Vivern a virtual environment for multiscale visualization and modeling of DNA nanostructures

DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design of such structures. However, as such structures are often spatially complex, their assembly and analysis are complicated. Since virtual reality (VR) was proven to be advantageous for such spatial-related tasks and there are no existing VR solutions focused on this domain, we propose Vivern, a VR application that allows domain experts to design and visually examine DNA origami nanostructures. Our approach presents different abstracted visual representations of the nanostructures, various color schemes, and an ability to place several DNA nanostructures and proteins in one environment, thus allowing for the detailed analysis of complex assemblies. We also present two novel examination tools, the Magic Scale Lens and the DNA Untwister, that allow the experts to visually embed different representations into local regions to preserve the context and support detailed investigation. To showcase the capabilities of our solution, prototypes of novel nanodevices conceptualized by our collaborating experts, such as DNA-protein hybrid structures and DNA origami superstructures, are presented. Finally, the results of two rounds of evaluations are summarized. They demonstrate the advantages of our solution, especially for scenarios where current desktop tools are very limited, while also presenting possible future research directions.Fil: Kutak, David. Masaryk University; República ChecaFil: Selzer, Matias Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingenieria de la Computacion. Laboratorio de Investigación y Desarrollo en Visualización yComputación Gráfica; ArgentinaFil: Byska, Jan. Masaryk University; República ChecaFil: Ganuza, María Luján. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingenieria de la Computacion. Laboratorio de Investigación y Desarrollo en Visualización yComputación Gráfica; ArgentinaFil: Barisic, Ivan. Austrian Institute of Technology; AustriaFil: Kozlikova, Barbora. Masaryk University; República ChecaFil: Miao, Haichao. Austrian Institute of Technology; Austri

Predictions for cold nuclear matter effects in p plus Pb collisions at root SNN =8.16 TeV

Predictions for cold nuclear matter effects on charged hadrons, identified light hadrons, quarkonium and heavy flavor hadrons, Drell-Yan dileptons, jets, photons, gauge bosons and top quark pairs produced in p+Pb collisions at, root S-NN = 8.16 TeV are compiled and, where possible, compared to each other. Predictions of the normalized ratios of p+Pb to p+ p cross sections are also presented for most of the observables, providing new insights into the expected role of cold nuclear matter effects. In particular, the role of nuclear parson distribution functions on particle production can now be probed over a wider range of phase space than ever before. (C) 2018 Elsevier B.V. All rights reserved.Peer reviewe

Novel tools and observables for jet physics in heavy-ion collisions

Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute "Novel tools and observables for jet physics in heavy-ion collisions" in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms

Novel tools and observables for jet physics in heavy-ion collisions

Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute 'Novel tools and observables for jet physics in heavy-ion collisions' in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms

Novel tools and observables for jet physics in heavy-ion collisions

Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute "Novel tools and observables for jet physics in heavy-ion collisions" in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms.Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute ‘Novel tools and observables for jet physics in heavy-ion collisions’ in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms.Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute 'Novel tools and observables for jet physics in heavy-ion collisions' in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms

Novel tools and observables for jet physics in heavy-ion collisions

© 2020 IOP Publishing Ltd. Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute 'Novel tools and observables for jet physics in heavy-ion collisions' in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms