Tarmo: A Framework for Parallelized Bounded Model Checking

This paper investigates approaches to parallelizing Bounded Model Checking (BMC) for shared memory environments as well as for clusters of workstations. We present a generic framework for parallelized BMC named Tarmo. Our framework can be used with any incremental SAT encoding for BMC but for the results in this paper we use only the current state-of-the-art encoding for full PLTL. Using this encoding allows us to check both safety and liveness properties, contrary to an earlier work on distributing BMC that is limited to safety properties only. Despite our focus on BMC after it has been translated to SAT, existing distributed SAT solvers are not well suited for our application. This is because solving a BMC problem is not solving a set of independent SAT instances but rather involves solving multiple related SAT instances, encoded incrementally, where the satisfiability of each instance corresponds to the existence of a counterexample of a specific length. Our framework includes a generic architecture for a shared clause database that allows easy clause sharing between SAT solver threads solving various such instances. We present extensive experimental results obtained with multiple variants of our Tarmo implementation. Our shared memory variants have a significantly better performance than conventional single threaded approaches, which is a result that many users can benefit from as multi-core and multi-processor technology is widely available. Furthermore we demonstrate that our framework can be deployed in a typical cluster of workstations, where several multi-core machines are connected by a network

Stereoscopic space map – semi-immersive configuration of 3Dstereoscopic tours in multi-display environments

Although large-scale stereoscopic 3D environments like CAVEs are a favorable location for group presentations, the perspective projection and stereoscopic optimization usually follows a navigator-centric approach. Therefore, these presentations are usually accompanied by strong side-effects, such as motion sickness which is often caused by a disturbed stereoscopic vision. The reason is that the stereoscopic visualization is usually optimized for the only head-tracked person in the CAVE – the navigator – ignoring the needs of the real target group – the audience. To overcome this misconception, this work proposes an alternative to the head tracking-based stereoscopic effect optimization. By using an interactive virtual overview map in 3D, the pre-tour and on-tour configuration of the stereoscopic effect is provided, partly utilizing our previously published interactive projection plane approach. This Stereoscopic Space Map is visualized by the zSpace 200®, whereas the virtual world is shown on a panoramic 330° CAVE2TM. A pilot expert study with eight participants was conducted using pre-configured tours through 3D models. The comparison of the manual and automatic stereoscopic adjustment showed that the proposed approach is an appropriate alternative to the nowadays commonly used head tracking-based stereoscopic adjustment

Towards a 3D Cell Model of Chlamydomonas reinhardtii (Workshop Abstract)

Biere N, Doebbe A, Rothe N, Huser T, Kruse O, Sommer B. Towards a 3D Cell Model of Chlamydomonas reinhardtii (Workshop Abstract). In: Sommer B, ed. Proceedings of the CELLmicrocosmos neXt workshop. Bielefeld: Bielefeld University; 2014: 9-10

Ultrahigh Ionic Exclusion through Carbon Nanomembranes.

Yang Y, Hillmann R, Qi Y, et al. Ultrahigh Ionic Exclusion through Carbon Nanomembranes. Advanced materials . 2020;32(8): e1907850.The collective "single-file" motion of water molecules through natural and artificial nanoconduits inspires the development of high-performance membranes for water separation. However, a material that contains a large number of pores combining rapid water flow with superior ion rejection is still highly desirable. Here, a 1.2 nm thick carbon nanomembrane (CNM) made from cross-linking of terphenylthiol (TPT) self-assembled monolayers is reported to possess these properties. Utilizing their extremely high pore density of 1 sub-nm channel nm-2 , TPT CNMs let water molecules rapidly pass, while the translocation of ions, including protons, is efficiently hindered. Their membrane resistance reaches 104 Omega cm2 in 1 m Cl- solutions, comparable to lipid bilayers of a cell membrane. Consequently, a single CNM channel yields an 108 higher resistance than pores in lipid membrane channels and carbon nanotubes. The ultrahigh ionic exclusion by CNMs is likely dominated by a steric hindrance mechanism, coupled with electrostatic repulsion and entrance effects. The operation of TPT CNM membrane composites in forward osmosis is also demonstrated. These observations highlight the potential of utilizing CNMs for water purification and opens up a simple avenue to creating 2D membranes through molecular self-assembly for highly selective and fast separations. © 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell

The structural modeling and representation of cells is a complex task as different microscopic, spectroscopic and other information resources have to be combined to achieve a three-dimensional representation with high accuracy. Moreover, to provide an appropriate spatial representation of the cell, a stereoscopic 3D (S3D) visualization is favorable. In this work, a structural cell model is created by combining information from various light microscopic and electron microscopic images as well as from publication-related data. At the mesoscopic level each cell component is presented with special structural and visual properties; at the molecular level a cell membrane composition and the underlying modeling method are discussed; and structural information is correlated with those at the functional level (represented by simplified energy-producing metabolic pathways). The organism used as an example is the unicellular Chlamydomonas reinhardtii, which might be important in future alternative energy production processes. Based on the 3D model, an educative S3D animation was created which was shown at conferences. The complete workflow was accomplished by using the open source 3D modeling software Blender. The discussed project including the animation is available from: http://Cm5.CELLmicrocosmos.or

rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations

Feiner R, Teschner J, Teschner K, et al. rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations. International Journal of Molecular Sciences. 2019;20(22): 5702.Recombinant adeno-associated viruses (rAAV) provide outstanding options for customization and superior capabilities for gene therapy. To access their full potential, facile genetic manipulation is pivotal, including capsid loop modifications. Therefore, we assessed capsid tolerance to modifications of the structural VP proteins in terms of stability and plasticity. Flexible glycine-serine linkers of increasing sizes were, at the genetic level, introduced into the 587 loop region of the VP proteins of serotype 2, the best studied AAV representative. Analyses of biological function and thermal stability with respect to genome release of viral particles revealed structural plasticity. In addition, insertion of the 29 kDa enzyme β-lactamase into the loop region was tested with a complete or a mosaic modification setting. For the mosaic approach, investigation of VP2 trans expression revealed that a Kozak sequence was required to prevent leaky scanning. Surprisingly, even the full capsid modification with β-lactamase allowed for the assembly of capsids with a concomitant increase in size. Enzyme activity assays revealed lactamase functionality for both rAAV variants, which demonstrates the structural robustness of this platform technology.</jats:p

Automatically Comparing Memory Consistency Models

A memory consistency model (MCM) is the part of a programming language or computer architecture specification that defines which values can legally be read from shared memory locations. Because MCMs take into account various optimisations employed by archi- tectures and compilers, they are often complex and counterintu- itive, which makes them challenging to design and to understand. We identify four tasks involved in designing and understanding MCMs: generating conformance tests, distinguishing two MCMs, checking compiler optimisations, and checking compiler mappings. We show that all four tasks are instances of a general constraint-satisfaction problem to which the solution is either a program or a pair of programs. Although this problem is intractable for automatic solvers when phrased over programs directly, we show how to solve analogous constraints over program executions, and then construct programs that satisfy the original constraints. Our technique, which is implemented in the Alloy modelling framework, is illustrated on several software- and architecture-level MCMs, both axiomatically and operationally defined. We automatically recreate several known results, often in a simpler form, including: distinctions between variants of the C11 MCM; a failure of the ‘SC-DRF guarantee’ in an early C11 draft; that x86 is ‘multi-copy atomic’ and Power is not; bugs in common C11 compiler optimisations; and bugs in a compiler mapping from OpenCL to AMD-style GPUs. We also use our technique to develop and validate a new MCM for NVIDIA GPUs that supports a natural mapping from OpenCL