Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations

Computation is one of the centerpieces of both the physical and biological sciences. A key thrust in computational science is the explicit mechanistic simulation of the spatiotemporal evolution of materials ranging from macromolecules to intermetallic alloys. However, our ability to simulate such systems is in the end always limited in both the spatial extent of the systems that are considered, as well as the duration of the time that can be simulated. As a result, a variety of efforts have been put forth that aim to finesse these challenges in both space and time through new techniques in which constraint is exploited to reduce the overall computational burden. The aim of this review is to describe in general terms some of the key ideas that have been set forth in both the materials and biological setting and to speculate on future developments along these lines. We begin by developing general ideas on the exploitation of constraint as a systematic tool for degree of freedom thinning. These ideas are then applied to case studies ranging from the plastic deformation of solids to the interactions of proteins and DNA

Self-adaptive Scouting---Autonomous Experimentation for Systems Biology

We introduce a new algorithm for autonomous experimentation. This algorithm uses evolution to drive exploration during scientific discovery. Population size and mutation strength are self-adaptive. The only variables remaining to be set are the limits and maximum resolution of the parameters in the experiment. In practice, these are determined by instrumentation. Aside from conducting physical experiments, the algorithm is a valuable tool for investigating simulation models of biological systems. We illustrate the operation of the algorithm on a model of HIV-immune system interaction. Finally, the difference between scouting and optimization is discussed

Sediment transport over static armour layers and its impact on bed stability

River morphodynamics and sediment transportRiver morphology and morphodynamic

Der Bibliotheksneubau der Hochschule für Technik, Wirtschaft und Kultur Leipzig

Der Neubau der Hochschulbibliothek der Hochschule für Technik, Wirtschaft und Kultur Leipzig (HTWK) ist ein Beispiel für ein durchgeführtes Bauprojekt des Vorhabens „Infrastruktur an Hochschulen“, finanziert mit Mitteln des Europäischen Fonds für regionale Entwicklung. Ziel der Förderung ist unter anderem, die baulichen Voraussetzungen für eine bessere Vernetzung der Forschung innerhalb der Hochschule, aber auch zu anderen Einrichtungen und Unternehmen zu schaffen. Die HTWK Leipzig konzentriert sich an ihrem Hauptstandort im Leipziger Süden auf beiden Seiten der Karl-Liebknecht-Straße. Ausgehend von dieser Zielstellung wurde für die Hochschul - bibliothek ein Neubau geschaffen, der sowohl in seiner Größe als auch in seiner Ausstattung den gewachsenen Ansprüchen an die Literatur- und Informationsversorgung der sich im Campus konzentrierenden Lehre und Forschung gerecht wird

Cell-Free Microfluidic Determination of P-glycoprotein Interactions with Substrates and Inhibitors

ABSTRACT: The membrane protein P-glycoprotein (P-gp) plays key roles in the oral bioavailability of drugs, their blood brain barrier passage as well as in multidrug resistance. For new drug candidates it is mandatory to study their interaction with P-gp, according to FDA and EMA regulations. The vast majority of these tests are performed using confluent cell layers of P-gp overexpressing cell lines that render these tests laborious. In this study, we introduce a cell-free microfluidic assay for the rapid testing of drug- P-gp interactions. Cell-derived vesicles are prepared from MDCKII-MDR1 overexpressing cells and immobilized on the surface of a planar microfluidic device. The drug is delivered continuously to the vesicles and calcein accumulation is monitored by means of a fluorescence assay and total internal reflection fluorescence (TIRF) microscopy. Only small amounts of compounds (~10μl) are required in concentrations of 5, 25 and 50μM for a test that provides within 5min information on the apparent dissociation constant of the drug and P-gp. We tested 10 drugs on-chip, 9 of which are inhibitors or substrates of P-glycoprotein and one negative control. We benchmarked the measured apparent dissociation constants against an alternative assay on a plate reader and reference data from FDA. These comparisons revealed good correlations between the logarithmic apparent dissociation constants (R2 = 0.95 with ATPase assay, R2 = 0.93 with FDA data) and show the reliability of the rapid on-chip test. The herein presented assay has an excellent screening window factor (Z'-factor) of 0.8, and is suitable for high-throughput testing

Skyrmion Lattice Phases in Thin Film Multilayer

Phases of matter are ubiquitous with everyday examples including solids and liquids. In reduced dimensions, particular phases, such as the two-dimensional (2D) hexatic phase and corresponding phase transitions occur. A particularly exciting example of 2D ordered systems are skyrmion lattices, where in contrast to previously studied 2D colloid systems, the skyrmion size and density can be tuned by temperature and magnetic field. This allows us to drive the system from a liquid phase to a hexatic phase as deduced from the analysis of the hexagonal order. Using coarse-grained molecular dynamics simulations of soft disks, we determine the skyrmion interaction potentials and we find that the simulations are able to reproduce the full two-dimensional phase behavior. This shows that not only the static behavior of skyrmions is qualitatively well described in terms of a simple two-dimensional model system but skyrmion lattices are versatile and tunable two-dimensional model systems that allow for studying phases and phase transitions in reduced dimensions.Comment: Corrected Acknowledgement