Stefanie Barz, Ivan Kassal, Martin Ringbauer1,∗, Yannick Ole Lipp, Borivoje Dakić, Alán Aspuru-Guzik, Philip Walther 1 Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria 2 Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, United States 3 Centre for Engineered Quantum Systems, Centre for Quantum Computing and Communication Technol...

1 School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, United States of America, 2 Bioinformatics and Research Computing, Whitehead Institute, Cambridge, Massachusetts, United States of America, 3 Department of Biological Sciences and School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America, 4 European Molecular ...

The environment adaptation capability of biological entities and systems unfolds solutions to challenging problems. Evolution constantly polishes up the solutions to be optimal. Computer scientists look into the phenomenon as guiding metaphors for problem solving; henceforth the Bio-inspired computing (BIC) comes into picture. BIC focuses on the designs and developments of computer algorithms a...

A new semantics in terms of Mean Field Equations is presented for WSCCS (Weighted Synchronous Calculus of Communicating Systems). The semantics captures the average behaviour of the system over time, but without computing the entire state space, therefore avoiding the state space explosion problem. This allows easy investigation of models with large numbers of components. The new semantics is s...

The International Olympiad in Informatics (IOI) is the premier competition in computing science for secondary education. The competition problems are algorithmic in nature, but the IOI Regulations do not clearly define the scope of the competition. The international olympiads in physics, chemistry, and biology do have an official syllabus, whereas the International Mathematical Olympiad has mad...

A typical computing environment for solving Grand Challenge Problems consists of a high performance graphics workstation acting as a front-end, connected to a variety of remote supercomputers. A Problem Solving Environment (PSE) is a system of programs designed to assist a scientist in solving his/her problems without detailed understanding of parallel machines, and guiding him/her through the ...

Programs of the NCBI BLAST family have been widely used for retrieving homologous sequences from existing databases. This article briefly introduces and evaluates a parallelized version of the BLAST algorithm, paraBLAST, using Message Passing Interface (MPI) on a multi-node compute cluster. A dynamical database fragmentation scheme based on the availability of a compute cluster is proposed. Its...

Genome rearrangement is an important area in computational biology and bioinformatics. The translocation operation is one of the popular operations for genome rearrangement. It was proved that computing the unsigned translocation distance is NP-hard. In this paper, we present a ð1:5þ Þ-approximation algorithm for computing the unsigned translocation distance that improves upon the best known 1....

The Metropolis algorithm [8] is a mainstay of scientific computing. Indeed it appears first on a list of the “Top Ten Algorithms” [12]. It gives a method for sampling from probability distributions on high-dimensional spaces when these distributions are only known up to a normalizing constant. For background and references to extensive applications in physics, chemistry, biology and statistics,...

The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, National Information Communications Technology Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, School of Engineering, Department of Computing and Information Systems, and Department of Mathematics and Statistics, The University of Melbourne, ...