Day 1 - June, 5th 2017

Session 1, 17:00-18:30

G. Jung, Iterative Reconstruction of Memory Kernels

G. T. Vu, Mean curvature as a guiding field for block copolymer conformation

C. Scherer, Evaluating many-body effects in systemtic coarse graining

Day 2 - June, 6th 2017

Session 2, 10:00-11:30

A. Disterhoft, A short introduction to weak formulations of partial differential
equations and galerkin methods

D. Spiller, Spinodal decomposition of polymer-solvent systems: first steps
towards treating 2D systems

P. Strasser, Energy-stable numerical schemes for multiscale simulations of
polymer-solvent mixtures

Session 3, 14:00-16:00

P. Koss, Estimation of crystal nucleation barriers for colloidal crystals from
computer simulations

F. Knoch, Time-dependent nonequilibrium Markov state modeling

S. Wörner, Kinetic properties of liquid crystals from coarse-grained and atomistic
molecular dynamics simulations

F. Kössel, A kinetic theory for dynamics of self-propelled magnetic suspensions

Day 3 - June, 7th 2017

Free time suggestion: group trip by ship to Bregenz and hiking on the "Pfänder" for a beautiful view over the Bodensee.

Day 4 - June, 8th 2017

Session 4, 10:00-11:30

T. Pal, All-atom molecular dynamics simulation of ionic liquid films on silica
surface

D. Lesnicki, Understanding water relaxation at interfaces

V. R. Ardham, A thermodynamic model to simulate particles at an oil-water
interface

Session 5, 14:00-16:00

H. Guzman, Scalable and fast heterogeneous molecular simulation with
predictive parallelization schemes

M. Heidari, Chemical potential calculation of dense fluids using hamiltonian
adaptive resolution simulation

S. Stalter, Molecular dynamics simulations in hybrid particle-continuum
schemes: pitfalls and caveats

Session 6, 18:00-19:00

S. Köhler, Computer simulations at BASF

Day 5 - June, 9th 2017

Session 7, 10:00-11:00

D. Reith, Autonomous cars at Bosch

Session 8, 11:00-12:00

K. Schäfer, Refolding dynamics of molecular constructs after a force
quench

S. Jaschonek, Molecular dynamics simulations of phase transition in phospholipid bilayers

Session 9, 18:00-19:00

B. Trefz, IT Consulting

Day 6 - June, 10th 2017

Session 10, 10:00-11:00

T. Kemmer, Efficient nonlocal protein electrostatics in the Julia programming
language

F. Padua, File locking and concurrency control for filesystems: understanding
real-word applications

Iterative Reconstruction of Memory Kernels

G. Jung, F. Schmid

Institut für Physik, Johannes Gutenberg-Universität Mainz, Germany

In recent years it has become increasingly popular to construct coarse-grained
models with Non-Markovian dynamics in order 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 all-atom
simulations. In this talk we will present the iterative memory reconstruction (IMR) [1],
which is the first iterative method suggested in the field of Non-Markovian
modeling. This new extraction technique shows various similarities to the
reconstruction of static potentials via inverse Monte Carlo (IMC) [2] or iterative
Boltzmann inversion (IBI) [3] . The big advantage compared to previously proposed
techniques (e.g. [4, 5]) is the efficient reconstruction of coarsegrained models that
have precisely the same dynamical properties as the original finegrained
systems.

We demonstrate the performance of the above described methods at the example
of the anomalous diffusion of a single colloid. For this system we are able to
reconstruct realistic coarse-grained models for timesteps about 200 times larger then
the original molecular dynamics simulations.

[1] G. Jung and F. Schmid, submitted to JCTC

[2] A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52, 3730 (1995)

[3] D. Reith, M. Pütz, F. Müller-Plathe, Comp. Chem. 24, 1624 (2003)

[4] H. K. Shin, C. Kim, P. Talkner and E. K. Lee, Chem. Phys. 375, 316 (2010)

[5] A. Carof, R. Vuilleumier and B. Rotenberg, J. Chem. Phys. 140, 124103
(2014)

Mean curvature as a guiding field for block copolymer conformation

G. T. Vu, A. Abate, L. Gómez, A. Pezzutti, R. Register, D. Vega, F. Schmid

Experimental data on cylinder-forming block copolymer thin films deposited on
curved substrates and free standing membranes show that the local orientation of the
pattern are strongly coupled with the geometry in which the system is embedded. This
coupling affects defect dynamics and also the shape developed by free-standing
membranes. Here we performed self-consistent field theory (SCFT) calculations to
determine how equilibrium configurations and the elastic bending constants are
affected by a geometric field. The stability of the block copolymer thin film against
dewetting due to curvature is also analysed. In good agreement with experiments,
it is found that the competition between the strong length scale selectivity
imposed by the block copolymer structure and curvature dictates pattern
orientation.

Evaluating many-body effects in systematic coarse graining

Christoph Scherer

Particle based coarse-graining (CG) is a systematic way of reduction of
the number of degrees of freedom describing a physical system. It involves
three steps: choice of the CG degrees of freedom, identification of a merit
function which quantifies the difference between the fine- and coarse-grained
representations, and determination of the CG potential energy surface (PES). The
entire procedure is sensitive to the number and types of basis-functions employed
in the CG representations: for example, the incorporation of nonbonded
three-body interactions in a coarse-grained water model helps to reproduce both
thermodynamic and structural properties [1,2]. In this work, we investigate the
effect of extending the basis set to three-body interactions for several organic
solvents and formulate clear criteria for when these many-body terms are
required. The coarse-graining scheme is implemented in the VOTCA-CSG toolkit
[3].

[1] V. Molinero, E. B. Moore, J. Phys. Chem. B, 113, 4008 (2009)

[2] L. Larini, L. Lu, G.A. Voth, J. Chem. Phys. 132, 164107 (2010)

[3] V. Rühle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem. Theory.
Comput. 5, 3211 (2009)

A Short Introduction to Weak Formulations of Partial
Differential Equations and Galerkin Methods

Alexej Disterhoft

Partial differential equations (PDEs) are fundamental to physics and chemistry;
often used to describe a wide variety of phenomena. Unfortunately, predominantly
only simple examples can be solved analytically. Most PDEs do not even have a
solution in the classical sense. The concept of weak solutions lifts some of these
problems. For many PDEs, this theoretic framework not only answers the question
whether a (unique) solution exists, but also allows the construction of computational
methods to calculate approximations. Exemplary applications of this framework, and
so-called Galerkin methods based thereon, are presented.

Spinodal Decomposition of Polymer-Solvent Systems: First
Steps Towards Treating 2d Systems

Dominic Spiller, Burkhard Dünweg, Maria Lukacova and Paul Strasser

We investigate the dynamics of a polymer system falling out of solution, using two
complementary methodological approaches: On the one hand, viscoelastic
Cahn-Hilliard (CH) continuum equations are solved numerically on a grid
(contribution by Paul Strasser). On the other hand, we use a coupled Lattice
Boltzmann (LB) / Molecular Dynamics (MD) scheme to simulate a bead-spring model
for a system of chain molecules in a hydrodynamic background, where the solvent
quality is taken into account by the strength of the non-bonded monomer-monomer
interaction. Since the CH calculations are done in two dimensions, we modify
our three-dimensional simulation code in order to study two dimensions
as well; this is done via a suitable external confining potential. For such a
system, we study and test in detail how the virial equation of state must be
evaluated, in order to obtain a suitable parametrization of the continuum
free-energy functional. First numerical results on these investigations will be
presented.

Energy-stable numerical schemes for multiscale simulations
of polymer-solvent mixtures

Paul Strasser

Introducing energy stable numerical schemes to solve a macroscopic equation
system aiming at the modeling of the dynamics of polymer-solvent mixtures. Focus is
the time discretization of the system, since the space discretization done by a
combined Finite Difference / Finite Volume scheme is known to conserve physical
quantities. 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 to compare the dynamics of
both time scales.

Estimation of crystal nucleation barriers for colloidal
crystals from computer simulations

P. Koss

A fluid in equilibrium in a finite volume, with a density exceeding the onset of
freezing, may exhibit phase coexistence of a crystal nucleus surrounded by
liquid. In classical nucleation theory, the barrier of homogeneous nucleation is
given by two contributions, the energy gain of creating a droplet and the
energy loss due to surface tension of the newly created interface. Using a
computational method suitable for the estimation of the chemical potential
of dense fluids we obtain the excess free energy due to the surface of the
crystalline nucleus. Our novel analysis method is appropriate for crystal nuclei of
all shapes without suffering from ambiguities occurring when one needs
a microscopic identification of the crystalline droplet. We report that the
nucleation barrier for a soft version of the effective Asakura-Oosawa model[1] is
compatible with a spherical shape, and consistent with classical nucleation theory
[2].

[1] M. Dijkstra, R. van Roij and R. Evans, Phys. Rev. E 59, 5744-5771 (1999).

[2] A. Statt, P. Virnau, and K. Binder, Phys. Rev. Lett. 114, 026101 (2015).

Time-dependent nonequilibrium Markov state modeling

Fabian Knoch, Ken Schäfer, Gregor Diezemann and Thomas Speck.

A major current challenge in statistical mechanics poses the systematic
construction of coarse-grained Markov state models that are dynamically consistent,
and moreover might be used for systems driven out of thermal equilibrium. We
previously introduced a novel prescription that extends the Markov state modeling
approach to systems with dynamics breaking detailed-balance. Here, we introduce
the concept of nonequilibrium Markov state modeling to systems driven
by general time-dependent periodic as well as nonperiodic protocols. We
illustrate our new methodology for both types of driving protocols by giving two
examples: alanine dipeptide exposed to an oscillating electric field and the
Calix[4]arene-catenane dimer elongated employing a constant-velocity pulling
protocol.

Kinetic properties of liquid crystals from coarse-grained and
atomistic molecular dynamics simulations

Svenja Wörner, Joseph Rudzinski, Kurt Kremer, and Tristan Bereau

Max-Planck-Institut für Polymerforschung, Mainz, Germany

Liquid crystals display liquid-like behavior while maintaining a long-range
crystalline order, giving rise to unique material properties. To understand
macroscopic processes, e.g. phase transitions, large systems need to be studied on
time scales not accessible by atomistic models. Coarse grained models make these
sizes and time scales accessible.

In this work we investigate the liquid crystal mesogen 8AB8, containing a stiff,
photoisomerizable azobenzene core with flexible alkyl tails. Mukherjee et al. have
previously developed a coarse-grained model of 8AB8, which displays the
correct thermodynamic and structural properties. Not only is it able to form a
smectic phase, the model also reproduces the transition temperature of the
disordered to smectic phase transition of the underlying atomistic model.
Reducing the degrees of freedom usually leads to a non-trivial modification of the
timescales for different processes sampled by the coarse-grained model. Two
well-characterized translocation pathways in the smectic A phase are studied in
detail, utilizing a Markov state model framework to systematically assess the
differences in the transport kinetics between the coarse-grained and atomistic
models. Investigating the precise source of the discrepancies between the two
models implicates an approach for reparametrization of the coarse-grained
model.

A kinetic theory for dynamics of self-propelled magnetic
suspensions

Fabian Rouven Kössel and Sara Jabbari-Farouji

Inspired by novel dynamical patterns in magnetotactic bacteria, we present a
minimal kinetic model for dilute suspensions of magnetic self-propelled particles. Our
kinetic theory couples a Fokker-Planck equation of active particles in an external
magnetic field to a Stokes flow equation. Including the hydrodynamic stress
contributions of self- propulsion and magnetic torque in the Stokes flow allows us to
investigate, the interplay between internal and external drives on the dynamics and
effective viscosity of active suspensions. Through the linear stability analysis and full
numerical simulations of our model, we ex- amine the role of the external
magnetic field on stability of aligned suspensions and their complex flow
patterns.

All-Atom Molecular Dynamics Simulation of Ionic Liquid
films on Silica Surface

Tamisra Pal and Michael Vogel

Institut für Festkörperphysik Technische Universität Darmstadt , 64289 Darmstadt
, Germany

Room temperature ionic liquid films in confined geometries have been recognized
for their significant interfacial properties in electrochemical and electronic
devices. Depending on the hydrophobicity of the anions, we chose ionic liquid
1-butyl-3-methylimidazolium cation with hexafluorophosphate ([Bmim][PF6]) and
tetrafluoroborate ([Bmim][BF4]) counterparts. Here, the dynamical and structural
properties of these ionic liquid confined between amorphous silica slabs have been
investigated by all-atom molecular dynamics simulation studies at 300 K. Relative
number densities of the ions are calculated near the surface, as well as in the middle of
the slit. The more hydrophilic [BF4]- ions tend to stay closer to the slab wall than
symmetric [PF6]-, whereas the [Bmim]+ ions always resides in the next layer
forming a bi-layered arrangement from the wall. A preferred orientation has
been observed for the cations with their methyl groups pointing towards
the slab surface and the butyl tail projected inwards. The middle of the slit
displays more of a bulk behavior in terms of density and ion diffusivities. We
have performed spatially-resolved analysis of the mean square displacement
(MSD) and incoherent intermediate scattering function (ISF) to understand
the very sluggish and heterogeneous dynamics of these ionic liquids in the
vicinity of the silica surface, which need to be considered when designing
applications.

Vibrational energy relaxation at water interfaces from ab
initio molecular dynamics simulations

Dominika Lesnicki, Marialore Sulpizi

Department of Physics, Johannes Gutenberg University Mainz (JGU Mainz)
Staudingerweg 7, 55128 Mainz - Germany

Ab initio molecular dynamics simulations represent a versatile approach to
investigate the structure and dynamics of water interfaces, especially in the cases of
heterogeneous systems where less computationally demanding techniques, such as
force field approaches are not easily transferable. Recently, ab initio simulations have
been used to calculate Sum Frequency Generation spectra, also thanks to new
developments in the calculations of the response functions, which make use of
velocity-velocity correlation functions incorporating the appropriate selection rules
[1,2].

We present here a new approach to investigate vibrational energy relaxation at
water interfaces from the analysis of ab initio molecular dynamics trajectories. We
follow the energy relaxation from a locally excited vibrational state using suitable
descriptors based on vibrational density of states.

Our method is applied to different water systems, including bulk water and
fluorite/water interfaces at different pH. In the case of the fluorite/water interface at
low pH we find that water behaves similarly to bulk water, while, in the case of high
pH, instead, the energy relaxation is much slower. A molecular interpretation of the
different time scales is provided.

[1] R Khatib, EHG Backus, M Bonn, MJ Perez-Haro, MP Gaigeot, M Sulpizi,
Scientific Reports, 6 (2016)

[2] R. Khatib and M Sulpizi, J. Phys. Chem. Letters, 8, 6 (2017)

A thermodynamic model to simulate particles at an oil-water
interface

Vikram Reddy Ardham, Frédéric Leroy

Technische Universität Darmstadt, Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany

Liquid-liquid interfaces offer a suitable environment to facilitate self-assembly of
nano-particles driven by the free energy difference between the bulk and interface.
Particularly, water-oil interfaces have been exploited to synthesize networks of
graphene particles that are highly inter-connected and only up to a few layers thick. To
simulate and study these systems, we develop and evaluate a thermodynamic method
to generate models that are thermodynamically consistent with a reference system.
The models here mean the different interaction potentials that are to be used to
simulate particles using molecular simulation methods. We reformulate the wetting
coefficient (!)^{1} for a particle in a two-phase media in terms of an easily computable
work of adhesion^{2} and then use this as reference to generate models with different
resolutions (all-atom/coarse-grained). We observe that the wetting coefficient
accurately determines the equilibrium position of a particle where only dispersion
forces are dominant. We however, observed that reproducing the thermodynamics
does not necessarily reproduce the structural properties and must be taken care of
separately by choosing appropriate liquid models. Further, we illustrate the
applicability of method by simulating a relatively large water-oil interface with
graphene particles forming an inter-connected network using a coarse-grain
model.

[1] Sumita, M.; Sakata, K.; Asai, S.; Miyasaka, K.; Nakagawa, H. Polym. Bull. 1991, 25
(2), 265-271.

[2] Ardham, V. R.; Deichmann, G.; van der Vegt, N. F. A.; Leroy, F. J. Chem. Phys.
2015, 143 (24).

Scalable and fast heterogeneous molecular simulation with
predictive parallelization schemes

Horacio V. Guzman, Kurt Kremer, and Torsten Stuehn

Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany Christoph Junghans

Computer, Computational, and Statistical Sciences Division, Los Alamos National
Laboratory, Los Alamos, NM 87545, USA

Abstract: Multiscale and inhomogeneous molecular systems are challenging
topics in the eld of molecular simulation. In particular, modeling biological systems in
the context of multiscale simulations and exploring material properties are driving a
permanent development of new simulation methods and optimization algorithms. In
computational terms, those methods require parallelization schemes that make a
productive use of computational resources for each simulation and from its genesis.
Here, we introduce the heterogeneous domain decomposition algorithm which is a
combination of an heterogeneity sensitive spatial domain decomposition with an a
priori sliding subdomain-walls procedure. The algorithm modeling is presented for
dual resolution systems and inhomogeneous binary fluids, in terms of scaling
properties as a function of the size of the low-resolution region and the high-to-low
resolutions ratio. We also show the algorithm competences, by comparing it to
both static domain decomposition algorithms and dynamic load balancing
schemes. Mainly, two representative molecular systems have been simulated and
compared to the heterogeneous domain decomposition proposed in this
work. These two systems comprise an adaptive resolution simulation of a
biomolecule solvated in water and a phase separated binary Lennard-Jones
fluid.

Chemical Potential Calculation of Dense Fluids using
Hamiltonian Adaptive Resolution Simulation

Maziar Heidari, Robinson Cortes-Huerto, Kurt Kremer, Raffaello Potestio

The calculation of chemical potential of fluids is a relevant and challenging
problem in computational chemistry and physics. Here, we propose a method which
employs the recently multi-scale Hamiltonian Adaptive Resolution Simulation
(H-AdResS) method to calculate the chemical potential of dense fluids. In H-AdResS,
the simulation domain is subdivided in regions of high and low resolutions, coupled
through a hybrid region. Since the dynamics of particles are obtained from a global
Hamiltonian, the generated statistical ensembles of the system are well-defined. In
our method, the fluid within the high resolution region is coupled with an ideal gas of
non-interacting particles, and to enforce a uniform density profile an external force is
computed on-the-fly and applied. Then the converged compensation forces are
integrated across the hybrid region to obtain the Gibbs free energy difference
between the two resolutions. The resulting Gibbs free energy is related to
the excess chemical potential of the fluid with respect to the ideal gas. We
validated this method by calculating the excess chemical potentials of fluid
mixtures.

Molecular dynamics simulations in hybrid particle-continuum
schemes: Pitfalls and caveats

Stefanie Stalter, Nehzat Emamy, Leonid Yelash, Mária Lukácová, Peter
Virnau

We aim to develop an efficient reduced-order hybrid multiscale method in order
to simulate complex fluids. With help of the heterogeneous multiscale method
(HMM), that makes use of the scale separation into macro- and microlevels, the
method combines the continuum and the molecular description. The missing
information on the macro-level is the unknown stress-tensor, evaluated by means of a
molecular dynamics (MD) simulation under shear on the micro-level. In this talk I will
discuss pitfalls and caveats, which arise for this application of MD simulations. This
includes the choice of optimum system sizes, thermostats and realistic shear rates,
which can be achieved.

Efficient nonlocal protein electrostatics in the Julia
programming language

Thomas Kemmer, Andreas Hildebrandt

Software in the field of computational science is generally exposed to
a particularly restrictive set of requirements, mainly owing to the natural
complexity of its tasks and the algorithms to solve them. Inevitably, these
requirements influence the choice of programming language, not only demanding a
certain ease of use - allowing rapid prototyping and, thus, rapid adaption to
changes in the experimental or theoretical setup - but also the computational
efficiency to solve the tasks within a given set of time or hardware constraints.
Computational efficiency becomes of particular importance in the case of multi-scale
environments, such as the simulation of electrostatic interactions between
biomolecules in highly structured solvents. One major challenge in this context is
the treatment of the latter, as strong simplifications of the solvent structure
invariably lead to considerable inaccuracies in the estimated potentials and free
energies. Here, we present efficient protein electrostatics computations as a
showcase example for the cross-platform and open-source Julia programming
language, which provides a positive user experience comparable to Python or
MATLAB alongside high-performance capabilities known from C and C++. By
modeling water in an implicit but nonlocal fashion, we account for correlation of
molecular polarization due to the water network around the solute and sustain
accuracy without suffering from infeasible runtimes as compared to the explicit
case.

File locking and concurrency control for filesystems:
understanding real-word applications

Federico Padua

File locking is a form of serialization used by parallel filesystems to prevent data
corruption or other bugs in case many programs or many processes access the same
files at the same time. This is the case for a single MPI program, in which many
processes read and write a single shared file or multiple files during the run. If
user-level filesystems aim to replace some key functionalities of kernel level
filesystems, then it becomes important to verify whether such a filesystem needs to
support any form of concurrency control or none. In case a form of concurrency
control is needed, it's also important to asses which one would be the best
option.

Our interest in studying concurrent file accesses and file locking is motivated by one
section of the POSIX specification:

"This volume of POSIX.1-2008 does not specify behavior of concurrent writes to a file
from multiple processes. Applications should use some form of concurrency control."
It then becomes fundamental that filesystem designers take into account this possible
issue when developing their filesystems: either some form of concurrency control is
needed or not.

This mandates a clear understanding and study of real world applications that run in
HPC centers.

We hope that the study we are embarking on will open up a discussion and a rethinking of some assumptions. For instance, previous works tried to explore the benefits of optimistic concurrency control in the HPC context. We plan first to assess to what extent ad-hoc file system developers should care about concurrency control or not, to support one design choice over another: this can justify optimistic or pessimistic approaches.

In the case of more general purpose filesystems in HPC clusters, such as GPFS and
Lustre, the default to concurrency control is to employ a pessimistic approach using
some kind of distributed locking (with different level of granularity). We plan to use
the study to provide a solid experimental foundation to see whether this pessimistic
approach is needed even in the case of general purpose filesystems to correctly
support HPC applications.

## Calendar

## Contact

- Scientific Coordinator of the TRR 146
- Dr. Giovanni Settanni
- Staudingerweg 9
- D-55128 Mainz
- trr146JYHGgwpB@bDoDcuni-mainz.de