Technical University of Denmark

About: Technical University of Denmark is a education organization based out in Kongens Lyngby, Hovedstaden, Denmark. It is known for research contribution in the topics: Population & Catalysis. The organization has 24126 authors who have published 66394 publications receiving 2443649 citations. The organization is also known as: Danmarks Tekniske Universitet & DTU.

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

Abstract: Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.

Phonon-limited mobility in n -type single-layer MoS 2 from first principles

Abstract: We study the phonon-limited mobility in intrinsic $n$-type single-layer MoS${}_{2}$ for temperatures $Tg100$ K. The materials properties including the electron-phonon interaction are calculated from first principles and the deformation potentials and Fr\"ohlich interaction in single-layer MoS${}_{2}$ are established. The calculated room-temperature mobility of $\ensuremath{\sim}$410 cm${}^{2}$V${}^{\ensuremath{-}1}$s${}^{\ensuremath{-}1}$ is found to be dominated by optical phonon scattering via intra and intervalley deformation potential couplings and the Fr\"ohlich interaction. The mobility is weakly dependent on the carrier density and follows a $\ensuremath{\mu}\ensuremath{\sim}{T}^{\ensuremath{-}\ensuremath{\gamma}}$ temperature dependence with $\ensuremath{\gamma}=1.69$ at room temperature. It is shown that a quenching of the characteristic homopolar mode, which is likely to occur in top-gated samples, increases the mobility with $\ensuremath{\sim}$70 cm${}^{2}$V${}^{\ensuremath{-}1}$s${}^{\ensuremath{-}1}$ and can be observed as a decrease in the exponent to $\ensuremath{\gamma}=1.52$. In comparison to recent experimental findings for the mobility in single-layer MoS${}_{2}$ ($\ensuremath{\sim}$200 cm${}^{2}$V${}^{\ensuremath{-}1}$s${}^{\ensuremath{-}1}$), our results indicate that mobilities close to the intrinsic phonon-limited mobility can be achieved in two-dimensional materials via dielectric engineering that effectively screens static Coulomb scattering on, e.g., charged impurities.

Ammonia synthesis from first-principles calculations.

Abstract: The rate of ammonia synthesis over a nanoparticle ruthenium catalyst can be calculated directly on the basis of a quantum chemical treatment of the problem using density functional theory. We compared the results to measured rates over a ruthenium catalyst supported on magnesium aluminum spinel. When the size distribution of ruthenium particles measured by transmission electron microscopy was used as the link between the catalyst material and the theoretical treatment, the calculated rate was within a factor of 3 to 20 of the experimental rate. This offers hope for computer-based methods in the search for catalysts.

New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria

Abstract: Use of the green fluorescent protein (Gfp) from the jellyfish Aequorea victoria is a powerful method for nondestructive in situ monitoring, since expression of green fluorescence does not require any substrate addition. To expand the use of Gfp as a reporter protein, new variants have been constructed by the addition of short peptide sequences to the C-terminal end of intact Gfp. This rendered the Gfp susceptible to the action of indigenous housekeeping proteases, resulting in protein variants with half-lives ranging from 40 min to a few hours when synthesized in Escherichia coli and Pseudomonas putida. The new Gfp variants should be useful for in situ studies of temporal gene expression.