monitoring - such as the realizability of all truth values - can be transferred to the robust setting. We show that LTL formulas with robust semantics can be monitored by deterministic automata, and provide tight bounds on the size of the constructed automaton. Lastly, we report on a prototype implementation and compare it to the LTL monitor of Bauer et al. on a sample of examples

Synthesis of Eight-Arm, Branched Oligonucleotide Hybrids and Studies on the Limits of DNA-Driven Assembly

Oligonucleotide hybrids with organic cores as rigid branching elements and four or six CG dimer strands have been shown to form porous materials from dilute aqueous solution. In order to explore the limits of this form of DNA-driven assembly, we prepared hybrids with three or eight DNA arms via solution-phase syntheses, using <i>H</i>-phosphonates of protected dinucleoside phosphates. This included the synthesis of (CG)₈TREA, where TREA stands for the tetrakis­[4-(resorcin-5-ylethynyl)­phenyl]­adamantane core. The ability of the new compounds to assemble in a DNA-driven fashion was studied by UV-melting analysis and NMR, using hybrids with self-complementary CG zipper arms or non-self-complementary TC dimer arms. The three-arm hybrid failed to form a material under conditions where four-arm hybrids did so. Further, the assembly of TREA hybrids appears to be dominated by hydrophobic interactions, not base pairing of the DNA arms. These results help in the design of materials forming by multivalent DNA–DNA interactions

Synthesis of Eight-Arm, Branched Oligonucleotide Hybrids and Studies on the Limits of DNA-Driven Assembly

Oligonucleotide hybrids with organic cores as rigid branching elements and four or six CG dimer strands have been shown to form porous materials from dilute aqueous solution. In order to explore the limits of this form of DNA-driven assembly, we prepared hybrids with three or eight DNA arms via solution-phase syntheses, using <i>H</i>-phosphonates of protected dinucleoside phosphates. This included the synthesis of (CG)₈TREA, where TREA stands for the tetrakis­[4-(resorcin-5-ylethynyl)­phenyl]­adamantane core. The ability of the new compounds to assemble in a DNA-driven fashion was studied by UV-melting analysis and NMR, using hybrids with self-complementary CG zipper arms or non-self-complementary TC dimer arms. The three-arm hybrid failed to form a material under conditions where four-arm hybrids did so. Further, the assembly of TREA hybrids appears to be dominated by hydrophobic interactions, not base pairing of the DNA arms. These results help in the design of materials forming by multivalent DNA–DNA interactions