Classical molecular dynamics simulation of a macromolecule requires the use of an eecient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplect...

This report documents the program and the outcomes of the Seminar 11151 ‘Formal Methods in Molecular Biology’ that took place in Dagstuhl, Germany, on 10.–15. April, 2011. The most recent advances in Systems Biology were discussed, as well as and the contribution of computational formalisms to the modeling of biological systems, with the focus on stochasticity. About 30 talks were given. The pa...

It is now generally accepted in microbial ecology that cultivation-based approaches provide an incomplete picture of microbial diversity in the gastrointestinal (GI) tract because only a minority of microbes can be obtained in culture. Therefore, the application of molecular approaches, especially those focused on 16S ribosomal RNA (rRNA) sequence diversity, have become popular as they enable r...

In 2008, molecular methods continue to be mainstream in environmental engineering research. Fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis continue to be popular tools to track differences in microbial community composition over time and space. Fluorescent in situ hybridization (FISH) of wh...

Screening tests to detect Chlamydia trachomatis infections have advanced to permit the detection of nucleic acids from organisms. The development of these molecular assays that can detect and amplify the specific nucleic acids from the genes of C. trachomatis are called nucleic acid amplification tests (NAATs) and they have expanded the range of available specimen types to include noninvasive s...