Place, Space, and Motion

(a) Topics and Goals. The Junior Research Group »Place, Space and Motion« investigates the role of spatial concepts in physical theories in the millennium from Plato (4th century BCE) through Philoponus and Simplicius (6th century CE). In particular, we examine the explicit theoretical views of ancient physicists and philosophers concerning space, the spatial features of bodies, and the existence of isomorphisms among space, change, and time. Projects are devoted to issues in Plato’s Timaeus and Aristotle’s Physics, and to the interwoven reception of these texts in Middle Platonism and Late Platonism. We trace the evolving answers given to such central questions as whether space is metaphysically basic or is rather dependent upon bodies or even non-spatial entities (such as souls); the possibility of empty space; the causal role of space in nature; how spatial structures make certain kinds of change possible or necessary. The group aims to produce a series of essays and commentaries examining key texts of Plato and Aristotle and tracing the reception and transformation of their views in Middle- and Late Platonism. (b) Methods. The group engages in close reading and interpretation of ancient texts, with the aim of constructing a history of engagement with the questions indicated above. The main areas of expertise brought to bear on the relevant texts lie in classical philology, history of ideas, history of science, and systematic philosophy. In a weekly research seminar, individual research projects and results are presented in detail and discussed in the light of these varied disciplines and skill sets. (c) State of Discussion. Relevant texts are interpreted both internally and in the light of their relationships with earlier sources and later readings. In this way a narrative is emerging of development and interrelationship among ancient theories of space – a narrative with some shape and coherence, but without the suppression of details and uncertainties. The group is also beginning to pay more attention to epistemological issues, concerning the sources of theoretical knowledge about space, and the evolving standards of argument, justification, and presentation of such knowledge

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair.

Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns of NHEJ are strongly biased by sequence context, but these studies were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ∼1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB repair of 6872 synthetic target sequences, introduced into a human cell line via lentiviral infection. We find that: (i) insertions are dominated by 1 bp events templated by sequence immediately upstream of the cleavage site, (ii) deletions are predominantly associated with microhomology and (iii) targets exhibit variable but reproducible diversity with respect to the number and relative frequency of the mutational outcomes to which they give rise. From these data, we trained a model that uses local sequence context to predict the distribution of mutational outcomes. Exploiting the bias of NHEJ outcomes towards microhomology mediated events, we demonstrate the programming of deletion patterns by introducing microhomology to specific locations in the vicinity of the DSB site. We anticipate that our results will inform investigations of DSB repair mechanisms as well as the design of CRISPR/Cas9 experiments for diverse applications including genome-wide screens, gene therapy, lineage tracing and molecular recording

One million indents, a hardness (and modulus) story

Advances in nanomechanical testing have progressed to a point where high-speed mapping and large data sets have become achievable. An Edisonian approach to indentation spacing and rate determines the experimental parameters that are then applied to a modern Damascene steel. One million indents were then performed over a period of less than 6 days thereby mapping out an area of 1mm x 1mm with a spacing of 1µm. To make sense of the data, artificial intelligence algorithms are used to provide an analysis of the hardness and modulus data. Please click Additional Files below to see the full abstract

North Atlantic Deep Water Production during the Last Glacial Maximum.

Changes in deep ocean ventilation are commonly invoked as the primary cause of lower glacial atmospheric CO2. The water mass structure of the glacial deep Atlantic Ocean and the mechanism by which it may have sequestered carbon remain elusive. Here we present neodymium isotope measurements from cores throughout the Atlantic that reveal glacial-interglacial changes in water mass distributions. These results demonstrate the sustained production of North Atlantic Deep Water under glacial conditions, indicating that southern-sourced waters were not as spatially extensive during the Last Glacial Maximum as previously believed. We demonstrate that the depleted glacial δ(13)C values in the deep Atlantic Ocean cannot be explained solely by water mass source changes. A greater amount of respired carbon, therefore, must have been stored in the abyssal Atlantic during the Last Glacial Maximum. We infer that this was achieved by a sluggish deep overturning cell, comprised of well-mixed northern- and southern-sourced waters.Sample material was provided by the Godwin Laboratory for Paleoclimate Research at the University of Cambridge, the International Ocean Discovery Program, the GeoB Core Repository at the MARUM – Center for Marine Environmental Sciences, University of Bremen and Petrobras. Jo Kerr and Aurora Elmore are thanked for providing additional samples. The data reported in this paper are listed in supplementary information and archived in Pangaea (www.pangaea.de). Thiago Pereira dos Santos is thanked for providing the unpublished age model data for GL1090; Jo Clegg and Vicky Rennie are thanked for technical support and Natalie Roberts for helpful discussions. Radiocarbon analyses were supported by NERC radiocarbon grant 1752.1013 and Nd isotope analyses by NERC grant NERC NE/K005235/1 and NERC NE/F006047/1 to AMP. JNWH was supported by a Rutherford Memorial Scholarship. SM was funded through the DFG Research Center/Cluster of Excellence “The Ocean in the Earth System”. CMC acknowledges financial support from FAPESP (Grant 2012/17517-3).This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by Nature Publishing Group

Resistivity-driven State Changes in Vertically Stratified Accretion Disks

We investigate the effect of shear viscosity and Ohmic resistivity on the magnetorotational instability (MRI) in vertically stratified accretion disks through a series of local simulations with the Athena code. First, we use a series of unstratified simulations to calibrate physical dissipation as a function of resolution and background field strength; the effect of the magnetic Prandtl number, Pm = viscosity/resistivity, on the turbulence is captured by ~32 grid zones per disk scale height, H. In agreement with previous results, our stratified disk calculations are characterized by a subthermal, predominately toroidal magnetic field that produces MRI-driven turbulence for |z| < 2 H. Above |z| = 2 H, magnetic pressure dominates and the field is buoyantly unstable. Large scale radial and toroidal fields are also generated near the mid-plane and subsequently rise through the disk. The polarity of this mean field switches on a roughly 10 orbit period in a process that is well-modeled by an alpha-omega dynamo. Turbulent stress increases with Pm but with a shallower dependence compared to unstratified simulations. For sufficiently large resistivity, on the order of cs H/1000, where cs is the sound speed, MRI turbulence within 2 H of the mid-plane undergoes periods of resistive decay followed by regrowth. This regrowth is caused by amplification of toroidal field via the dynamo. This process results in large amplitude variability in the stress on 10 to 100 orbital timescales, which may have relevance for partially ionized disks that are observed to have high and low accretion states.Comment: very minor changes, accepted to Ap

Mary Clifford Webster Darling Correspondence

Entries include some correct biographical information typed by the Maine State Library and handwritten correspondence on a Fredericka Manor card and plain paper stationery