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Fréchet differentiability of molecular distribution functions II: the Ursell function
Martin Hanke
Letters in Mathematical Physics108 (2),307-329 (2017);

Fréchet differentiability of molecular distribution functions I. $$L^\infty $$ L ∞ analysis
Martin Hanke
Letters in Mathematical Physics108 (2),285-306 (2017);

Well-Posedness of the Iterative Boltzmann Inversion
Martin Hanke
Journal of Statistical Physics170 (3),536-553 (2017);

A unique juxtaglomerular apparatus in the river ray, Potamotrygon humerosa, a freshwater stingray
E. R. Lacy, E. Reale
Zoomorphology137 (1),155-164 (2017);

Energy-Stable Numerical Schemes for Multiscale Simulations of Polymer–Solvent Mixtures
Mária Lukáčová-Medvid’ová, Burkhard Dünweg, Paul Strasser, Nikita Tretyakov
in Mathematical Analysis of Continuum Mechanics and Industrial Applications II, Mathematics for Industry,Pages153-165,Springer Singapore (2017);

Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles
Santosh Kumar Meena, Claire Goldmann, Douga Nassoko, Mahamadou Seydou, Thomas Marchandier, Simona Moldovan, Ovidiu Ersen, François Ribot, Corinne Chanéac, Clément Sanchez, David Portehault, Frederik Tielens, Marialore Sulpizi
ACS Nano11 (7),7371-7381 (2017);

Numerical analysis of the Oseen-type Peterlin viscoelastic model by the stabilized Lagrange-Galerkin method. Part I: a nonlinear scheme
Lukáčová-Medviďová, M.; Mizerová, H.; Notsu, H.; Tabata, M.
ESAIM Math. Model. Numer. Anal. 51 (5),1637–1661. (2017);
URL: https://www.esaim-m2an.org/

We present a nonlinear stabilized Lagrange–Galerkin scheme for the Oseen-type Peterlin viscoelastic model. Our scheme is a combination of the method of characteristics and Brezzi Pitkäranta’s stabilization method for the conforming linear elements, which yields an efficient computation with a small number of degrees of freedom. We prove error estimates with the optimal convergence order without any relation between the time increment and the mesh size. The result is valid for both the diffusive and non-diffusive models for the conformation tensor in two space dimensions. We introduce an additional term that yields a suitable structural property and allows us to obtain required energy estimate. The theoretical convergence orders are confirmed by numerical experiments. In a forthcoming paper, Part II, a linear scheme is proposed and the corresponding error estimates are proved in two and three space dimensions for the diffusive model.

Effects of Silica Surfaces on the Structure and Dynamics of Room-Temperature Ionic Liquids: A Molecular Dynamics Simulation Study
Tamisra Pal, Constantin Beck, Dominik Lessnich, Michael Vogel
The Journal of Physical Chemistry C122 (1),624-634 (2017);

Force probe simulations using a hybrid scheme with virtual sites
Ken Schäfer, Marco Oestereich, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics147 (13),134909 (2017);

Implicit-explicit and explicit projection schemes for the unsteady incompressible Navier–Stokes equations using a high-order dG method
Nehzat Emamy, Florian Kummer, Markus Mrosek, Martin Karcher, Martin Oberlack
Computers & Fluids154,285-295 (2017);

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats
S. Stalter, L. Yelash, N. Emamy, A. Statt, M. Hanke, M. Lukáčová-Medvid’ová, P. Virnau
Computer Physics Communications, (2017);

Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles
Hamed Sharifi Dehsari, Maziar Heidari, Anielen Halda Ribeiro, Wolfgang Tremel, Gerhard Jakob, Davide Donadio, Raffaello Potestio, Kamal Asadi
Chemistry of Materials29 (22),9648-9656 (2017);

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Horacio V. Guzman, Christoph Junghans, Kurt Kremer, Torsten Stuehn
Physical Review E96 (5), (2017);

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales
Biswaroop Mukherjee, Christine Peter, Kurt Kremer
The Journal of Chemical Physics147 (11),114501 (2017);

Conditional Reversible Work Coarse-Grained Models of Molecular Liquids with Coulomb Electrostatics – A Proof of Concept Study on Weakly Polar Organic Molecules
Gregor Deichmann, Nico F. A. van der Vegt
Journal of Chemical Theory and Computation13 (12),6158-6166 (2017);

Evaluation of mapping schemes for systematic coarse graining of higher alkanes
Marco Dallavalle, Nico F. A. van der Vegt
Physical Chemistry Chemical Physics19 (34),23034-23042 (2017);

Flow properties and hydrodynamic interactions of rigid spherical microswimmers
Tapan Chandra Adhyapak, Sara Jabbari-Farouji
Physical Review E96 (5), (2017);

The Hydrophobic Effect and the Role of Cosolvents
Nico F. A. van der Vegt, Divya Nayar
The Journal of Physical Chemistry B121 (43),9986-9998 (2017);

Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry
Divya Nayar, Angelina Folberth, Nico F. A. van der Vegt
Physical Chemistry Chemical Physics19 (28),18156-18161 (2017);

Free-energy barriers for crystal nucleation from fluid phases
Peter Koß, Antonia Statt, Peter Virnau, Kurt Binder
Physical Review E96 (4), (2017);

Frequency-dependent hydrodynamic interaction between two solid spheres
Gerhard Jung, Friederike Schmid
Physics of Fluids29 (12),126101 (2017);

Dynamic Density Functional Theories for Inhomogeneous Polymer Systems Compared to Brownian Dynamics Simulations
Shuanhu Qi, Friederike Schmid
Macromolecules50 (24),9831-9845 (2017);

Fréchet differentiability of molecular distribution functions I. $$L^\infty $$ L ∞ analysis
Martin Hanke
Letters in Mathematical Physics108 (2),285-306 (2017);

Anomalous critical slowdown at a first order phase transition in single polymer chains
Shuangshuang Zhang, Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Dadong Yan, Friederike Schmid
The Journal of Chemical Physics147 (6),064902 (2017);

Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory
Shuanhu Qi, Friederike Schmid
Soft Matter13 (43),7938-7947 (2017);

Communication: Is a coarse-grained model for water sufficient to compute Kapitza conductance on non-polar surfaces?
Vikram Reddy Ardham, Frédéric Leroy
The Journal of Chemical Physics147 (15),151102 (2017);
URL: http://aip.scitation.org/doi/10.1063/1.5003199

Coarse-grained models have increasingly been used in large-scale particle-based simulations. However, due to their lack of degrees of freedom, it is a priori unlikely that they straightforwardly represent thermal properties with the same accuracy as their atomistic counterparts. We take a first step in addressing the impact of liquid coarse-graining on interfacial heat conduction by showing that an atomistic and a coarse-grained model of water may yield similar values of the Kapitza conductance on few-layer graphene with interactions ranging from hydrophobic to mildly hydrophilic. By design the water models employed yield similar liquid layer structures on the graphene surfaces. Moreover, they share common vibration properties close to the surfaces and thus couple with the vibrations of graphene in a similar way. These common properties explain why they yield similar Kapitza conductance values despite their bulk thermal conductivity differing by more than a factor of two.

Well-Posedness of the Iterative Boltzmann Inversion
Martin Hanke
Journal of Statistical Physics170 (3),536-553 (2017);

An inverse problem in statistical mechanics
Martin Hanke
in Oberwolfach Reports,Editor:Gerhard Huisken,ChapterReport No. 08/2017,EMS,Zürich,Series:Oberwolfach Reports, Vol.14 (2017);

Simulating copolymeric nanoparticle assembly in the co-solvent method: How mixing rates control final particle sizes and morphologies
Simon Keßler, Klaus Drese, Friederike Schmid
Polymer126,9-18 (2017);

Phase behavior of active Brownian disks, spheres, and dimers
Jonathan Tammo Siebert, Janina Letz, Thomas Speck, Peter Virnau
Soft Matter13 (5),1020-1026 (2017);

An improved dissipative coupling scheme for a system of Molecular Dynamics particles interacting with a Lattice Boltzmann fluid
Nikita Tretyakov, Burkhard Dünweg
Computer Physics Communications216,102-108 (2017);

Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness
Stefan Jaschonek, Gregor Diezemann
The Journal of Chemical Physics146 (12),124901 (2017);

Nonequilibrium Markov state modeling of the globule-stretch transition
Fabian Knoch, Thomas Speck
Physical Review E95 (1), (2017);

Role of Dynamic Heterogeneities in Ionic Liquids: Insights from All-Atom and Coarse-Grained Molecular Dynamics Simulation Studies
Tamisra Pal, Michael Vogel
ChemPhysChem18 (16),2233-2242 (2017);

Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces
Vikram Reddy Ardham, Frédéric Leroy
The Journal of Chemical Physics147 (7),074702 (2017);
URL: http://dx.doi.org/10.1063/1.4999337

In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics.

Numerical analysis of the Oseen-type Peterlin viscoelastic model by the stabilized Lagrange-Galerkin method, Part II: A linear scheme
M. Lukacova-Medvidova, H. Mizerova, H. Notsu, M. Tabata
Mathematical Modelling and Numerical Analysis , (2017);

This is the second part of our error analysis of the stabilized Lagrange–Galerkin scheme applied to the Oseen-type Peterlin viscoelastic model. Our scheme is a combination of the method of characteristics and Brezzi–Pitkäranta’s stabilization method for the conforming linear elements, which leads to an efficient computation with a small number of degrees of freedom. In this paper, Part II, we apply a semi-implicit time discretization which yields the linear scheme. We concentrate on the diffusive viscoelastic model, i.e. in the constitutive equation for time evolution of the conformation tensor diffusive effects are included. Under mild stability conditions we obtain error estimates with the optimal convergence order in two and three space dimensions. The theoretical convergence orders are confirmed by numerical experiments.

Thermodynamic formalism for transport coefficients with an application to the shear modulus and shear viscosity
Thomas Palmer, Thomas Speck
The Journal of Chemical Physics146 (12),124130 (2017);

Estimation of the critical behavior in an active colloidal system with Vicsek-like interactions
Benjamin Trefz, Jonathan Tammo Siebert, Thomas Speck, Kurt Binder, Peter Virnau
The Journal of Chemical Physics146 (7),074901 (2017);

The PCPDTBT Family: Correlations between Chemical Structure, Polymorphism, and Device Performance
G. L. Schulz, F. S. U. Fischer, D. Trefz, A. Melnyk, A. Hamidi-Sakr, M. Brinkmann, D. Andrienko, S. Ludwigs
Macromolecules50 (4),1402-1414 (2017);

Conformations and orientational ordering of semiflexible polymers in spherical confinement
Andrey Milchev, Sergei A. Egorov, Arash Nikoubashman, Kurt Binder
The Journal of Chemical Physics146 (19),194907 (2017);

Role of the Intercrystalline Tie Chains Network in the Mechanical Response of Semicrystalline Polymers
Sara Jabbari-Farouji, Olivier Lame, Michel Perez, Joerg Rottler, Jean-Louis Barrat
Physical Review Letters118 (21), (2017);

Iterative Reconstruction of Memory Kernels
Gerhard Jung, Martin Hanke, Friederike Schmid
Journal of Chemical Theory and Computation13 (6),2481-2488 (2017);

In recent years, it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the extraction of the dynamical properties, namely, the memory kernel, from equilibrium all-atom simulations. In this article, we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed noniterative techniques, it ensures by construction that the target correlation functions of the original fine-grained systems are reproduced accurately by the coarse-grained system, regardless of time step and discretization effects. Furthermore, we also propose a new numerical integrator for generalized Langevin equations that is significantly more accurate than the more commonly used generalization of the velocity Verlet integrator. We demonstrate the performance of the above-described methods using the example of backflow-induced memory in the Brownian diffusion of a single colloid. For this system, we are able to reconstruct realistic coarse-grained dynamics with time steps about 200 times larger than those used in the original molecular dynamics simulations.

Asymptotic preserving IMEX finite volume schemes for low Mach number Euler equations with gravitation
G. Bispen, M. Lukacova-Medvidova, L. Yelash
J. Comput. Phys. 335,222-248 (2017);

Global existence result for the generalized Peterlin viscoelastic model
Maria Lukacova - Medvidova, Hana Mizerova, Sarka Necasova, Michael Renardy
SIAM J. Math. Anal.,1-14 (2017);
URL: https://www.siam.org/journals/sima.php

We consider a class of differential models of viscoelastic fluids with diffusive stress. These constitutive models are motivated by Peterlin dumbbell theories with a nonlinear spring law for an infinitely extensible spring. A diffusion term is in- cluded in the constitutive model. Under appropriate assumptions on the nonlinear constitutive functions, we prove global existence of weak solutions for large data. For creeping flows and two-dimensional flows, we prove global existence of a classical solution under stronger assumptions.

The electromagnetic nature of protein-protein interactions
Hildebrandt, A.K., Kemmer, T.. and Hildebrandt, A.
in Conductive polymers: Electrical interactions in cell biology and medicine,Ze Zhang, Mahmoud Rouabhia, Simon E. Moulton, CRC Press (2017);

Energy-stable numerical schemes for multiscale simulations of polymer-solvent mixtures
M. Lukacova-Medvidova, B. Duenweg, P. Strasser, N. Tretyakov
in Mathematical Analysis of Contimuum Mechanics and Industrial Applications II ,Editor:Patrick van Meurs, Masato Kimura, Hirofumi Notsu,ChapterChap5: Interface Dynamics ,Pages1-12,Springer International Publishing AG/ Eds. Patrick van Meurs, Masato Kimura, Hirofumi Notsu (2017);
URL: https://link.springer.com/chapter/10.1007/978-981-10-6283-4_13

We present a new second order energy dissipative numerical scheme to treat macroscopic equations aiming at the modeling of the dynamics of complex polymer-solvent mixtures. These partial differential equations are the Cahn-Hilliard equation for diffuse interface phase fields and the Oldroyd-B equations for the hydrodynamics of the polymeric mixture. A second order combined finite volume / finite difference method is applied for the spatial discretization. A complementary approach to study the same physical system is realized by simulations of a microscopic model based on a hybrid Lattice Boltzmann / Molecular Dynamics scheme. These latter simulations provide initial conditions for the numerical solution of the macroscopic equations. This procedure is intended as a first step towards the development of a multiscale method that aims at combining the two models.

Reduced-order hybrid multiscale method combining the molecular dynamics and the discontinuous Galerkin method
N. Emamy, M. Lukácová-Medvid’ová, S. Stalter, P. Virnau, L. Yelash
VII International Conference on Computational Methods for Coupled Problems in Science and Engineering, Coupled Problems 2017,1-15. (2017);
URL: http://congress.cimne.com/coupled2017/frontal/default.asp

We present a new reduced-order hybrid multiscale method to simulate complex fluids. The method combines the continuum and molecular descriptions. We follow the framework of the heterogeneous multi-scale method (HMM) that makes use of the scale separation into macro- and micro-levels. On the macro-level, the governing equations of the incompressible flow are the continuity and momentum equations. The equations are solved using a high-order accurate discontinuous Galerkin Finite Element Method (dG) and implemented in the BoSSS code. The missing information on the macro-level is represented by the unknown stress tensor evaluated by means of the molecular dynamics (MD) simulations on the micro-level. We shear the microscopic system by applying Lees-Edwards boundary conditions and either an isokinetic or Lowe-Andersen thermostat. The data obtained from the MD simulations underlie large stochastic errors that can be controlled by means of the least-square approximation. In order to reduce a large number of computationally expensive MD runs, we apply the reduced order approach. Numerical experiments confirm the robustness of our newly developed hybrid MD-dG method.

Self-Assembly of Polymeric Particles in Poiseuille Flow: A Hybrid Lattice Boltzmann/External Potential Dynamics Simulation Study
Johannes Heuser, G. J. Agur Sevink, Friederike Schmid
Macromolecules50 (11),4474-4490 (2017);

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics
G. J. A. Sevink, F. Schmid, T. Kawakatsu, G. Milano
Soft Matter13 (8),1594-1623 (2017);

π+–π+ stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces
Fujie Tang, Tatsuhiko Ohto, Taisuke Hasegawa, Mischa Bonn, and Yuki Nagata
Phys. Chem. Chem. Phys.19,2850 (2017);
URL: http://pubs.rsc.org/is/content/articlehtml/2016/cp/c6cp07034e

The interfacial structure of room temperature ionic liquids (RTILs) controls many of the unique properties of RTILs, such as the high capacitance of RTILs and the efficiency of charge transport between RTILs and electrodes. RTILs have been experimentally shown to exhibit interfacial molecular layering structures over a 10 Å length scale. However, the driving force behind the formation of these layered structures has not been resolved. Here, we report ab initio molecular dynamics simulations of imidazolium RTIL/air and RTIL/graphene interfaces along with force field molecular dynamics simulations. We find that the π+–π+ interaction of imidazolium cations enhances the layering structure of RTILs, despite the electrostatic repulsion. The length scales of the molecular layering at the RTIL/air and RTIL/graphene interfaces are very similar, manifesting the limited effect of the substrate on the interfacial organization of RTILs.

MERCURY: a Transparent Guided I/O Framework for High Performance I/O Stacks
Giuseppe Congiu, Matthias Grawinkel, Federico Padua, James Morse, Tim Süß and André Brinkmann
in 25th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2017),IEEE Press (2017);

The performance gap between processors and I/O represents a serious scalability limitation for applications running on computing clusters. Parallel file systems often provide mechanisms that allow programmers to disclose their I/O pattern knowledge to the lower layers of the I/O stack through a hints API. This information can be used by the file system to boost the application performance. Unfortunately, programmers rarely make use of these features, missing the opportunity to exploit the full potential of the storage system. In this paper we propose MERCURY, a transparent guided I/O framework able to optimize file I/O patterns in scientific applications, allowing users to control the I/O behavior of applications without modifications. This is done by exploiting the hints API provided by the back-end file system to guide data prefetching. MERCURY efficiently converts numerous small read requests into a few larger requests. Furthermore, it increases the I/O bandwidth, reduces the number of I/O requests, and ultimately the application running time. Moreover, we also propose a Linux kernel modification that allows network file systems, specifically Lustre, to work with our guided I/O framework through the posix_fadvise interface.


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