scenery: Flexible Virtual Reality Visualization on the Java VM

Life science today involves computational analysis of a large amount and variety of data, such as volumetric data acquired by state-of-the-art microscopes, or mesh data from analysis of such data or simulations. Visualization is often the first step in making sense of data, and a crucial part of building and debugging analysis pipelines. It is therefore important that visualizations can be quickly prototyped, as well as developed or embedded into full applications. In order to better judge spatiotemporal relationships, immersive hardware, such as Virtual or Augmented Reality (VR/AR) headsets and associated controllers are becoming invaluable tools. In this work we introduce scenery, a flexible VR/AR visualization framework for the Java VM that can handle mesh and large volumetric data, containing multiple views, timepoints, and color channels. scenery is free and open-source software, works on all major platforms, and uses the Vulkan or OpenGL rendering APIs. We introduce scenery's main features and example applications, such as its use in VR for microscopy, in the biomedical image analysis software Fiji, or for visualizing agent-based simulations.Comment: Added IEEE DOI, version published at VIS 201

Non-adiabatic and time-resolved photoelectron spectroscopy for molecular systems

We quantify the non-adiabatic contributions to the vibronic sidebands of equilibrium and explicitly time-resolved non-equilibrium photoelectron spectra for a vibronic model system of Trans-Polyacetylene. Using exact diagonalization, we directly evaluate the sum-over-states expressions for the linear-response photocurrent. We show that spurious peaks appear in the Born-Oppenheimer approximation for the vibronic spectral function, which are not present in the exact spectral function of the system. The effect can be traced back to the factorized nature of the Born-Oppenheimer initial and final photoemission states and also persists when either only initial, or final states are replaced by correlated vibronic states. Only when correlated initial and final vibronic states are taken into account, the spurious spectral weights of the Born-Oppenheimer approximation are suppressed. In the non-equilibrium case, we illustrate for an initial Franck-Condon excitation and an explicit pump-pulse excitation how the vibronic wavepacket motion of the system can be traced in the time-resolved photoelectron spectra as function of the pump-probe delay

How honeybees defy gravity with royal jelly to raise queens

The female sex in honeybees (Apis spp.) comprises a reproductive queen and a sterile worker caste. Nurse bees feed all larvae progressively with a caste-specific food jelly until the prepupal stage. Only those larvae that are exclusively fed a large amount of royal jelly (RJ) develop into queens [1]. RJ is a composite secretion of two specialized head glands: the mandibular glands, which produce mainly fatty acids [2], and the hypopharyngeal glands, which contribute proteins, primarily belonging to the major royal jelly protein (MRJP) family [3]. Past research on RJ has focused on its nutritional function and overlooked its central role with regard to the orientation of the larva in the royal brood cell. Whereas workers are reared in the regular horizontal cells of the comb, the queen cells are specifically built outside of the normal comb area to accommodate for the larger queen [4, 5]. These cells hang freely along the bottom of the comb and are vertically oriented, opening downward [6]. Queen larvae are attached by their RJ diet to the cell ceiling. Thus, the physical properties of RJ are central to successful retention of larvae in the cell. Here, we show that the main protein of RJ (MRJP1) polymerizes in complex with another protein, apisimin, into long fibrous structures that build the basis for the high viscosity of RJ to hold queen larvae on the RJ surface.Document S1. Figures S1–S4 and Table S1.Data S1. Mass Spectrometric Identification of OligoMRJP1, MonoMRJP1, and Apisimin, Related to Figure 1.The German Research Foundation (Deutsche Forschungsgemeinschaft - DFG, grant MO 373/32-1 to R.F.A.M.) and an ERASMUS + exchange program grant to C.I.M.http://www.sciencedirect.com/science/journal/09609822am2018Zoology and Entomolog

Comparative study of an Eden model for the irreversible growth of spins and the equilibrium Ising model

The Magnetic Eden Model (MEM) with ferromagnetic interactions between nearest-neighbor spins is studied in $(d+1)-$dimensional rectangular geometries for $d = 1,2$. In the MEM, magnetic clusters are grown by adding spins at the boundaries of the clusters. The orientation of the added spins depends on both the energetic interaction with already deposited spins and the temperature, through a Boltzmann factor. A numerical Monte Carlo investigation of the MEM has been performed and the results of the simulations have been analyzed using finite-size scaling arguments. As in the case of the Ising model, the MEM in $d = 1$ is non-critical (only exhibits an ordered phase at $T= 0$). In $d = 2$ the MEM exhibits an order-disorder transition of second-order at a finite temperature. Such transition has been characterized in detail and the relevant critical exponents have been determined. These exponents are in agreement (within error bars) with those of the Ising model in 2 dimensions. Further similarities between both models have been found by evaluating the probability distribution of the order parameter, the magnetization and the susceptibility. Results obtained by means of extensive computer simulations allow us to put forward a conjecture which establishes a nontrivial correspondence between the MEM for the irreversible growth of spins and the equilibrium Ising model. This conjecture is certainly a theoretical challenge and its confirmation will contribute to the development of a framework for the study of irreversible growth processes.Comment: 21 pages, 11 figure

Magnetoresistance through a single molecule

The use of single molecules to design electronic devices is an extremely challenging and fundamentally different approach to further downsizing electronic circuits. Two-terminal molecular devices such as diodes were first predicted [1] and, more recently, measured experimentally [2]. The addition of a gate then enabled the study of molecular transistors [3-5]. In general terms, in order to increase data processing capabilities, one may not only consider the electron's charge but also its spin [6,7]. This concept has been pioneered in giant magnetoresistance (GMR) junctions that consist of thin metallic films [8,9]. Spin transport across molecules, i.e. Molecular Spintronics remains, however, a challenging endeavor. As an important first step in this field, we have performed an experimental and theoretical study on spin transport across a molecular GMR junction consisting of two ferromagnetic electrodes bridged by a single hydrogen phthalocyanine (H2Pc) molecule. We observe that even though H2Pc in itself is nonmagnetic, incorporating it into a molecular junction can enhance the magnetoresistance by one order of magnitude to 52%.Comment: To appear in Nature Nanotechnology. Present version is the first submission to Nature Nanotechnology, from May 18th, 201

Combining scanning probe microscopy and x-ray spectroscopy

A new versatile tool, combining Shear Force Microscopy and X-Ray Spectroscopy was designed and constructed to obtain simultaneously surface topography and chemical mapping. Using a sharp optical fiber as microscope probe, it is possible to collect locally the visible luminescence of the sample. Results of tests on ZnO and on ZnWO4 thin layers are in perfect agreement with that obtained with other conventional techniques. Twin images obtained by simultaneous acquisition in near field of surface topography and of local visible light emitted by the sample under X-Ray irradiation in synchrotron environment are shown. Replacing the optical fibre by an X-ray capillary, it is possible to collect local X-ray fluorescence of the sample. Preliminary results on Co-Ti sample analysis are presented

A call for public archives for biological image data

Public data archives are the backbone of modern biological and biomedical research. While archives for biological molecules and structures are well-established, resources for imaging data do not yet cover the full range of spatial and temporal scales or application domains used by the scientific community. In the last few years, the technical barriers to building such resources have been solved and the first examples of scientific outputs from public image data resources, often through linkage to existing molecular resources, have been published. Using the successes of existing biomolecular resources as a guide, we present the rationale and principles for the construction of image data archives and databases that will be the foundation of the next revolution in biological and biomedical informatics and discovery.Comment: 13 pages, 1 figur