Analog Computing for Molecular Dynamics

Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model inspired by force fields which are popular in molecular dynamics. We demonstrate a setup which simulate a single water molecule in time. To the best of our knowledge such a simulation has never been done on analog computers before. Important implementation aspects of the model, such as scaling, data range and circuit design, are highlighted. We also analyze the performance and compare the solution with a numerical approach.Comment: 9 pages, 9 figures, submitted to Emerging Topics in Computing, IEEE Tran

Solving Partial Differential Equations with Monte Carlo / Random Walk on an Analog-Digital Hybrid Computer

Current digital computers are about to hit basic physical boundaries with respect to integration density, clock frequencies, and particularly energy consumption. This requires the application of new computing paradigms, such as quantum and analog computing in the near future. Although neither quantum nor analog computer are general purpose computers they will play an important role as co-processors to offload certain classes of compute intensive tasks from classic digital computers, thereby not only reducing run time but also and foremost power consumption. In this work, we describe a random walk approach to the solution of certain types of partial differential equations which is well suited for combinations of digital and analog computers (hybrid computers). The experiments were performed on an Analog Paradigm Model-1 analog computer attached to a digital computer by means of a hybrid interface. At the end we give some estimates of speedups and power consumption obtainable by using future analog computers on chip.Comment: 9 pages, 7 figures. Proceeding for the MikroSystemTechnik Kongress 2023 (VDE Verlag MST Kongress 2023

The role of the cortical cytoskeleton

We generated Dictyostelium double mutants lacking the two F-actin crosslinking proteins alpha-actinin and gelation factor by inactivating the corresponding genes via homologous recombination. Here we investigated the consequences of these deficiencies both at the single cell level and at the multicellular stage. We found that loss of both proteins severely affected growth of the mutant cells in shaking suspension, and led to a reduction of cell size from 12 microns in wild-type cells to 9 microns in mutant cells. Moreover the cells did not exhibit the typical polarized morphology of aggregating Dictyostelium cells but had a more rounded cell shape, and also exhibited an increased sensitivity towards osmotic shock and a reduced rate of phagocytosis. Development was heavily impaired and never resulted in the formation of fruiting bodies. Expression of developmentally regulated genes and the final developmental stages that were reached varied, however, with the substrata on which the cells were deposited. On phosphate buffered agar plates the cells were able to form tight aggregates and mounds and to express prespore and prestalk cell specific genes. Under these conditions the cells could perform chemotactic signalling and cell behavior was normal at the onset of multicellular development as revealed by time-lapse video microscopy. Double mutant cells were motile but speed was reduced by approximately 30% as compared to wild type. These changes were reversed by expressing the gelation factor in the mutant cells. We conclude that the actin assemblies that are formed and/or stabilized by both F-actin crosslinking proteins have a protective function during osmotic stress and are essential for proper cell shape and motility

Влияние исходного структурно-фазового состояния низкоуглеродистых малолегированных сталей на формирование структуры и свойств лазерных сварных соединений

В результате комплексных структурных исследований показано, что исходное структурно-фазовое состояние определяет формирование разного типа структур в зоне сплавления, зонах термического влияния и разный уровень микротвердости стали. В стали с меньшим содержанием углерода и исходной мелкозернистой, однородной феррито-бейнитной структурой при лазерной сварке сформирован сварной шов с лучшими механическими свойствами за счет получения в структуре феррита и гранулярного бейнита, чем в стали с более высоким содержанием углерода и феррито-перлитной крупнозернистой структурой.As a result of complex structural studies, it has been shown that the initial structural-phase state determines the formation of different types of structures in the fusion zone, heat-affected zones and different levels of steel microhardness. Steels with a lower carbon content and an initial fine-grained homogeneous ferrite-bainite structure during laser welding form a weld with better mechanical properties due to the production of ferrite and granular bainite in the structure than steels with a higher carbon content and a ferrite-pearlite coarse-grained structure

The Shahre Javan Community Detailed Plan : Planning for a Climate Responsive and Sustainable Iranian Urban Quarter

Zugleich gedruckt veröffentlicht im Universitätsverlag der TU Berlin unter der ISBN 978-3-7983-2451-0.This report presents the major accomplishments of the ‘Shahre Javan Community’ pilot project as the main pilot project of the German-Iranian Young Cities research project,. ‘Shahre Javan’ is Farsi and stands for ‘Young City’. The pilot project uses an integrated planning and research process to explore aspects of energy and resource efficiency, climate and environmentally conscious solutions for urban form, architecture, landscape planning, transportation planning, water and energy management, and environmental assessment. It is about the upgraded Iranian detailed plan (‘Tarh-e Tafsili’) for a nearly 45 ha large pilot project area in the southern part of the Hashtgerd New Town, Iran. It includes innovations derived during the strategically integrative urban development and research process, in an effort to reach more climate responsive and more sustainable urban development. Thus, several of the presented solutions go above and beyond the standard content of an Iranian detailed plan. Hence, this publication does not present the or an approved formal Iranian detailed plan. Rather, it combines a reflection of research background, approach, and process with a kind of a hybrid detailed plan report which includes common Iranian detailed plan contents and new and innovative elements as well as research findings going beyond the detailed plan scale and content. Printed Version published by Universitätsverlag der TU Berlin (www.univerlag.tu-berlin.de), ISBN 978-3-7983-2451-

Renewable Energies in Germany – A Biography of the Innovation Process

In den letzten 20 Jahren konnten in Deutschland zuvor nicht für möglich gehaltene Wachstumsquoten in den Branchen der erneuerbaren Energien im Stromsektor umgesetzt werden. Das Forschungsprojekt „Innovationsbiographie der erneuerbaren Energien“ untersuchte in einer Querschnittsbetrachtung rückblickend die Innovationsverläufe der erneuerbaren Energien zur Stromerzeugung: Biogasverstromung, Photovoltaik, Windenergie, Tiefengeothermie und Wasserkraft. Die nun vorliegende Studie gibt Aufschluss darüber, welche zentralen Einflussfaktoren und Akteure auf den Innovationsprozess der erneuerbaren Energien fördernd – oder auch hemmend – einwirkten. Die einzelnen Sparten der erneuerbaren Energien im Stromsektor weisen individuelle Innovationsbedingungen, Verläufe und Dynamiken auf. Es wird aber auch eine gewisse Regelhaftigkeit deutlich: die Innovationsprozesse verlaufen nicht stetig bzw. linear, sondern weisen Brüche und Entwicklungsknicks auf. Auf Phasen hoher Innovationsdynamik können Phasen der Stagnation oder Krisen folgen, die eine Herausforderung für die Steuerung darstellen. Die Ergebnisse des Forschungsvorhabens beleuchten die Vielschichtigkeit und das Auf und Ab von Innovationsverläufen der erneuerbaren Energien. Die Erfolge sind Ergebnis einer Koordinationsleistung staatlicher, privater und gesellschaftlicher Akteure. Auch übergeordnete Rahmenbedingungen, technische Voraussetzungen oder gesellschaftliche Einflüsse spielten im Sektor der erneuerbaren Energien eine entscheidende Rolle. Auf Seiten der Politik ist daher systemisches Denken und Handeln gefragt. Nur dann können Wirkungszusammenhänge zwischen den unterschiedlicher Einflussfaktoren erkannt, interpretiert und durch adäquate Maßnahmen politisch gesteuert werden. Online-Version, im Universitätsverlag der TU Berlin (www.univerlag.tu-berlin.de) erschienen.For the past 20 years we have witnessed growth rates of electricity generation from renewable energies in Germany that were not considered possible before. The interdisciplinary research project “Innovationsbiographie der erneuerbaren Energien“ (biography of the innovation process of renewable energies) examined with a cross-sectional, retrospective approach the innovation pathways of five energy sources for renewable electricity generation: biomass, photovoltaic, deep geothermal energy, wind power and hydroelectricity. This study sheds light on the – supportive and inhibitive - influencing factors and on the decisive actors within the innovation process of renewable energies. The individual branches of renewable energies in the electricity sector possess unique innovation conditions, pathways and dynamics. Yet there appears to be a certain pattern: the innovation processes do not proceed continuously or linear, but they exhibit phases of breaks and ruptures. Phases of high innovative dynamics may be followed by phases of stagnation or crises, which pose a challenge for political steering. The results of the research project highlight the multi-layered character and the ups and downs in the innovation paths of renewable energies. The successes are a result of the coordination capabilities of governmental, private and societal actors. Just as well, overarching framework conditions, technical preconditions or societal influences play a decisive role within the sector of renewable energies. Hence there is a constant need for systemic thinking and acting on the side of politics. This is the only way to discover and interpret the interdependencies between different influencing factors and to allow for political steering by adequate measures. Online-Version, published by Universitätsverlag der TU Berlin (www.univerlag.tu-berlin.de)

Bovine herpesvirus 5 BICP0 complements the bovine herpesvirus 1 homolog

Bovine herpesvirus 1 (BoHV-1) and BoHV-5 are closely related (82% amino acid identity) but differ strongly in neuropathogenesis. The immediate-early gene for BICP0 is less conserved (70% amino acid identity) and may contribute to a dissimilar phenotype. A peculiar difference is a guanosine hexamer in the BICP0-1 gene which aligns with only five guanosines in the BICP0-5 gene and therefore results in a frameshift in the latter open reading frame. Thus, the C-terminal amino acid sequence (residues 643–676 of BICP0-1 vs. 655–720 of BICP0-5) is completely different. We introduced the BICP0-5 frameshift into the BoHV-1 genome cloned as a bacterial artificial chromosome (BoHV-1 BAC) using the Red recombination system with galK selection and counterselection. Transfection of MDBK cells with the resulting BAC produced recombinant virus that replicated like wild type BoHV-1 in vitro. Attempts to exchange the entire BICP0-1 gene by the BoHV-5 homolog using the same approach failed repeatedly. Therefore, we cotransfected purified BICP0/galK+-BoHV-1 BAC DNA with a recombination plasmid coding for BICP0-5 with or without a HA tag into MDBK cells. BoHV-1 recombinants expressing the respective proteins were characterized. In vitro, all recombinants grew to similar titers as the parental viruses, which demonstrates that BICP0-5 compensates for the growth defect of BICP0/galK+-BoHV-1 and functionally complements BICP0-1 of BoHV-1. We conclude that BICP0 may be suitable to positively select BoHV-1 recombinants with deletions or insertions of additional genes of interest