University of Potsdam

About: University of Potsdam is a education organization based out in Potsdam, Germany. It is known for research contribution in the topics: Population & Computer science. The organization has 9629 authors who have published 26740 publications receiving 759745 citations. The organization is also known as: Universität Potsdam.

Time-dependent configuration-interaction calculations of laser-pulse-driven many-electron dynamics: Controlled dipole switching in lithium cyanide

Abstract: We report simulations of laser-driven many-electron dynamics by means of the time-dependent configuration interaction singles (doubles) approach. The method accounts for the correlation of ground and excited states, is capable of describing explicitly time-dependent, nonlinear phenomena, and is systematically improvable. Lithium cyanide serves as a molecular test system in which the charge distribution and hence the dipole moment are shown to be switchable, in a controlled fashion, by (a series of) laser pulses which induce selective, state-to-state electronic transitions. One focus of our time-dependent calculations is the question of how fast the transition from the ionic ground state to a specific excited state that is embedded in a multitude of other states can be made, without creating an electronic wave packet.

Multi-shot ASP solving with clingo

Abstract: We introduce a new flexible paradigm of grounding and solving in Answer Set Programming (ASP), which we refer to as multi-shot ASP solving, and present its implementation in the ASP system clingo. Multi-shot ASP solving features grounding and solving processes that deal with continuously changing logic programs. In doing so, they remain operative and accommodate changes in a seamless way. For instance, such processes allow for advanced forms of search, as in optimization or theory solving, or interaction with an environment, as in robotics or query answering. Common to them is that the problem specification evolves during the reasoning process, either because data or constraints are added, deleted, or replaced. This evolutionary aspect adds another dimension to ASP since it brings about state changing operations. We address this issue by providing an operational semantics that characterizes grounding and solving processes in multi-shot ASP solving. This characterization provides a semantic account of grounder and solver states along with the operations manipulating them. The operative nature of multi-shot solving avoids redundancies in relaunching grounder and solver programs and benefits from the solver's learning capacities. clingo accomplishes this by complementing ASP's declarative input language with control capacities. On the declarative side, a new directive allows for structuring logic programs into named and parameterizable subprograms. The grounding and integration of these subprograms into the solving process is completely modular and fully controllable from the procedural side. To this end, clingo offers a new application programming interface that is conveniently accessible via scripting languages. By strictly separating logic and control, clingo also abolishes the need for dedicated systems for incremental and reactive reasoning, like iclingo and oclingo, respectively, and its flexibility goes well beyond the advanced yet still rigid solving processes of the latter.

Inferring hypotheses on functional relationships of genes: Analysis of the Arabidopsis thaliana subtilase gene family.

Abstract: The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative bioinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co-regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades. Supplemental material is available in the Plant Subtilase Database (PSDB) (http://csbdb.mpimp-golm.mpg.de/psdb.html), as well as from the CSB.DB (http://csbdb.mpimp-golm.mpg.de).