The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA–RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de.

We address the problem of reconstructing spatially-varying BRDFs from a small set of image measurements. This is a fundamentally under-constrained problem, and previous work has relied on using various regularization priors or on capturing many images to produce plausible results. In this work, we present MaterialGAN , a deep generative convolutional network based on StyleGAN2, trained to synthesize realistic SVBRDF parameter maps. We show that MaterialGAN can be used as a powerful material prior in an inverse rendering framework: we optimize in its latent representation to generate material maps that match the appearance of the captured images when rendered. We demonstrate this framework on the task of reconstructing SVBRDFs from images captured under flash illumination using a hand-held mobile phone. Our method succeeds in producing plausible material maps that accurately reproduce the target images, and outperforms previous state-of-the-art material capture methods in evaluations on both synthetic and real data. Furthermore, our GAN-based latent space allows for high-level semantic material editing operations such as generating material variations and material morphing.

Summary: Studies on proteins are often restricted to highly simplified models to face the immense computational complexity of the associated problems. Constraint-based protein structure prediction (CPSP) tools is a package of very fast algorithms for ab initio optimal structure prediction and related problems in 3D HP-models [cubic and face centered cubic (FCC)]. Here, we present CPSP-web-tools, an interactive online interface of these programs for their immediate use. They include the first method for the direct prediction of optimal energies and structures in 3D HP side-chain models. This newest extension of the CPSP approach is described here for the first time.Availability and Implementation: Free access at http://cpsp.informatik.uni-freiburg.deContact: cpsp@informatik.uni-freiburg.de; cpsp@informatik.uni-freiburg.de

Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce , a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested 's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while is the only available tool for such models.

Efficient exploitation of exascale architectures requires rethinking of the numerical algorithms used in many large-scale applications. These architectures favor algorithms that expose ultra fine-grain parallelism and maximize the ratio of floating point operations to energy intensive data movement. One of the few viable approaches to achieve high efficiency in the area of PDE discretizations on unstructured grids is to use matrix-free/partially assembled high-order finite element methods, since these methods can increase the accuracy and/or lower the computational time due to reduced data motion. In this paper we provide an overview of the research and development activities in the Center for Efficient Exascale Discretizations (CEED), a co-design center in the Exascale Computing Project that is focused on the development of next-generation discretization software and algorithms to enable a wide range of finite element applications to run efficiently on future hardware. CEED is a research partnership involving more than 30 computational scientists from two US national labs and five universities, including members of the Nek5000, MFEM, MAGMA and PETSc projects. We discuss the CEED co-design activities based on targeted benchmarks, miniapps and discretization libraries and our work on performance optimizations for large-scale GPU architectures. We also provide a broad overview of research and development activities in areas such as unstructured adaptive mesh refinement algorithms, matrix-free linear solvers, high-order data visualization, and list examples of collaborations with several ECP and external applications.

An active flow control application on a realistic wing design could be leveraged by a scalable, fully implicit, unstructured, finite-element flow solver and high-performance computing resources. This article describes the active flow control application; summarizes the main features in the implementation of a massively parallel turbulent flow solver, PHASTA; and demonstrates the method's strong scalability at extreme scale.

The Parallel Unstructured Mesh Infrastructure (PUMI) is designed to support the representation of, and operations on, unstructured meshes as needed for the execution of mesh-based simulations on massively parallel computers. In PUMI, the mesh representation is complete in the sense of being able to provide any adjacency of mesh entities of multiple topologies in O(1) time, and fully distributed to support relationships of mesh entities across multiple memory spaces in a manner consistent with supporting massively parallel simulation workflows. PUMI's mesh maintains links to the high-level model definition in terms of a model topology as produced by CAD systems, and is specifically designed to efficiently support evolving meshes as required for mesh generation and adaptation. To support the needs of parallel unstructured mesh simulations, PUMI also supports a specific set of services such as the migration of mesh entities between parts while maintaining the mesh adjacencies, maintaining read-only mesh entity copies from neighboring parts (ghosting), repartitioning parts as the mesh evolves, and dynamic mesh load balancing. Here we present the overall design, software structures, example programs, and performance results. The effectiveness of PUMI is demonstrated by its applications to massively parallel adaptive simulation workflows.

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