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Effective use of parallel and distributed computing in science depends upon multiple interdependent entities and activities that form an ecosystem. Active engagement between application users and technology catalysts is a crucial activity…
Combinatorial decision problems arise in many different domains such as scheduling, routing, packing, bioinformatics, and many more. Despite recent advances in developing scalable solvers, there are still many problems which are often very…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
There is a growing need to integrate sustainability into tertiary mathematics education given the urgency of addressing global environmental challenges. This paper presents four case studies from Australian university courses that…
The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques of growing interest for early-stage drug discovery is de novo…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the…
The development of critical systems is becoming more and more complex. The overall tendency is that development costs raise. In order to cut cost of development, companies are forced to build systems from proven components and larger new…
The great promise of quantum computers comes with the dual challenges of building them and finding their useful applications. We argue that these two challenges should be considered together, by co-designing full-stack quantum computer…
A widely used strategy to reduce the computational cost in quantum-chemical calculations is to partition the system into an active subsystem, which is the focus of the computational efforts and an environment that is treated at a lower…
This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda…
The increased energy and power density required in modern electronics poses a challenge for designing new dielectric polymer materials with high energy density while maintaining low loss at high applied electric fields. Recently, an…
The 4th Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 2010) is organized in Jena as a satellite event of the Eleventh International Conference on Membrane Computing (CMC11). Biological membranes play a…
Nowadays, we are witnessing the advent of the Internet of Things (EC) with numerous devices performing interactions between them or with end users. The huge number of devices leads to huge volumes of collected data that demand the…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…