Adiabatic response for Lindblad dynamics

We study the adiabatic response of open systems governed by Lindblad evolutions. In such systems, there is an ambiguity in the assignment of observables to fluxes (rates) such as velocities and currents. For the appropriate notion of flux, the formulas for the transport coefficients are simple and explicit and are governed by the parallel transport on the manifold of instantaneous stationary states. Among our results we show that the response coefficients of open systems, whose stationary states are projections, is given by the adiabatic curvature.Comment: 33 pages, 4 figures, accepted versio

Adiabatic theorems for generators of contracting evolutions

We develop an adiabatic theory for generators of contracting evolution on Banach spaces. This provides a uniform framework for a host of adiabatic theorems ranging from unitary quantum evolutions through quantum evolutions of open systems generated by Lindbladians all the way to classically driven stochastic systems. In all these cases the adiabatic evolution approximates, to lowest order, the natural notion of parallel transport in the manifold of instantaneous stationary states. The dynamics in the manifold of instantaneous stationary states and transversal to it have distinct characteristics: The former is irreversible and the latter is transient in a sense that we explain. Both the gapped and gapless cases are considered. Some applications are discussed.Comment: 31 pages, 4 figures, replaced by the version accepted for publication in CM

Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P

Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyltRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation

Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy

10.1111/1755-0998.12314Molecular Ecology Resources152329-33

Die frührömische Holz-Kies-Straße im Murnauer Moos - Untersuchung des ehemaligen Verlaufs mittels Georadar (GPR)

Declarative Networking is a recent, viable approach to make distributed programming easier, which is becoming increasingly popular in systems and networking community. It offers the programmer a declarative, rule-based language, called P2, for writing distributed applications in an abstract, yet expressive way. This approach, however, imposes new challenges on analysis and verification methods when they are applied to P2 programs. Reasoning about P2 computations is beyond the scope of existing tools since it requires handling of program states defined in terms of collections of relations, which store the application data, together with multisets of tuples, which represent communication events in-flight. In this paper, we propose a cardinality abstraction technique that can be used to analyze and verify P2 programs. It keeps track of the size of relations (together with projections thereof) and multisets defining P2 states, and provides an appropriate treatment of declarative operations, e.g., indexing, unification, variable binding, and negation. Our cardinality abstraction-based verifier successfully proves critical safety properties of a P2 implementation of the Byzantine fault tolerance protocol Zyzzyva, which is a representative and complex declarative networking application