2019

Baz, J ; Held, C ; Pleiss, Jürgen ; Hansen, N: Thermophysical properties of glyceline-water mixtures investigated by molecular modelling. In: Physical Chemistry Chemical Physics, Physical Chemistry Chemical Physics. Bd. 21 (2019), S. 6467–6476
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@article{Baz2019, author = {Baz, J and Held, C and Pleiss, Jürgen and Hansen, N}, itb_ag = {pleiss}, journal = {Physical Chemistry Chemical Physics}, orcid = {0000-0003-1045-8202}, pages = {6467 - 6476}, staffids = {2660}, title = {Thermophysical properties of glyceline-water mixtures investigated by molecular modelling.}, volume = 21, year = 2019 }
Gralka, Patrick ; Becher, Michael ; Braun, Matthias ; Frieß, Florian ; Müller, Christoph ; Rau, Tobias ; Schatz, Karsten ; Schulz, Christoph ; u. a.: MegaMol -- a comprehensive prototyping framework for visualizations. In: The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1817--1829
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@article{Gralka2019Megamol, abstract = {We present MegaMol, a low-overhead prototyping framework for interactive visualization of large scientific data sets. We give a brief summary of related work for context and then focus on a comprehensive overview of the core architecture of the framework. This is followed by the existing and novel features and techniques in MegaMol that define its current functionality. MegaMol has originally been developed to support the visualization and analysis of particle-based data sets that, for instance, come from molecular dynamics simulations. Meanwhile, the software has evolved beyond that. New algorithms and techniques have been implemented to handle many diverse tasks, including information visualization. Additionally, improvements have been made on the software engineering side to make MegaMol more accessible for domain scientists, like an easy-to-handle scripting interface.}, author = {Gralka, Patrick and Becher, Michael and Braun, Matthias and Frieß, Florian and Müller, Christoph and Rau, Tobias and Schatz, Karsten and Schulz, Christoph and Krone, Michael and Reina, Guido and Ertl, Thomas}, doi = {10.1140/epjst/e2019-800167-5}, issn = {1951-6401}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1817--1829}, title = {MegaMol -- a comprehensive prototyping framework for visualizations}, url = {https://doi.org/10.1140/epjst/e2019-800167-5}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
Link
https://doi.org/10.1140/epjst/e2019-800167-5
Hirschmann, S. ; Glass, C. W. ; Pflüger, D.: Enabling Unstructured Domain Decompositions for Inhomogeneous Short-Range Molecular Dynamics in ESPResSo. Particle Methods in Natural Science and Engineering. In: Holm, C. ; Ertl, T. ; Schmauder, S. ; Kästner, J. ; Groß, J. (Hrsg.) The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1779–1788
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@article{hirschmann2019enabling, author = {Hirschmann, S. and Glass, C. W. and Pflüger, D.}, editor = {Holm, C. and Ertl, T. and Schmauder, S. and Kästner, J. and Groß, J.}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1779-1788}, title = {Enabling Unstructured Domain Decompositions for Inhomogeneous Short-Range Molecular Dynamics in ESPResSo. Particle Methods in Natural Science and Engineering.}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
Maier, F. C. ; Fyta, M.: Influence of dynamics on the conductance across functionalized electrodes for biodetection. (2019)
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@article{maier2019influence, author = {Maier, F. C. and Fyta, M.}, title = {Influence of dynamics on the conductance across functionalized electrodes for biodetection.}, year = 2019 }
Maier, F. C. ; Sarap, C. S. ; Dou, M. ; Sivaraman, G. ; Fyta, M.: Diamondoid-functionalized nanogaps: From small molecules to electronic biosensing. In: Holm, C. ; Ertl, T. ; Schmauder, S. ; Kästner, J. ; Groß, J. (Hrsg.) The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019b), Nr. 14, S. 1681--1692
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@article{maier2019diamondoidfunctionalized, author = {Maier, F. C. and Sarap, C. S. and Dou, M. and Sivaraman, G. and Fyta, M.}, editor = {Holm, C. and Ertl, T. and Schmauder, S. and Kästner, J. and Groß, J.}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1681--1692}, title = {Diamondoid-functionalized nanogaps: From small molecules to electronic biosensing.}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
Maier, F. C. ; Dou, M. ; Fyta, M.: Solvent effects in the transmission across diamondoid-functionalized gaps reading-out DANN. (2019a)
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@article{maier2019solvent, author = {Maier, F. C. and Dou, M. and Fyta, M.}, title = {Solvent effects in the transmission across diamondoid-functionalized gaps reading-out DANN.}, year = 2019 }
Oprzeska-Zingrebe, Ewa Anna ; Kohagen, Miriam ; Kästner, Johannes ; Smiatek, Jens: Unfolding of DNA by co-solutes: insights from Kirkwood--Buff integrals and transfer free energies. In: Holm, C. ; Ertl, T. ; Schmauder, S. ; Kästner, J. ; Groß, J. (Hrsg.) The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1665--1679
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@article{Oprzeska-Zingrebe2019, abstract = {Many organic co-solutes are known to stabilize or to destabilize native structures of proteins or DNA. Most of these effects can be explained by co-solute binding or exclusion mechanisms. A beneficial approach to study the underlying principles relies on the computation of Kirkwood--Buff integrals, which can be also used to derive detailed expressions for transfer free energies and changes of the chemical equilibrium between the unfolded and the native states. In this article, we use the framework of Kirkwood--Buff theory in order to study the influence of ectoine on the stability of short DNA hairpins. Our results highlight a strong binding of ectoine, which reveals a pronounced destabilization of DNA in good agreement with experimental findings.}, author = {Oprzeska-Zingrebe, Ewa Anna and Kohagen, Miriam and K{\"a}stner, Johannes and Smiatek, Jens}, doi = {10.1140/epjst/e2019-800163-5}, editor = {Holm, C. and Ertl, T. and Schmauder, S. and Kästner, J. and Groß, J.}, issn = {1951-6401}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1665--1679}, title = {Unfolding of DNA by co-solutes: insights from Kirkwood--Buff integrals and transfer free energies.}, url = {https://doi.org/10.1140/epjst/e2019-800163-5}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
Link
https://doi.org/10.1140/epjst/e2019-800163-5
Reina, Guido ; Gralka, Patrick ; Ertl, Thomas: A decade of particle-based scientific visualization. In: Holm, C. ; Ertl, T. ; Schmauder, S. ; Kästner, J. ; Groß, J. (Hrsg.) The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1705--1723
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@article{Reina2019Scivis, abstract = {In this manuscript, we review the evolution of atomistic visualization over the last 12 years and put the development of the community in context with our own efforts within the DFG collaborative research center 716. The goal is to provide a comprehensive summary of all relevant work that has been conducted under the auspices of project D.3. In this project, we focused on the visualization and analysis of particle-based data sets, and on how to bring these visualizations onto the workstation of domain scientists without the need for a large rendering infrastructure. We discuss how our decisions and goals evolved over time and show the success stories and publications. Finally, we give an outlook on the challenges that still require additional research and to which extent the requirements and constraints of current research have changed the way visualization works after these 12 years.}, author = {Reina, Guido and Gralka, Patrick and Ertl, Thomas}, doi = {10.1140/epjst/e2019-800172-4}, editor = {Holm, C. and Ertl, T. and Schmauder, S. and Kästner, J. and Groß, J.}, issn = {1951-6401}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1705--1723}, title = {A decade of particle-based scientific visualization}, url = {https://doi.org/10.1140/epjst/e2019-800172-4}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
Link
https://doi.org/10.1140/epjst/e2019-800172-4
Schatz, Karsten ; Krone, Michael ; Pleiss, Jürgen ; Ertl, Thomas: Interactive visualization of biomolecules’ dynamic and complex properties. In: Holm, C. ; Ertl, T. ; Schmauder, S. ; Kästner, J. ; Groß, J. (Hrsg.) The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1725--1739
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@article{schatz2019interactive, abstract = {In this paper, we review the advances in molecular visualization over the last 12 years and put the development of the community in context with our own efforts in the DFG Collaborative Research Center (CRC) 716. This includes advances in the field of molecular surface computation and rendering, interactive extraction of protein cavities, and comparative visualization for biomolecules. Our main focus was on the development of methods that assist the interactive and explorative visual analysis of large, dynamic molecular data sets on single desktop computers. To meet this goal, we often developed GPU-accelerated algorithms, which is in line with the general research direction of the field. Over the last years, we made seminal contributions to the field of molecular visualization, which partially still constitute the state of the art development or provided the basis for follow-up works}, author = {Schatz, Karsten and Krone, Michael and Pleiss, Jürgen and Ertl, Thomas}, doi = {https://doi.org/10.1140/epjst/e2019-800162-y}, editor = {Holm, C. and Ertl, T. and Schmauder, S. and Kästner, J. and Groß, J.}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1725--1739}, title = {Interactive visualization of biomolecules' dynamic and complex properties}, url = {https://epjst.epj.org/articles/epjst/abs/2019/02/epjst1800162/epjst1800162.html}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
Link
https://epjst.epj.org/articles/epjst/abs/2019/02/epjst1800162/epjst1800162.html
Zhou, Liang ; Weiskopf, Daniel: Multivariate Visualization of Particle Data. In: The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019), Nr. 14, S. 1741--1756
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@article{zhou2019multivariate, author = {Zhou, Liang and Weiskopf, Daniel}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1741--1756}, title = {Multivariate Visualization of Particle Data.}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }

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