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.

Predicting Secretory Proteins with SignalP

Abstract: SignalP is the currently most widely used program for prediction of signal peptides from amino acid sequences. Proteins with signal peptides are targeted to the secretory pathway, but are not necessarily secreted. After a brief introduction to the biology of signal peptides and the history of signal peptide prediction, this chapter will describe all the options of the current version of SignalP and the details of the output from the program. The chapter includes a case study where the scores of SignalP were used in a novel way to predict the functional effects of amino acid substitutions in signal peptides.

An analysis of ductile rupture in notched bars

Abstract: Ductile fracture in axisymmetric and plane strain notched tensile specimens is analyzed numerically, based on a set of elastic-plastic constitutive relations that account for the nucleation and growth of microvoids. Final material failure by void coalescence is incorporated into the constitutive model via the dependence of the yield function on the void volume fraction. In the analyses the material has no voids initially; but as the voids nucleate and grow, the resultant dilatancy and pressure sensitivity of the macroscopic plastic flow influence the solution significantly. Considering both a blunt notch geometry and a sharp notch geometry in the computations permits a study of the relative roles of high strain and high triaxiality on failure. Comparison is made with published experimental results for notched tensile specimens of high-strength steels. All axisymmetric specimens analyzed fail at the center of the notched section, whereas failure initiation at the surface is found in plane strain specimens with sharp notches, in agreement with the experiments. The results for different specimens are used to investigate the circumstances under which fracture initiation can be represented by a single failure locus in a plot of stress triaxiality vs effective plastic strain.

Acoustofluidics 7: The acoustic radiation force on small particles

Abstract: In this paper, Part 7 of the thematic tutorial series “Acoustofluidics – exploiting ultrasonic standing waves, forces and acoustic streaming in microfluidic systems for cell and particle manipulation ”, we present the theory of the acoustic radiation force; a second-order, time-averaged effect responsible for the acoustophoretic motion of suspended, micrometre-sized particles in an ultrasound field.

NetMHCpan, a method for MHC class I binding prediction beyond humans

Abstract: Binding of peptides to major histocompatibility complex (MHC) molecules is the single most selective step in the recognition of pathogens by the cellular immune system. The human MHC genomic region (called HLA) is extremely polymorphic comprising several thousand alleles, each encoding a distinct MHC molecule. The potentially unique specificity of the majority of HLA alleles that have been identified to date remains uncharacterized. Likewise, only a limited number of chimpanzee and rhesus macaque MHC class I molecules have been characterized experimentally. Here, we present NetMHCpan-2.0, a method that generates quantitative predictions of the affinity of any peptide–MHC class I interaction. NetMHCpan-2.0 has been trained on the hitherto largest set of quantitative MHC binding data available, covering HLA-A and HLA-B, as well as chimpanzee, rhesus macaque, gorilla, and mouse MHC class I molecules. We show that the NetMHCpan-2.0 method can accurately predict binding to uncharacterized HLA molecules, including HLA-C and HLA-G. Moreover, NetMHCpan-2.0 is demonstrated to accurately predict peptide binding to chimpanzee and macaque MHC class I molecules. The power of NetMHCpan-2.0 to guide immunologists in interpreting cellular immune responses in large out-bred populations is demonstrated. Further, we used NetMHCpan-2.0 to predict potential binding peptides for the pig MHC class I molecule SLA-1*0401. Ninety-three percent of the predicted peptides were demonstrated to bind stronger than 500 nM. The high performance of NetMHCpan-2.0 for non-human primates documents the method’s ability to provide broad allelic coverage also beyond human MHC molecules. The method is available at http://www.cbs.dtu.dk/services/NetMHCpan .