Widefield phototransient imaging for visualizing 3D motion of resonant particles in scattering environments

: Identifying, visualising and ultimately tracking dynamically moving non-fluorescent nanoparticles in the presence of non-specific scattering is a long-standing challenge across the nano- and life-sciences. In this work we demonstrate that our recently developed ultrafast holographic transient (UHT) microscope is ideally suited for meeting this challenge. We show that UHT microscopy allows reliably distinguishing off-resonant, dielectric, from resonant, metallic, nanoparticles, based on the phototransient signal: a pre-requisite for single-particle tracking in scattering environments. We then demonstrate the capability of UHT microscopy to holographically localize in 3D single particles over large volumes of view. Ultimately, we combine the two concepts to simultaneously track several tens of freely diffusing gold nanoparticles, within a 110 × 110 × 110 μm volume of view at an integration time of 10 ms per frame, while simultaneously recording their phototransient signals. The combined experimental concepts outlined and validated in this work lay the foundation for background-free 3D single-particle tracking applications or spectroscopy in scattering environments and are immediately applicable to systems as diverse as live cells and tissues or supported heterogeneous catalysts

Michigan molecular interactions r2: from interacting proteins to pathways

Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. This article describes the resulting MiMI Release 2 (MiMIr2). New functionality includes extension from proteins to genes and to pathways; identification of highlighted sentences in source publications; seamless two-way linkage with Cytoscape; query facilities based on MeSH/GO terms and other concepts; approximate graph matching to find relevant pathways; support for querying in bulk; and a user focus-group driven interface design. MiMI is part of the NIH's; National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: http://mimi.ncibi.org

The nature of singlet exciton fission in carotenoid aggregates.

Singlet exciton fission allows the fast and efficient generation of two spin triplet states from one photoexcited singlet. It has the potential to improve organic photovoltaics, enabling efficient coupling to the blue to ultraviolet region of the solar spectrum to capture the energy generally lost as waste heat. However, many questions remain about the underlying fission mechanism. The relation between intermolecular geometry and singlet fission rate and yield is poorly understood and remains one of the most significant barriers to the design of new singlet fission sensitizers. Here we explore the structure-property relationship and examine the mechanism of singlet fission in aggregates of astaxanthin, a small polyene. We isolate five distinct supramolecular structures of astaxanthin generated through self-assembly in solution. Each is capable of undergoing intermolecular singlet fission, with rates of triplet generation and annihilation that can be correlated with intermolecular coupling strength. In contrast with the conventional model of singlet fission in linear molecules, we demonstrate that no intermediate states are involved in the triplet formation: instead, singlet fission occurs directly from the initial 1B(u) photoexcited state on ultrafast time scales. This result demands a re-evaluation of current theories of polyene photophysics and highlights the robustness of carotenoid singlet fission.This work was supported by the EPSRC (UK) (EP/G060738/ 1), the European Community (LASERLAB-EUROPE, grant agreement no. 284464, EC’s Seventh Framework Programme; and Marie-Curie ITN-SUPERIOR, PITN-GA-2009-238177), and the Winton Programme for the Physics of Sustainability. G.C. acknowledges support by the European Research Council Advanced Grant STRATUS (ERC-2011-AdG No. 291198). J.C. acknowledges support by the Royal Society Dorothy Hodgkin Fellowship and The University of Sheffield’s Vice- Chancellor’s Fellowship scheme.This is the final published version. It was first made available by ACS at http://pubs.acs.org/doi/abs/10.1021/jacs.5b01130

Imaging the boundaries—innovative tools for microscopy of living cells and real-time imaging

Recently, light microscopy moved back into the spotlight, which is mainly due to the development of revolutionary technologies for imaging real-time events in living cells. It is truly fascinating to see enzymes “at work” and optically acquired images certainly help us to understand biological processes better than any abstract measurements. This review aims to point out elegant examples of recent cell-biological imaging applications that have been developed with a chemical approach. The discussed technologies include nanoscale fluorescence microscopy, imaging of model membranes, automated high-throughput microscopy control and analysis, and fluorescent probes with a special focus on visualizing enzyme activity, free radicals, and protein–protein interaction designed for use in living cells

Ready for Prime Time, - Yes, Industrial-Grade Modelling Tools can be Used in Education

It has been stated that industrial-grade modelling tools are unsuit- able for teaching modelling. In this paper, we present our experience with a university course on software modelling. In the first year of the course, we used a commercial modelling tool, in the second year the open- source alternative Papyrus. Both tools are considered to be of industrial grade and used in industry. Our quantitative analysis shows that the industrial-grade modelling tools with all their complexity did not have a negative impact on the students’ experience of modelling. This shows that industrial-grade modelling tools can be used in the classroom. We analyse why our experience differs from published accounts and conclude that the availability of a tool champion and tailored instruction mate- rial is key. From this, we derive recommendations for teacher support from tool-providers (vendors and open source), research directions for researchers and teachers, and for training efforts in the industry