Jan Westerholm

We construct holonomic quantum gates for qubits that are encoded in the near-degenerate vibrational E doublet of a deformable three-body system. Using Kendall's shape theory, we derive the Wilczek-Zee connection that governs adiabatic transport within the E manifold. We show that its restricted holonomy group is SU ( 2 ) , implying universal single-qubit control by closed loops in shape space. We provide explicit loops implementing a π / 2 phase gate and a Hadamard-type gate. For two-qubit operations, we outline how linked holonomic cycles in arrays generate a controlled Chern-Simons phase, enabling an entangling controlled- X () gate. We present a Ramsey-echo interferometric protocol that measures the Wilson loop trace of the Wilczek-Zee connection for a control cycle, providing a gauge-invariant signature of the non-Abelian holonomy. As a physically realizable demonstrator, we propose bond-length modulations of a Cs( 6 s )-Cs( 6 s )-Cs( n d 3 / 2 ) Rydberg trimer in optical tweezers and specify operating conditions that suppress leakage out of the E manifold.

The universality of interfacial roughness in growing epithelial tissue has remained a controversial issue. Kardar-Parisi-Zhang (KPZ) and molecular beam epitaxy (MBE) universality classes have been reported among other behaviors including a total lack of universality. Here, we simulate tissues using the cellsim3d kinetic division model for deformable cells to investigate cell-colony scaling. With seemingly minor model changes, it can reproduce both KPZ- and MBE-like scaling in configurations that mimic the respective experiments. Tissue growth with strong cell-cell adhesion in a linear geometry is KPZ like, while weakly adhesive tissues in a radial geometry are MBE like. This result neutralizes the apparent scaling controversy.

Seawaters exhibit various types of cyclic and trend-like temporal alterations in their biological, physical, and chemical processes. Surface water dynamics may vary, for instance, when the timings, durations, or amplitudes of seasonal developments of water properties alter between years and locations. We introduce a workflow using remote sensing to identify surface waters undergoing similar dynamics. The method, called ocean surface dynamics partitioning, classifies pixels based on their temporal change patterns instead of their properties at successive time snapshots. We apply an efficient parallel computing method to calculate Dynamic Time Warping (DTW) time series distances of large datasets of Earth Observation MERIS-instrument reflectance data R_rs(510 nm) and R_rs(620 nm), and produce a matrix of time series distances between 12,252 locations/time series in the Baltic Sea, for both wavelengths. We define cluster prototypes by hierarchical clustering of distance matrices and use them as initial prototypes for an iterative process of partitional clustering in order to identify areas that have similar reflectance dynamics. Lastly, we compute distances from the time series of the reflectance data to selected physical factors (wind, precipitation, and changes in sea surface temperature) obtained from Copernicus data archives. The workflow is reproducible and capable of managing large datasets in reasonable computation times and identifying areas of distinctive dynamics. The results show spatially coherent and logical areas without a priori information about the locations of the satellite image time series. The alignments of the reflectance time series vs. the observational time series of the physical environment clarify the causalities behind the cluster formation. We conclude that following the changes in an aquatic realm by biogeochemical observations at certain temporal intervals alone is not sufficient to identify environmental shifts. We foresee that the changes in dynamics are a sensitive measure of environmental threats and therefore they will be important to follow in the future.

The breakthrough of GPS-equipped smartphones has enabled the collection of track data from human mobility on massive scales that can be used in route recommendation, urban planning and traffic management. In this work we present a fast map server that can generate and visualize heat maps of popular routes online from massive sports track data based on client preferences, e.g., running routes lasting less than an hour. The heat maps shown respect user privacy by not showing routes with less than a predefined number of different users, for instance five. The results are represented to the client using a dynamic tile layer. The current implementation uses data collected by the Sports Tracker mobile application with over 800,000 different tracks and 2.8 billion GPS data points. Stress tests indicate that the server can handle hundreds of simultaneous client requests in a single server configuration.

A central task in protein sequence characterization is the use of a sequence database homology search tool to find similar protein sequences in other individuals or species. PSI-BLAST is a widely used module of the BLAST package that calculates a position-specific score matrix from the best matching sequences and performs iterated searches using a method to avoid many similar sequences for the score. For some queries and parameter settings, PSI-BLAST may find many similar high-scoring matches, and therefore up to 80% of the total run time may be spent in this procedure. In this article, we present code optimizations that improve the cache utilization and the overall performance of this procedure. Measurements show that, for queries where the number of similar matches is high, the optimized PSI-BLAST program may be as much as 2.9 times faster than the original program.