Periodically driven stochastic un- and refolding transitions of biopolymers

Mechanical single molecule experiments probe the energy profile of biomolecules. We show that in the case of a profile with two minima (like folded/unfolded) periodic driving leads to a stochastic resonance-like phenomenon. We demonstrate that the analysis of such data can be used to extract four basic parameters of such a transition and discuss the statistical requirements of the data acquisition. As advantages of the proposed scheme, a polymeric linker is explicitly included and thermal fluctuations within each well need not to be resolved.Comment: 7 pages, 5 figures, submitted to EP

Tube Width Fluctuations in F-Actin Solutions

We determine the statistics of the local tube width in F-actin solutions, beyond the usually reported mean value. Our experimental observations are explained by a segment fluid theory based on the binary collision approximation (BCA). In this systematic generalization of the standard mean-field approach effective polymer segments interact via a potential representing the topological constraints. The analytically predicted universal tube width distribution with a stretched tail is in good agreement with the data.Comment: Final version, 5 pages, 4 figure

Coupling JOREK and STARWALL for Non-linear Resistive-wall Simulations

The implementation of a resistive-wall extension to the non-linear MHD-code JOREK via a coupling to the vacuum-field code STARWALL is presented along with first applications and benchmark results. Also, non-linear saturation in the presence of a resistive wall is demonstrated. After completion of the ongoing verification process, this code extension will allow to perform non-linear simulations of MHD instabilities in the presence of three-dimensional resistive walls with holes for limited and X-point plasmas.Comment: Contribution for "Theory Of Fusion Plasmas, Joint Varenna - Lausanne International Workshop, Villa Monastero, Varenna, Italy (27.-31.8.2012)", accepted for publication in Journal of Physics Conference Serie

funcX: A Federated Function Serving Fabric for Science

Exploding data volumes and velocities, new computational methods and platforms, and ubiquitous connectivity demand new approaches to computation in the sciences. These new approaches must enable computation to be mobile, so that, for example, it can occur near data, be triggered by events (e.g., arrival of new data), be offloaded to specialized accelerators, or run remotely where resources are available. They also require new design approaches in which monolithic applications can be decomposed into smaller components, that may in turn be executed separately and on the most suitable resources. To address these needs we present funcX---a distributed function as a service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. funcX's endpoint software can transform existing clouds, clusters, and supercomputers into function serving systems, while funcX's cloud-hosted service provides transparent, secure, and reliable function execution across a federated ecosystem of endpoints. We motivate the need for funcX with several scientific case studies, present our prototype design and implementation, show optimizations that deliver throughput in excess of 1 million functions per second, and demonstrate, via experiments on two supercomputers, that funcX can scale to more than more than 130000 concurrent workers.Comment: Accepted to ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC 2020). arXiv admin note: substantial text overlap with arXiv:1908.0490

Non-linear Simulations of MHD Instabilities in Tokamaks Including Eddy Current Effects and Perspectives for the Extension to Halo Currents

The dynamics of large scale plasma instabilities can strongly be influenced by the mutual interaction with currents flowing in conducting vessel structures. Especially eddy currents caused by time-varying magnetic perturbations and halo currents flowing directly from the plasma into the walls are important. The relevance of a resistive wall model is directly evident for Resistive Wall Modes (RWMs) or Vertical Displacement Events (VDEs). However, also the linear and non-linear properties of most other large-scale instabilities may be influenced significantly by the interaction with currents in conducting structures near the plasma. The understanding of halo currents arising during disruptions and VDEs, which are a serious concern for ITER as they may lead to strong asymmetric forces on vessel structures, could also benefit strongly from these non-linear modeling capabilities. Modeling the plasma dynamics and its interaction with wall currents requires solving the magneto-hydrodynamic (MHD) equations in realistic toroidal X-point geometry consistently coupled with a model for the vacuum region and the resistive conducting structures. With this in mind, the non-linear finite element MHD code JOREK has been coupled with the resistive wall code STARWALL, which allows to include the effects of eddy currents in 3D conducting structures in non-linear MHD simulations. This article summarizes the capabilities of the coupled JOREK-STARWALL system and presents benchmark results as well as first applications to non-linear simulations of RWMs, VDEs, disruptions triggered by massive gas injection, and Quiescent H-Mode. As an outlook, the perspectives for extending the model to halo currents are described.Comment: Proceeding paper for Theory of Fusion Plasmas (Joint Varenna-Lausanne International Workshop), Varenna, Italy (September 1-5, 2014); accepted for publication in: to Journal of Physics: Conference Serie

Masked millennial-scale climate variations in South West Africa during the last glaciation

To address the connection between tropical African vegetation development and high-latitude climate change we present a high-resolution pollen record from ODP Site 1078 (off Angola) covering the period 50–10 ka BP. Although several tropical African vegetation and climate reconstructions indicate an impact of Heinrich Stadials (HSs) in Southern Hemisphere Africa, our vegetation record shows no response. Model simulations conducted with an Earth System Model of Intermediate Complexity including a dynamical vegetation component provide one possible explanation. Because both precipitation and evaporation increased during HSs and their effects nearly cancelled each other, there was a negligible change in moisture supply. Consequently, the resulting climatic response to HSs might have been too weak to noticeably affect the vegetation composition in the study area. Our results also show that the response to HSs in southern tropical Africa neither equals nor mirrors the response to abrupt climate change in northern Africa