EPJ Special Topics (EPJ ST)

Open Access

Editorial

Particle methods in natural science and engineering p. 1493

Christian Holm, Thomas Ertl, Siegfried Schmauder, Johannes Kästner and Joachim Gross

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-900008-2

Fully implicit time integration in truly incompressible SPH p. 1501

Manuel Hopp-Hirschler and Ulrich Nieken

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800152-6

Developing coarse-grained models for agglomerate growth p. 1515

Milena Smiljanic, Rudolf Weeber, Dirk Pflüger, Christian Holm and Andreas Kronenburg

Published online: 08 March 2019

DOI: 10.1140/epjst/e2018-800177-y

On the use of transport properties to discriminate Mie-type molecular models for 1-propanol optimized against VLE data p. 1529

Jörg Baz, Niels Hansen and Joachim Gross

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800178-4

Studying equilibria of polymers in solution by direct molecular dynamics simulations: poly(N-isopropylacrylamide) in water as a test case p. 1547

Edder J. García and Hans Hasse

Published online: 08 March 2019

DOI: 10.1140/epjst/e2018-800171-y

Precipitation, planar defects and dislocations in alloys: Simulations on Ni₃Si and Ni₃Al precipitates p. 1559

Stephen Hocker, Hansjörg Lipp and Siegfried Schmauder

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800154-6

A wide-range modeling approach for the thermal conductivity and dielectric function of solid and liquid aluminum p. 1575

Eugen Eisfeldeugen, Hans-Rainer Trebin and Johannes Roth

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800165-5

Vacancy defect centers in diamond: influence of surface termination p. 1591

Jens Hertkorn, Jörg Wrachtrup and Maria Fyta

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800190-2

High-order Particle-In-Cell simulations of laser-plasma interaction p. 1603

Stephen M. Copplestone, Marcel Pfeiffer, Stefanos Fasoulas and Claus-Dieter Munz

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800160-y

Performance of state-of-the-art force fields for atomistic simulations of silicon at high electronic temperatures p. 1615

Bernd Bauerhenne and Martin E. Garcia

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800181-3

Molecular simulations of enzymes under non-natural conditions p. 1631

Valerio Ferrario and Jürgen Pleiss

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800174-4

Modeling the current modulation of dsDNA in nanopores – from mean-field to atomistic and back p. 1639

Florian Weik, Kai Szuttor, Jonas Landsgesell and Christian Holm

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800189-3

Copper coordination in formylglycine generating enzymes p. 1657

Sonia Álvarez-Barcia and Johannes Kästner

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800149-7

Unfolding of DNA by co-solutes: insights from Kirkwood–Buff integrals and transfer free energies p. 1665

Ewa Anna Oprzeska-Zingrebe, Miriam Kohagen, Johannes Kästner and Jens Smiatek

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800163-5

Diamondoid-functionalized nanogaps: from small molecules to electronic biosensing p. 1681

Frank C. Maier, Chandra S. Sarap, Maofeng Dou, Ganesh Sivaraman and Maria Fyta

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800157-0

Dynamics of the full-length yeast Hsp90 dimer p. 1693

Florian Kandzia and Martin Zacharias

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800164-y

A decade of particle-based scientific visualization p. 1705

Guido Reina, Patrick Gralka and Thomas Ertl

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800172-4

Interactive visualization of biomolecules’ dynamic and complex properties - State of the art and project review p. 1725

Karsten Schatz, Michael Krone, Jürgen Pleiss and Thomas Ertl

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800162-y

Multivariate visualization of particle data p. 1741

Liang Zhou and Daniel Weiskopf

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800158-6

Adaptive grid implementation for parallel continuum mechanics methods in particle simulations p. 1757

Miriam Mehl and Michael Lahnert

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800161-5

Enabling unstructured domain decompositions for inhomogeneous short-range molecular dynamics in ESPResSo p. 1779

Steffen Hirschmann, Colin W. Glass and Dirk Pflüger

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800159-0

ESPResSo 4.0 – an extensible software package for simulating soft matter systems p. 1789

Florian Weik, Rudolf Weeber, Kai Szuttor, Konrad Breitsprecher, Joost de Graaf, Michael Kuron, Jonas Landsgesell, Henri Menke, David Sean and Christian Holm

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800186-9

MegaMol – a comprehensive prototyping framework for visualizations p. 1817

Patrick Gralka, Michael Becher, Matthias Braun, Florian Frieß, Christoph Müller, Tobias Rau, Karsten Schatz, Christoph Schulz, Michael Krone, Guido Reina and Thomas Ertl

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800167-5

IMD – the ITAP molecular dynamics simulation package p. 1831

Johannes Roth, Eugen Eisfeld, Dominic Klein, Stephen Hocker, Hansjörg Lipp and Hans-Rainer Trebin

Published online: 08 March 2019

DOI: 10.1140/epjst/e2019-800147-7

EPJ

European Physical Journal - Special Topics

Volume 227 / No 14 (2019)

Particle Methods in Natural Science and Engineering

Particle Methods in Natural Science and Engineering

Particle methods in natural science and engineering p. 1493

Fully implicit time integration in truly incompressible SPH p. 1501

Developing coarse-grained models for agglomerate growth p. 1515

On the use of transport properties to discriminate Mie-type molecular models for 1-propanol optimized against VLE data p. 1529

Studying equilibria of polymers in solution by direct molecular dynamics simulations: poly(N-isopropylacrylamide) in water as a test case p. 1547

Precipitation, planar defects and dislocations in alloys: Simulations on Ni₃Si and Ni₃Al precipitates p. 1559

A wide-range modeling approach for the thermal conductivity and dielectric function of solid and liquid aluminum p. 1575

Vacancy defect centers in diamond: influence of surface termination p. 1591

High-order Particle-In-Cell simulations of laser-plasma interaction p. 1603

Performance of state-of-the-art force fields for atomistic simulations of silicon at high electronic temperatures p. 1615

Molecular simulations of enzymes under non-natural conditions p. 1631

Modeling the current modulation of dsDNA in nanopores – from mean-field to atomistic and back p. 1639

Copper coordination in formylglycine generating enzymes p. 1657

Unfolding of DNA by co-solutes: insights from Kirkwood–Buff integrals and transfer free energies p. 1665

Diamondoid-functionalized nanogaps: from small molecules to electronic biosensing p. 1681

Dynamics of the full-length yeast Hsp90 dimer p. 1693

A decade of particle-based scientific visualization p. 1705

Interactive visualization of biomolecules’ dynamic and complex properties - State of the art and project review p. 1725

Multivariate visualization of particle data p. 1741

Adaptive grid implementation for parallel continuum mechanics methods in particle simulations p. 1757

Enabling unstructured domain decompositions for inhomogeneous short-range molecular dynamics in ESPResSo p. 1779

ESPResSo 4.0 – an extensible software package for simulating soft matter systems p. 1789

MegaMol – a comprehensive prototyping framework for visualizations p. 1817

IMD – the ITAP molecular dynamics simulation package p. 1831

Conference announcements

EPJ

European Physical Journal - Special Topics

Volume 227 / No 14 (2019)

Particle Methods in Natural Science and Engineering

Particle Methods in Natural Science and Engineering

Particle methods in natural science and engineering p. 1493

Fully implicit time integration in truly incompressible SPH p. 1501

Developing coarse-grained models for agglomerate growth p. 1515

On the use of transport properties to discriminate Mie-type molecular models for 1-propanol optimized against VLE data p. 1529

Studying equilibria of polymers in solution by direct molecular dynamics simulations: poly(N-isopropylacrylamide) in water as a test case p. 1547

Precipitation, planar defects and dislocations in alloys: Simulations on Ni3Si and Ni3Al precipitates p. 1559

A wide-range modeling approach for the thermal conductivity and dielectric function of solid and liquid aluminum p. 1575

Vacancy defect centers in diamond: influence of surface termination p. 1591

High-order Particle-In-Cell simulations of laser-plasma interaction p. 1603

Performance of state-of-the-art force fields for atomistic simulations of silicon at high electronic temperatures p. 1615

Molecular simulations of enzymes under non-natural conditions p. 1631

Modeling the current modulation of dsDNA in nanopores – from mean-field to atomistic and back p. 1639

Copper coordination in formylglycine generating enzymes p. 1657

Unfolding of DNA by co-solutes: insights from Kirkwood–Buff integrals and transfer free energies p. 1665

Diamondoid-functionalized nanogaps: from small molecules to electronic biosensing p. 1681

Dynamics of the full-length yeast Hsp90 dimer p. 1693

A decade of particle-based scientific visualization p. 1705

Interactive visualization of biomolecules’ dynamic and complex properties - State of the art and project review p. 1725

Multivariate visualization of particle data p. 1741

Adaptive grid implementation for parallel continuum mechanics methods in particle simulations p. 1757

Enabling unstructured domain decompositions for inhomogeneous short-range molecular dynamics in ESPResSo p. 1779

ESPResSo 4.0 – an extensible software package for simulating soft matter systems p. 1789

MegaMol – a comprehensive prototyping framework for visualizations p. 1817

IMD – the ITAP molecular dynamics simulation package p. 1831

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Conference announcements

Precipitation, planar defects and dislocations in alloys: Simulations on Ni₃Si and Ni₃Al precipitates p. 1559