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CompMat2014

International symposium and workshop

Computational condensed matter:

advances and challenges

7 – 9 September 2014

Whitehaven, The Lake District, UK

Co-sponsored by

Materials Chemistry Division

http://www.j-octa.com

J-OCTA is a multi-scale simulation software for

soft matter. J-OCTA supports understanding of

mechanisms and estimation of material properties

from the atomistic scale to the micrometer scale, in

the research and development of high functional

materials

Polymers (www.mdpi.com/journal/polymers), an international, open

access journal of polymer science, provides an interdisciplinary forum

for publishing papers which advance the fields of polymerization

methods, theory, simulation, and modeling, understanding of new

physical phenomena, advances in characterization techniques, and

harnessing of self-assembly and biological strategies for producing

complex multifunctional structures.

Prizes are offered by

Computational Materials Science






The symposium brings together world-leading experts, young researches and PhD students in

computational soft matter, solid state physics and their interface. The small size of the symposium

allows for maximum discussion and networking. The symposium is held at Westlakes Science

and Technology Park, situated on the fringe of the Lake District National Park in Cumbria

between the sea-cost town of Whitehaven and Ennerdale Water, the most westerly and most

tranquil of the lakes.

On Sunday, 7 September 2014, there is a pre-symposium workshop intended for PhD students and

post-doctoral fellows.

The symposium marks 10 years since the Computational Physics Group has been founded at the

University of Central Lancashire (UCLan) in Preston, UK, on 1st September 2004.

On 1st September 2014 the group moved to the University of Lincoln, UK, to found the new

School of Mathematics and Physics.

Scientific Program Committee & Organizing Committee

Manuela Mura

Marco Pinna

Andrei Zvelindovsky (Chair)

CompMat2014 - Computational condensed matter: advances and challenges

2

Program

Saturday, 6 September

17:30 - 21:00 Dinner at Summergrove Halls (courtesy of UCLan/Lincoln Computational Physics Group)

Sunday, 7 September

Pre-symposium workshop

Summergrove Halls

Page

09:00 - 10:00 Lev Kantorovich Theoretical insight into the role of kinetics in atomic-scale surface

processes

7

10:00 - 11:00 Toshihiro Kawakatsu Hybrid field theories for complex domains in polymer/membrane

systems

7

11:00 - 12:00 Lianheng Tong CP2K: an ab initio materials simulation code – introduction and

highlight of recent developments

8

12:00 - 13:00 Lunch

13:00 - 14:00 Attilio Vargiu A (short and incomplete) introduction to force-field based molecular

simulations

8

14:00 - 15:00 Ignacio Pagonabarraga Introduction to mesoscopic computational approaches for the dynamics

of soft matter

9

15:00 - 15:30 Coffee break

15:30 - 16:30 David (Qiang) Wang A brief introduction to Monte Carlo simulations

9

16:30 Bus to Waterfront

Symposium

17:00 - 22:00 Welcome Reception at the Waterfront Restaurant (A buffet dinner in reception style sponsored by J-OCTA, JSOL)

22:00 Bus to Summergrove Halls

7 – 9 September 2014, Whitehaven, the Lake District, UK

3

Monday, 8 September

Symposium

Westlakes Science & Technology Park

8:30 Bus from Summergrove Halls to Westlakes S&T Park

Page

9:00 Welcome

9:15 -10:15 Guest Experimentalist - Philip Moriarty The Pauli principle in probe microscopy

10

10:15 -10:45 Coffee

10:45 -11:15 Lev Kantorovich The generalized Langevin equation: an efficient approach to non-

equilibrium molecular dynamics of open systems

12

11:15 - 11:35 Sanliang Ling Size really does matter: insights into electron and hole stability in TiO2

from hybrid density functional calculations

17

11:35 - 12:05 Luciano Colombo Elastic properties of SCBI metal-polymer nano composites

11

12:05 - 13:30 Lunch

13:30 - 14:00 Ignacio Pagonabarraga Entropic electrokinetics: dynamics of charged tracers and electrolytes

under strong confinement

14

14:00 - 14:20 Andela Saric Crucial role of non-specific interactions in amyloid nucleation

17

14:20 - 14:40 Attilio Vargiu AntibioticDB: a database of antibiotic parameters, dynamics and

properties

18

14:40 - 15:10 Fernando Peruani Collective motion in heterogeneous media and in confined geometries

15

15:10 - 17:00 Tea + Posters

20

17:00 - 18:00 Keynote - Daan Frenkel The role of entropy and cooperativity in complex self assembly

10

18:15 Bus to Moresby Hall

19:00 Dinner at Moresby Hall



4

Tuesday, 9 September

Westlakes Science & Technology Park

8:30 Bus from Summergrove Halls to Westlakes S&T Park

Page

9:00 - 9:30 Andrew Masters The molecular segregation of tri-butyl phosphate in an organic diluent

and its relevance to nuclear extraction processes

13

9:30 - 10:00 Kostas Daoulas Studying fluctuations and Frank elastic constants in polymer nematics

with coarse-grained models

12

10:00 - 10:30 Coffee

10:30 - 11:00 Agur Sevink Challenges in coarse-grained modeling of biomimetic systems

15

11:00 - 11:30 Toshihiro Kawakatsu Field theories for shape deformations of vesicles

13

11:30 - 11:50 Tom Underwood Lattice-switch Monte Carlo: a method for precise phase diagram

prediction

19

11:50 - 12:10 Hossein Eslami Molecular dynamics simulation of a silica-poly(methyl methacrylate)

nanocomposite

18

12:10 - 13:30 Lunch

13:30 - 14:00 Marcus Müller Studying the kinetics of copolymer self-assembly

14

14:00 - 14:30 David (Qiang) Wang Novel, efficient, and accurate methods for calculating pressure in

polymer lattice Monte Carlo simulations

16

14:30 - 15:00 Dick Bedeaux Curvature dependence of the heat and mass transfer resistances of the

surface of nano bubbles and droplets

11

15:00 - 15:20 Mariano Galvagno Continuous and discontinuous dynamic unbinding transitions in

dragged-out film flows

19

15:20 - 17:00 Tea + Posters + Prizes

20

17:00 - 17:30 Mark W. Matsen Monte Carlo field-theoretic simulations applied to block copolymer

melts

14

17:30 - 18:00 Ryoichi Yamamoto Direct numerical simulations of swimming particles

16


5

18:15 Bus to Moresby Hall

19:00 - 20:00 Elysia String Quartet

20:00 Dinner at Moresby Hall


Elysia String Quartet

9 September 2014 at Moresby Hall

Edwin Schreiber, Jane Guilfoyle - violins, Penny Legat - viola, Jane Dutton - cello.

The Elysia String Quartet is based in the South Lakes and performs for conferences, weddings and other events

throughout Cumbria and Lancashire. We are very pleased to be playing for the CompMat2014 Symposium.

www.elysiastringquartet.co.uk

http://www.elysiastringquartet.co.uk/


7

Abstracts

Pre-symposium workshop

Theoretical insight into the role of kinetics in atomic-scale surface processes

J. Bamidele (1), D. Abbasi-Pérez (2), R. Turansky (3), J.M. Recio (2), I. Stich (3), L. Kantorovich (1*)

(1) King’s College London, UK

(2) Universidad de Oviedo, Spain

(3) Institute of Physics, Slovak Academy of Sciences, Slovak Republic

There has been a considerable research done on various aspects of nanoscience, however, insufficient attention is still

being paid to understanding kinetics of the corresponding atomic-scale processes at play. In this talk I’ll present our

recent theoretical results in which combining van der Waals corrected density functional theory calculations and Kinetic

Monte Carlo modeling resulted in greater understanding of the experimental findings. Two examples will be presented.

In the first one I’ll show how the theoretical modeling uncovered an intricate mechanism of the vertical manipulation of

“super”-Cu atoms on the c(6x2)-Cu(110) surface with the tip of Atomic Force Microscope, and explain why the

contrast remains unchanged (in collaboration with Prof. Y. Sugawara et al., Osaka University). In the second example

I’ll present our study on kinetics of 1D self-assembly of [1,1’;4’,1’’]-terphenyl-3,3“-dicar-bonitrile molecules on the

Ag(111) surface. We show that the molecules diffuse on the surface by “walking” on their two “legs”, and that

observed structures [1] can only be explained by thermal cis-to-trans isomerization of the molecules stimulated by

formation of double hydrogen bonds with the adjacent trans isomer. These transformations lead to growth of 1D

filaments seen in experiments [1].

[1] M. Marschall et al., ChemPhysChem, 11 (2010) 1446

————

Hybrid field theories for complex domains in polymer/membrane systems

T. Kawakatsu

Department of Physics, Tohoku University, Sendai 980-8578, Japan

It is well-known that multi-component polymeric materials and solutions of amphiphilic molecules show nano-scale

(typically of the order of 10-100 nm) domain structures induced by microphase separation. Typical examples can be

found in block copolymer melts and surfactant solutions. To characterize the equilibrium structures of these nano-

domains, we can rely on density functional theories such as self-consistent field (SCF) theory and Ginzburg-Landau

(GL) theory coupled with computer simulation techniques. These techniques have been successfully used to study

equilibrium domain morphologies and phase diagrams of block copolymer [1] and polymer nano composites [2]. It is

quite important to extend these density functional theories to dynamical problems when we study dynamical properties

of the nano domains, for example the rhelogical properties of phase separated dense polymer systems as viscoelastic

bodies. For this purpose, we developed dynamic version of the SCF theories by introducing the microscopic chain

dynamics and/or external force field such as an electric field [3-6]. Further extension can be realized by introducing

microscopic chemical details into the density-functional theory. To realize such a modeling, we proposed a hybrid

technique where we combine molecular dynamics simulations and SCF theory [7,8]. Using this hybrid approach, one

can simulate a large scale systems of mesophases of block copolymers and biomembranes.

[1] M.W. Matsen and S.F. Bates, Macromolecules, 29 (1996) 1091.

[2] Y. Wu, G. Cheng, K. Katsov, S.W.Sides, J. Wang, J. Tang, G.H. Fredrickson, M. Moskovits and G.D. Stucky,

Nature Materials, 3 (2004) 816.


8

[3] T. Honda and T. Kawakatsu, in “Nanostructured Soft Matter”, A.V. Zvelindovsky, ed., (Springer-Verlag, Berlin,

2007), 461.

[4] T. Kawakatsu, in “Understanding Soft Condensed Matter via Modeling and Computations”, Wenbing Hu and An-

Chang Shi, eds., (World Scientific, Singapore, 2010) p.105.

[5] D. Ly, M. Pinna, T. Honda, T. Kawakatsu, and A.V. Zvelindovsky, J. Chem. Phys. 138 (2013) 074904.

[6] T. Shima, H. Kuni, Y. Okabe, M. Doi, X.-F.Y uan, and T. Kawakatsu, Macromolecules, 36 (2003) 9199.

[7] A. De Nicola, Y. Zhao, T. Kawakatsu, D. Roccatano and G. Milano, Theoretical Chemistry Accounts, 131 (2012)

1167.

[8] Y. Zhao, A. De Nicola, T. Kawakatsu and G. Milano, J. Comput. Chem. 33 (2012) 868.

————

CP2K: an ab initio materials simulation code - introduction and highlight of recent developments

Iain Bethune (1), Lev Kantorovich (2), Ben Slater (3), Lianheng Tong (2*), Matt Watkins (4)

(1) EPCC, The University of Edinburgh, UK

(2) Department of Physics, King's College London, UK

(3) Department of Chemistry, University College London, UK

(4) Department of Physics and Astronomy, University College London, UK

CP2K (www.cp2k.org) is a freely available open-source program for atomistic simulation, best known for its

implementation of the Quickstep (Gaussian and Plane Waves, GPW) linear-scaling Density Functional Theory (DFT)

method [1]. CP2K also provides a wide range of capabilities beyond the basic DFT, from classical potentials, semi-

empirical methods, hybrid DFT functionals, to Moller-Plesset 2nd order perturbation theory (MP2). In this talk we will

give a general overview of the CP2K code and its applications. In particular, we will highlight the recent work of

implementing the Filtered Matrix Diagonalisation method in CP2K. Filtered diagonalisation [2] allows the run-time

construction of a tailored contracted basis set, which are fully optimised for the system configuration, at every energy

minimisation step. The contracted basis functions are developed for each atom from localised subsets of the Kohn-

Sham matrix, allowing systematic and automated convergence to the basis set limit. This contracted basis set will be of

minimal size, and thus makes the diagonalisation and calculation of the Kohn-Sham energy and orbitals much faster

than the traditional diagonalisation methods. The full density matrix can be obtained by reverse transforming from the

contracted basis set to the original basis set. The Filtered diagonalisation method is ideal for calculations, such as for

metals, where the use of direct diagonalisation of the Kohn-Sham matrix is preferred over other methods, such as the

Orbital Transformation method or Order-N approaches which enforce truncation in density and Kohn-Sham matrices.

[1] VandeVondele et al., Comput. Phys. Commun., 167 (2005) 103

[2] Rayson et al., Phys. Rev. B, 80 (2009) 205104

————

A (short and incomplete) introduction to force-field based molecular simulations

Attilio Vittorio Vargiu

Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. 8, km 0.700, 09042 Monserrato (CA), Italy

In this lecture I will introduce the principles of all-atom classic molecular dynamics simulations, with examples in the

field of soft (biological) matter. I will first introduce the force-field concept in the framework of molecular mechanics

and I will describe some of the most used protocols used for parameters fitting. Then, I will outline the hottest research

subjects in the development of more accurate force-fields. In the last part of the lecture I will show a few successful

examples of all-atom molecular dynamics applied to biological problems.

————


9

Introduction to mesoscopic computational approaches for the dynamics of soft matter

I. Pagonabarraga

Dept. Fundamemtal Physics, University of Barcelona, 08028-Barcelona, Spain

In this lecture I will describe the need to develop computational methods to address the dynamics of heterogeneous

systems. In these systems a molecular description does not allow to reach the relevant time and length scales in which

these systems evolve and develop emergent structures. I will discuss the challenges and limitations of such an approach

and will describe reference approaches based on particle dynamics (e.g. dissipative particle dynamics) and on kinetic

theories (e.g. lattice Boltzmann).

————

A brief introduction to Monte Carlo simulations

Q. Wang

Department of Chemical and Biological Engineering, Colorado State University, USA

In this lecture I will explain the basic idea of Monte Carlo simulations, and introduce the commonly used Metropolis

sampling and Wang-Landau sampling.

————


10

Symposium

Keynote

The role of entropy and cooperativity in complex self assembly

Daan Frenkel

University of Cambridge, UK

————

Guest Experimentalist

The Pauli principle in probe microscopy

Philip Moriarty

School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, UK

Exceptionally clear images of intramolecular structure can now be attained in dynamic force microscopy (DFM)

through the combination of a passivated tip apex and operation in what has become known as the “Pauli exclusion

regime” of the tip-sample interaction [1-4]. I will discuss, from an experimentalist's perspective, a number of aspects of

the exclusion principle which underpin this ability to achieve submolecular resolution. My particular focus will be on

the interpretation of Pauli's principle in the context of interatomic and intermolecular interactions, what this means for

the quantitative analysis of ultrahigh resolution force microscopy data, and whether or not we really see chemical bonds

in DFM images [5].

[1] L. Gross, F. Mohn, N. Moll, P. Liljeroth, and G. Meyer. Science, 325 (2009) 1110

[2] Dimas G. de Oteyza, et al., Science, 340 (2013) 1434

[3] Jun Zhang, Pengcheng Chen, Bingkai Yuan, Wei Ji, Zhihai Cheng, and Xiaohui Qiu, Science 342 (2013) 611

[4] A. Sweetman, S.P. Jarvis, H. Sang, I. Lekkas, P. Rahe, Y. Wang, J. Wang, N. Champness, L. Kantorovich, and

P. Moriarty, Nature Comm. 5 (2014) 3931

[5] P. Hapala, G. Kichin, C.F. Wagner, S. Tautz, R. Temirov, and P. Jelinek, cond matt arXiv:1406.3562 (2014)

————


11

Invited

Curvature dependence of the heat and mass transfer resistances of the surface of nano bubbles and

droplets

D. Bedeaux (1*), Ø. Wilhelmsen (1), S. Kjelstrup (1), K. S. Glavatskiy (2)

(1) Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway

(2) Department of Applied Sciences, RMIT University, Melbourne, Australia

We analyze the curvature dependence of the heat and mass transfer resistances of the surface of nano bubbles and

droplets. For this we use an extension [1-7] of the so-called square gradient model introduced by van der Waals to

describe the density profile in a one-component fluid, and by Kahn and Hilliard for mixtures, to time dependent

problems. This enables us to calculate equilibrium and non-equilibrium density profiles for the two phase state.

Together with earlier derived integral relations [8] we are then able to calculate these resistances. It is found that the

resistances change considerably in the nanoscale range. This agrees with molecular dynamics results [9]. In earlier work

we studied the stability of nanoscale droplets and bubbles [10,11].

[1] D. Bedeaux, E. Johannessen and A. Røsjorde, The Nonequilibrium van der Waals Square Gradient Model I: The

Model and its Numerical Solution, Physica A 330 (2003) 329-353.

[2] E. Johannessen and D. Bedeaux, The Nonequilibrium van der Waals Square Gradient Model II: Local Equilibrium

of the Gibbs Surface, Physica A 330 (2003) 354-372.

[3] E. Johannessen and D. Bedeaux, The Nonequilibrium van der Waals Square Gradient Model III: Heat and Mass

Transfer Coefficients, Physica A 336 (2004) 252-270.

[4] K.S. Glavatskiy and D. Bedeaux, Non-equilibrium properties of a two-dimensional isotropic interface in a two-

phase mixture as described by the square gradient model. Phys. Rev. E 77 (2008) 061101-17.

[5] K.S. Glavatskiy and D. Bedeaux, Numerical solution and verification of local equilibrium for the flat interface in the

two-phase binary mixture, Phys. Rev. E 79 (2009) 031608, 1-19.

[6] K.S. Glavatskiy and D. Bedeaux, Transport of heat and mass in a two-phase mixture. From a continuous to a

discontinuous description, J. Chem. Phys. 133 (2010) 144709-17.

[7] K.S. Glavatskiy and D. Bedeaux, Resistances for heat and mass transfer through a liquid-vapor interface in a binary

mixture, J. Chem. Phys. 133 (2010) 234501.

[8] E. Johannessen and D. Bedeaux, Integral Relations for the Heat and Mass Transfer Resistivities of the Liquid-Vapor

Interface. Physica A 370 (2006) 258-274.

[9] A. Lervik, F. Bresme, S. Kjelstrup, D. Bedeaux and J.M. Rubi, Heat transfer in Protein-water interfaces, Phys.

Chem. Chem. Phys. 12 (2010) 1610-1617.

[10] K.S. Glavatskiy, D. Reguera, and D. Bedeaux, Effect of compressibility in bubble formation in closed systems, J.

Chem. Phys. 138 (2013) 204708-6.

[11] Ø. Wihelmsen, D. Bedeaux, S. Kjelstrup, D. Reguera, Thermodynamic stability of nanosized multicomponent

bubbles/droplets: The square gradient theory and the capillary approach, J. Chem. Phys. 140 (2014) 024704-9

————

Elastic properties of SCBI metal-polymer nano composites

L. Colombo

Department of Physics, University of Cagliari, Italy

Supersonic cluster beam implantation (SCBI) has proved to be an effective experimental technique to generate metal-

polymer nano composites useful for biomedical applications [1]. Large-scale molecular dynamics simulations are here

applied to characterise at the atomic scale che SCBI process [2,3] and to predict the elastic properties of an Au:PDMS

nano composite as a function of actual Au volume concentration [4].

[1] L. Ravagnan, G. Divitini, S. Rebasti, M. Marelli, P. Piseri, P. Milani, J. Phys. D: Appl. Phys. 42 082002 (2009)

[2] R. Cardia, C. Melis, L. Colombo, J. Appl. Phys. 113, 224307 (2013)

[3] C. Ghisleri, F. Borghi, L. Ravagnan, A. Podesta’, C. Melis, L. Colombo, P. Milani, J. Phys. D: Appl. Phys. 47,

015301 (2014)

[4] In preparation (2014)


12

Studying fluctuations and Frank elastic constants in polymer nematics with coarse-grained models

P. Gemünden, K. Kremer, K. Ch. Daoulas *

Max Planck Institute for Polymer Research, Mainz, Germany

Texture of polymeric liquid crystals (LC) is important for various technological applications. These include fabrication

of high strength materials [1] and manipulation of morphology of polymeric semiconductors [2]. The texture is affected

significantly by Frank elastic constants of the LC material, motivating their study with particle-based computer

simulations. In addition, such modeling studies can help to resolve certain controversies in earlier theories regarding,

e.g., the scaling of the splay constant with chain length [3-5]. Here nematic LC mesophases of poly(alkylthiophenes)

are considered, mapping the polymers onto a discrete worm-like chain model which has the same persistence length [6].

Non-bonded interactions are described by soft, directional potentials [6,7] inspired by mean-field studies of LC

polymers. The model can be seen as a soft tube enclosing the “hairy rod” of the thiophene-based molecule (Figure a).

The method enables us to equilibrate large samples of nematic morphologies (Figure b) with Monte Carlo schemes and

calculate density and local nematic director fluctuation spectra. From the spectra, the splay, twist, and bend Frank

constants are extracted. Their magnitudes are found to be similar to those reported in experiments on polymer nematics.

The dependence of the fluctuation spectra and the Frank elastic constants on molecular properties such as polymer

chain length is discussed and compared with predictions obtained from analytical theories [3-5].

[1] E. Samulski, Phys. Today, 35 (1982) 40

[2] N. Stingelin, Polym. Int., 61 (2012) 866

[3] P.G. de Gennes, Polymer Liquid Crystals, ch. 5, New York: Academic Press (1982).

[4] R.B. Mayer, Polymer Liquid Crystals, ch. 6, New York: Academic Press (1982).

[5] D.R. Nelson, Physica A, 177, (1991) 220

[6] K. Ch. Daoulas, V. Rühle, K. Kremer, J. Phys.: Condens. Matter, 24 (2012) 284121

[7] P. Gemünden, C. Poelking, K. Kremer, D. Andrienko, K. Ch. Daoulas, Macromolecules, 46 (2013) 5762

————

The generalized Langevin equation: an efficient approach to non-equilibrium molecular dynamics of

open systems

L. Stella (1), C. Lorenz (2) and L. Kantorovich (2*)

(1) Queen’s University Belfast, Belfast, UK

(2) King’s College London, London, UK

The Generalized Langevin Equation (GLE) has been recently [1] suggested to simulate the time evolution of classical

solid and molecular systems when considering general non-equilibrium processes. In this approach, a part of the whole

system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because

the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the

equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g.,

in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient

algorithms to solve the GLE for realistic memory kernels are highly non-trivial, especially if the memory kernels decay

non-exponentially. This is due to the fact that one has to generate a colored noise and take account of the memory

effects in a consistent manner. In this contribution, we present a simple, yet efficient, algorithm for solving the GLE for

practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator

coupled to a Debye bath.

[1] L. Kantorovich, Generalized Langevin equation for solids. I. Rigorous derivation and main properties. – Phys. Rev.

B 78 (2008) 094304.

————


13

Field theories for shape deformations of vesicles

Y. Oya, T. Kawakatsu *

Department of Physics, Tohoku University, Sendai 980-8578, Japan

Vesicle is a closed form of a bilayer composed of amphiphilic molecules. It is a simple model of bio-membrane and can

enclose polymers inside it. Typical exapmles are found in endocytosis, exocytosis, and drug-delivery systems. We

studied this system by simulations based on field theories. We adopt a coupled theory between phase field theory(PFT)

for deformation of the vesicle and self-consistent field theory(SCFT) for the polymer conformations [1]. This PFT-

SCFT method enables us to realize a soft confinement of polymers, which was difficult to simulate only by SCFT.

Using the PFT-SCFT method, we obtained a rich variety of vesicle shapes, for example symmetric dumbbell and

asymmetric pear shapes that can not be obtained by minimizing the free energy of the vesicle without the polymers [2].

We also examined shape deformations of vesicles in an external flow field. We derived the equation of motion of the

vesicle and the flow field based on the Onsager's variational principle. Using this formulation, we can quantitatively

determine the most stable steady state of the vesicle shape in the flow field [3].

[1] Y. Oya, K. Sato, T. Kawakatsu, Europhys. Lett., 94 (2011) 68004.

[2] Y. Oya and T. Kawakatsu, Europhys. Lett., in press (arXiv:1405.2201).

[3] Y. Oya and T. Kawakatsu, submitted (arXiv:1406.6184).

————

The molecular segregation of tri-butyl phosphate in an organic diluent and its relevance to nuclear

extraction processes.

L. Leay (1), A. Del Regno (2) and A. J. Masters (3*)

(1) Dalton Cumbrian Facility, Westlakes Science and Technology Park, Moor Row, Cumbria CA24 3HA

(2) Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL

(3) School of Chemical Engineering & Analytical Science, University of Manchester, Oxford Road, manchester M13 9PL

Tri-butyl phosphate (TBP) is used as a complexing agent in the PUREX liquid-liquid phase extraction process [1] for

recovering uranium and plutonium from spent nuclear reactor fuel. After the nuclear reaction has finished, the waste

material is dissolved in nitric acid. To this is added TBP and an organic diluent, usually odourless kerosene. The TBP

complexes selectively with uranyl and plutonium nitrate, and these metal nitrates move into the organic phase, thus

achieving the desired separation. Conventional activity models, however, have difficulty in predicting the

thermodynamics of this phase separation with good accuracy. One likely reason for this is that the organic phase is not a

conventional solution, as assumed in standard process models, but is instead a structured fluid. A number of

experimental and simulation studies have shown this to be highly likely [2]. The majority of these studies, though, have

considered the system in its full complexity. Thus the system might contain TBP, a hydrocarbon diluent, water, nitric

acid and a metal nitrate. Such a complex mixture, however, has a large number of degrees of freedom and this means

that a thorough analysis of the phase behaviour is extremely difficult. We have therefore elected to build up to the full

system in stages. We first use simulation to study a binary TBP/hydrocarbon system. This is studied over a range of

temperatures and compositions and we also vary the chain length of the hydrocarbon (hexane through to dodecane). We

find that this mixture is not a uniform solution. Instead the polar TBP molecules aggregate into a molecular-scale bi-

continuous micro-emulsion over a wide range of conditions. Experimental measurements of the diffusion constant of

TBP in these systems indicate an anomalously low diffusion constant, in keeping with the hypothesis of a structured

fluid. On adding water and nitric acid to the simulation, we observed a thickening of the micro-emulsion, with the water

and nitric acid incorporated into the mesh. Further simulations of the interface between the organic and aqueous phases

showed the formation of a TBP interfacial layer, from which the micro-emulsion filaments extend into the bulk organic

phase. We present simulation evidence that the mechanisms for metal transport between the phases is for the metal

nitrate the follow a continuous path of TBP filament into the bulk phase, thereby avoiding the need for unfavourable

contact with the non-polar hydrocarbon diluent. This may help explain the surprisingly rapid kinetics of mass transfer in

the PUREX process.

[1] Spent Fuel Reprocessing Options, IAEA-Tecdoc-1587, 2008

[2] For a recent review, see, e.g., Bauer, C., Baudin, P., Dufrêche, J. F., Zemb, T. and Diat, O., Eur. Phys. J. Special

Topics 213, 225 (2012)

————


14

Monte Carlo field-theoretic simulations applied to block copolymer melts

P. Stasiak (1), M.W. Matsen (2*)

(1) School of Mathematical and Physical Sciences, University of Reading, UK

(2) Waterloo Institute for Nanotechnology, University of Waterloo, Canada

Block copolymers are polymer molecules with two (or more) chemical distinct portions, generally labelled A and B.

The A and B components tend to be incompatible, which causes the molecules to self-assemble into various elaborate

nano-structures with their A and B blocks in separate A- and B-rich domains. Self-consistent field theory (SCFT) has

been remarkably successful in predicting the geometry of these ordered phases and the transitions between them, but

the theory has some short comings due to the fact it incorporates the mean-field approximation. Of course, this can be

overcome, in principle, by simulating the system with, for example, Monte Carlo methods. However, it is impractical to

perform conventional particle-based simulations for realistic conditions because polymer molecules are generally very

large. This obstacle has recently been overcome by applying a clever transformation that converts the particle-based

Hamiltonian into a mathematically equivalent field-based Hamiltonian. We demonstrate a variant of this method called

Monte Carlo field-theoretic simulations (MC-FTS), on the simple symmetric diblock copolymer melt.

————

Studying the kinetics of copolymer self-assembly

M. Müller *, D.-W. Sun, W. Li

Institute for Theoretical Physics, Georg-August University, Göttingen, Germany

Copolymers are string-like macromolecules that are comprised of two (or more) blocks. The incompatibility between

the segments of the different blocks gives rise to microphase separation into spatially modulated structures with a

periodicity of 5 -70 nm in the bulk. Much effort has been devoted to utilizing these soft materials as templates for

nanostructures, e.g., for integrated circuits and memory devices, and fabricating defect-free structures or structures that

differ from the thermodynamically stable morphologies in the bulk. Computational modeling can contribute to

optimizing material parameters such film thickness, interaction between copolymer blocks and substrate, geometry of

confinement, and it provides fundamental insights into the physical mechanisms of directing the self-assembly,

addressing both the equilibrium structure and thermodynamics and the kinetics of self-assembly. I will discuss highly

coarse-grained, top-down particle-based models that allow us to access the long time and large length scales associated

with self-assembly [1,2], review computational methods [2,3] to determine the free energy of self-assembled

structures [4,5] and to investigate the kinetic pathways of structure formation [6]. Opportunities for directing the kinetics of self-assembly by temporal changes of thermodynamic conditions will be discussed.

[1] M. M ller, J. tat. Phys., 145 ( 11), 967

[ ] M. M ller and J.J. de Pablo, Annual Rev. Mater. Res., 43 (2013), 1-34

[3] M. M ller and K.Ch. Daoulas, Phys. Rev. Lett., 1 7 ( 11), 78 1

[4] M. M ller, Phys. Rev. Lett., 1 9 ( 1 ), 878 1

[5] . Nagpal, M M ller, P.F. Nealey, and J.J. de Pablo, AC Macro Letters, 1 ( 1 ), 418

[6] M. M ller and D.W. un, Phys. Rev. Lett. 111 ( 13), 678 1

————

Entropic electrokinetics. Dynamics of charged tracers and electrolytes under strong confinement

I. Pagonabarraga

Dept. Fundamemtal Physics, University of Barcelona, 08028-Barcelona, Spain

I will analyze the dynamics of electrolytes under confinement. I will describe computational and theoretical methods

that allow us to understand how the heterogeneous spatial confinement (found in a wide variety of situations such as

porous media, or membrane ion channels) can modify qualitatively the dynamics and transport in charged fluids.

Understand the physical mechanisms controlling electrolyte dynamcs in such conditions will shade light on their

relevance in a wide variety of situations, ranging from nano- and micro-fluidic devices to biological systems. I will

show that when particles are suspended in an electrolyte confined between corrugated charged surfaces, electrokinetic

flows lead to a new set of phenomena such as particle separation, mixing for low-Reynolds micro- and nano-metric

devices and negative mobility.


15

Collective motion in heterogeneous media and in confined geometries

F. Peruani

Universite de Nice Sophia Antipolis, Nice, France

The rapidly expanding study of active particles has focused so far almost exclusively, theoretically as well as

experimentally, on the statistical description of particle motion in idealized, homogeneous spaces. However, the great

majority of natural active particle systems take place, in the wild, in heterogeneous media: from active transport inside

the cell, which occurs in a space that is filled by organelles and vesicles, to bacterial motion, which takes place in

highly heterogeneous environments such as the soil or complex tissues such as in the gastrointestinal tract. I will show

that the presence of spatial heterogeneities brings new physics unseen in homogeneous systems at the level of the

transport properties and collective dynamics of such systems. I will show first that a random distribution of “obstacles”

can lead to spontaneous trapping of active particles. uch “obstacles” represent undesirable areas that the active

particles avoid and may correspond to a source of a repellent chemical, a light gradient, or whatever threat sensed by

the moving particles. Inside traps, active particles exhibit a vortex-like motion and remain arbitrary long times. Particle

motion then becomes genuinely sub-diffusive. We also find that the presence of such obstacles has a dramatic effect on

the collective dynamics of usual self-propelled particle systems in two dimension. In particular, we observe: i) the

existence of an optimal (angular) noise amplitude that maximizes collective motion, and ii) quasi-long range order and

the existence of two critical points (cf. with the so-called Vicsek model in homogeneous spaces where order is long-

range and there is a unique critical point). Equally true and important is the fact that most active natural systems and

experiments are subject to boundary conditions. How a confined geometry affects the collective properties of such

active systems remains largely unexplored. I will show that often observed effect of accumulation of particles close to

walls as well as the boundary-following phenomenon can both be collective effects controlled by the alignment

strength. I will provide evidence that indicates that though a density-instability occurs at all system sizes, ordering

vanishes in the thermodynamical limit. This collection of results opens a new perspective for the design and control of

active particle systems.

[1] O. Chepizhko, E. Altmann, F. Peruani, PRL 110 (2013) 238101

[2] O. Chepizhko, F. Peruani, PRL 111 (2013) 160604

————

Challenges in coarse-grained modeling of biomimetic systems

G.J.A. Sevink *, M. I. Bulacu, M. Charlaganov, J.G.E.M. Fraaije

Faculty of Mathematics and Natural Sciences, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands

The key challenge in understanding soft material properties is the recognition that functional properties intricately relate

to structural/dynamic properties and that everything is connected: the experimentally accessible emergent properties are

a consequence of mechanisms at a variety of length/time scales, often down to the smallest scale in the system, and it is

the often strong correlation of these processes that renders them inseparable. Such issues are widespread but particularly

apparent in biology, where small sets of molecules involved in functional mechanisms perform their tasks within an

adaptive/responsive matrix, introducing an important (dynamic) coupling between the subsystem and the environment.

Ab initio and other finer-grained methods on one hand are unsuited for capturing most emergent soft matter properties,

while models that are able to capture emergent behavior, by relying on a considerable reduction of degrees of freedom

or coarsening, often lack the detail that is required for relevant and/or quantitative predictions. Here, I will review

recent work on lipid membrane (re)modeling [1,2,3] and discuss the challenges that we need to address for modeling

intricate phenomena in photosynthesis.

[1] G.J.A. Sevink, M. Charlaganov, J.G.E.M. Fraaije, Soft Matter, 9 (2013), 2816.

[2] G.J.A. Sevink, J.G.E.M. Fraaije, Soft Matter, 10 (2014), 5129.

[3] M.I. Bulacu, G.J.A. Sevink, Submitted to Soft Matter (2014).

————


16

Novel, efficient, and accurate methods for calculating pressure in polymer lattice Monte Carlo

simulations

Qiang (David) Wang

Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523-

1370, USA

Pressure calculation in polymer lattice Monte Carlo simulations is an important but nontrivial subject. The three classes

of existing methods – the test-chain insertion thermodynamic integration method [1] or the compressibility route [2],

the repulsive-wall method [3], and the hydrostatic equilibrium method [4] – all have their limitations and cannot be

used to accurately calculate the bulk pressure P at all polymer volume fractions f. Here we propose several novel

methods. We first introduce the Z method combining chain insertion/deletion with the Wang-Landau – Optimized

Ensemble (WL-OE) sampling to calculate P over a range of f in a single simulation, which is very efficient at low to

intermediate f and exhibits negligible finite-size effects. We then propose the repulsive plane with bridging bonds

(RPBB) method, which is similar to the repulsive-wall method [3] but eliminates its confinement effects, and use WL-

OE sampling to estimate the density of states of the contact number and the number of bridging bonds. This gives

efficient and accurate estimation of P, especially at high f where all the methods involving chain insertion/deletion fail.

We finally combine the Z method with RPBB method, which overcomes not only the limitation that the Z method

cannot be applied at high f, but also the drawback of RPBB method that two simulation runs are required to obtain P at

a single f-value. Our Z+RPBB method gives complete thermodynamics over the entire range of continuous and exact f-

values with negligible finite-size effects.

[1] H. Okamoto, J. Chem. Phys., 1976, 64, 2686; V. Ivanov et al., Phys. Rev. E, 2007, 76, 026702.

[2] M. Stukan et al., J. Chem. Phys., 2002, 117, 9934; A. Pelissetto, J. Chem. Phys., 2008, 129, 044901.

[3] R. Dickman, J. Chem. Phys., 1987, 87, 2246.

[4] C. Addison et al., ChemPhysChem, 2005, 6, 1760.

————

Direct numerical simulations of swimming particles

J.J. Molina, R. Yamamoto *

Department of Chemical Engineering, Kyoto University, Kyoto 615-8510, Japan

We have proposed to analyze the hydrodynamic interactions in a suspension of swimmers with respect to an effective

hydrodynamic diffusion coefficient, which only considers the fluctuating motion caused by the stirring of the fluid [1].

In this work, we study the diffusion of colloidal particles immersed in a bath of swimmers. To accurately resolve the

many-body hydrodynamic interactions responsible for this diffusion, we use a direct numerical simulation scheme

based on the Smooth Profile Method (SPM). We consider a squirmer model for the self-propelled swimmers, as it

accurately reproduces the flow field generated by real micro-organisms, such as bacteria or spermatozoa. We show that

the diffusion coefficients of the colloids are comparable with the effective diffusion coefficients of the swimmers,

provided that the concentration of swimmers is high enough. At low concentrations, the difference in the way colloids

and swimmers react to the flow leads to a significant reduction in the diffusion coefficient of the colloids. This is clearly

seen in the appearance of a negative-correlation region for the velocity-correlation function of the colloids, which does

not exist for the swimmers.

[1] J.J. Molina, Y. Nakayama and R. Yamamoto, Soft Matter 9, 4923 (2013).

————


17

Contributed talks

Size really does matter: insights into electron and hole stability in TiO2 from hybrid density

functional calculations

Sanliang Ling (1*), David O. Scanlon (1,2), Ben Slater (1)

(1) Department of Chemistry, University College London, London WC1H 0AJ, UK

(2) Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didco , Oxfordshire OX11 0DE, UK

Titanium dioxide (TiO2) is one of the most studied oxide semiconductors due to its efficiency in photocatalysis and

solar energy conversion. To produce a fundamental picture of the physical mechanism behind these applications, it is

very important to understand the behaviors of electrons and holes in TiO2. While it is generally believed that electron

polarons are formed in rutile and hole polarons are formed in anatase,[1] it is not clear whether there are hole polarons

in rutile and electron polarons in anatase. In a recent EPR experiment on rutile, Yang et al. found that the hole is

localised in a nonbonding p orbital on an oxygen ion,[2] and in another XPS experiment on a Nb-doped anatase thin

film, Bhachu et al. found coexisted electron polarons and delocalised electrons.[3] On the other hand, in a recent

theoretical study by Deak et al.,[1] it was shown that holes are delocalised in rutile and electrons are delocalised in

anatase, which are in contradiction with available experimental results. In this presentation, we present our recent

hybrid density functional calculations on Al-doped rutile and Nb-doped anatase at unprecedented levels of dilution,

through taking advantage of the recently implemented auxiliary density matrix method in the CP2K code.[4] We find

that the characterisation of electron and hole stability in TiO2 is sensitive to the size of supercell employed but

converges at cell sizes larger than those previously reported in the literature. Our study highlights the importance of

considering realistic defect concentrations in similar systems.

[1] Deak et al., Phys. Rev. B, 83, (2011) 155207

[2] Yang et al., Phys. Rev. B, 82, (2010) 035209

[3] Bhachu et al., Adv. Funct. Mater., DOI: 10.1002/adfm.201400338 (2014)

[4] Guidon et al., J. Chem. Theory Comput., 6, (2010) 2348

————

Crucial role of non-specific interactions in amyloid nucleation

A. Saric *, Y. Chebaro, T. P. J. Knowles, D. Frenkel

Department of Chemistry, University of Cambridge, United Kingdom

Oligomeric protein aggregates have been implicated as toxic agents in a wide range of amyloid-related diseases, such as

Alzheimer's and Parkinson's disease. Yet it has remained unsolved whether the oligomeric clusters are a necessary step

in the formation of amyloid fibrils, or just a dangerous by-product. Analogously, it has not been resolved if the amyloid

nucleation process is a classical one-step nucleation process, or a two-step process involving pre-nucleation clusters.

We combine atomistic and coarse-grained computer simulations to study the effect of non-specific attractions between

peptides on the primary nucleation process underlying amyloid fibrillization. We find that for peptides that do not

attract, the classical one-step nucleation mechanism is possible, but only at very high peptide concentrations. At low

peptide concentrations, which mimic the physiologically relevant regime, attractive inter-peptide interactions are

essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving

prefibrillar oligomers. We show that these aggregates not only help peptides meet each other, but create an environment

that facilitates the conversion of monomers into the beta-sheet rich form characteristic of fibrils. Nucleation then

typically does not proceed via the most prevalent oligomers, but via an oligomer size that is only observed in rare

fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation

of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism the critical nucleus

size increases both with an increase in concentration and in the inter-peptide interactions, in direct contrast with

predictions from classical nucleation theory.

————


18

AntibioticDB: a database of antibiotic parameters, dynamics and properties

A.V. Vargiu

Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. 8, km 0.700, 09042 Monserrato (CA), Italy

The study of the dynamical interaction between any drug and biomolecules including nucleic acids and proteins is of

paramount importance in medicinal chemistry and related fields. With respect to the past, the advent of specialized

machines and GPUs in the field of computational biology allows to investigate the dynamics of several biological

processes up to the millisecond timescale without loosing accuracy. A key ingredient of these simulations is the

parameterization of the systems under investigation. Despite the recent efforts in making the parameterization process

an affordable task for the scientific community, obtaining reliable force-fields for general molecules is often a non-

trivial job, requiring the use of different programs and in combination with chemical, physical, and biological intuition.

In this work, we present a (to our knowledge the first) database of about 30 molecules including antibiotics, anticancer

drugs, and inhibitors of bacterial membrane proteins. For each compound, we provide the General Amber Force Field

(GAFF) parameters for the most likely conformer at pH 7, together with an analysis of properties of interest, including

number and population of relevant structural clusters, number of H-bonds with the solvent, hydration shells, dihedral

angle populations, RMSF, hydrophobic and hydrophilic molecular surfaces, extracted from microsecond-long

molecular dynamics simulations in water and counter-ions. In addition, the database includes several key molecular

parameters, such as Bader charges and dipole moment, computed via DFT methods. The present database is intended as

a first attempt to describe the properties of a large collection of molecules of medicinal importance, but also as a way to

improve the existing data thanks to feedback from the end-users. This work constitutes the first step of a wider project

aiming at creating a database containing, for each compound, different force-field parameters with increasing level of

complexity and reliability. This project is being conducted within the TRANSLOCATION project funded by the IMI

consortium.

————

Molecular dynamics simulation of a silica-poly(methyl methacrylate) nanocomposite

Hossein Eslami (1,2*), Mohammad Rahimi (1,3), Florian Müller-Plathe (1)

(1) Eduard-Zintl Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität

Darmstadt, Alarich-Weiss-Straße 4, D-64287, Germany

(2) Department of Chemistry, College of Sciences, Persian Gulf University, Boushehr 75168, Iran

(3) Institute for Molecular Engineering, University of Chicago, 5747 South Ellis Avenue, Jones 222, Chicago, IL 60637, USA

Atomistic molecular dynamics simulations were performed on silica nanoparticles, of diameters 2 nm and 4 nm at

different grafting densities ranging from 0-1chain nm-2, in poly(methyl methacrylate). The effect of surface area,

surface curvature, grafting density, and hydrogen bonding on the alteration of local structural and dynamical properties

of the polymer, from their corresponding unperturbed values was investigated. A good comparison with experiment is

found regarding the amount of PMMA adsorbed on the silica surface, the height of the first density profile peak,

hydrogen bond formation between polymer and the surface, and the interphase thickness (determined in terms of

density profile convergence to bulk value). Dynamics deceleration at the interface is shown to depend on the surface

proximity, surface curvature, and the grafting density. The short-time dynamical properties (such as hydrogen bond

dynamics) are affected less by the surface, and hence, depend less on the surface features. Long-time dynamical

properties (such as the reorientation of chain’s end to end vector), however, are affected more in systems with bigger

nanoparticles and more densely grafted surfaces. The range of surface effects on both structural and dynamical

properties (interphase thickness) depends on the inherent length and time scales of those properties. A thicker

interphase is observed for global structural and long-time dynamical properties for chains in contact with a flatter and

more densely grafted surface.

————


19

Lattice-switch Monte Carlo: a method for precise phase diagram prediction

T. L. Underwood *, G. J. Ackland

School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK

One of the primary aims of theoretical materials science is the accurate determination of the phase diagram of a given

substance. Put another way: for a given substance, where in phase space do the phase transitions occur? This question is

difficult to answer for solid-solid transitions. Surprisingly, the difficulty is by no means limited to 'realistic' models of

solids: the location of the hcp-fcc transition for the Lennard-Jones solid – an archetype of a 'simple' model of a solid –

remained contentious until relatively recently [1]. The method which resolved the Lennard-Jones dispute – lattice-

switch Monte Carlo (LSMC) [2,3] - is the subject of this work. In LSMC a type of move is introduced which 'switches'

the underlying crystal lattice, while leaving the displacements of the particles from their lattice sites unchanged.

Furthermore, one preferentially biases microstates from which 'lattice switches' are more likely. The result is that

microstates pertaining to both crystal structures are explored in a single simulation of reasonable duration. Information

gathered during the simulation is then used to evaluate the free energy difference between the crystal structures – which

is zero at a transition point. As well as being both computationally efficient and relatively simple to implement, one

crucial benefit of this method is that it provides an uncertainty for the free energy difference. This uncertainty can of

course be reduced by increasing the simulation time. LSMC is a general technique, and can be applied to a variety of

crystal lattices and particle interactions; our ultimate aim is to interface the technique with ab initio codes. The method

has even been applied to a solid-fluid transition [4]. Here, I will focus on describing the technique, but will also present

some preliminary results pertaining to the iron fcc-bcc transition examined using embedded atom potentials.

[1] A. N. Jackson, A. D. Bruce, G. J. Ackland, PRE 65, 036710 (2002)

[2] A. D. Bruce, N. B. Wilding, G. J. Ackland, PRL 79, 3002 (1997)

[3] A. D. Bruce, A. N. Jackson, G. J. Ackland, N. B. Wilding, PRE 61, 906, (2000)

[4] N. B. Wilding, A. D. Bruce, PRL 85, 5138 (2000)

————

Continuous and discontinuous dynamic unbinding transitions in dragged-out film flows

M. Galvagno (1*), D. Tseluiko (1), H. Lopez (2), U. Thiele (1,3)

(1) Department of Mathematical Sciences, Loughborough University, UK

(2) School of Physics, University College Dublin, Ireland

(3) Institut fuer Theoretische Physik, Universitaet Muenster, Germany

When a plate is withdrawn from a liquid bath a coating layer is deposited whose thickness and homogeneity depend on

the velocity and the wetting properties of the plate. After reviewing previous works [1,2] we use a long-wave

mesoscopic hydrodynamic description that incorporates wettability via a Derjaguin (disjoining) pressure to analyse

steady meniscus profiles as the plate velocity and inclination angle are changed. We identify four qualitatively different

dynamic transitions between microscopic and macroscopic coatings that are out-of-equilibrium equivalents of known

equilibrium unbinding transitions, that is, continuous and discontinuous dynamic emptying transitions and

discontinuous and continuous dynamic wetting transitions [3]. We discuss several features that have no equivalent at

equilibrium, e.g., we show that the change from the continuous to the discontinuous dynamic emptying transition

involves the emergence of exponential snaking caused by the existence of infinitely many heteroclinic orbits close to a

heteroclinic chain in an appropriate 3d phase space [4].

[1] A. O. Parry et al., Phys. Rev. Lett. 108:246101, 2012

[2] J. Ziegler, J. H. Snoeijer, J. Eggers. Eur. Phys. J.-Spec. Top. 166:177-180, 2009

[3] M. Galvagno et al., Phys. Rev. Lett. 112, 137803, 2014

[4] D. Tseluiko, M. Galvagno, U. Thiele, Eur. Phys. J. E 37, 33, 2014

————


20

Posters

Cell dynamics simulation of sphere-forming diblock copolymers in thin films on chemically patterned

substrates

Maria Serral (1*), Marco Pinna (2), Josep Bonet Avalos (1), Andrei Zvelindovsky (2)

(1) Department of Chemical Engineering, University Rovira i Virgili, Tarragona, Spain

(2) Computational Physics Group and Institute for Nanotechnology and Bioengineering, University of Central Lancashire, Preston,

United Kingdom

Diblock copolymers are used to fabricate components or devices for many nanotechnological applications because they

can form a large variety of nanostructures [1]. These macromolecules consisting of two or more covalently bonded

blocks of chemically different monomers can self-assemble into distinct microdomains such as lamellae, cylinders,

spheres, etc. Long-range ordered structures can form in thin films on solid surfaces, aiming at producing patterned

media, among others [2]. Chemically patterned substrates are considered here among all other techniques to induce

highly-ordered structures [3]. We study the morphology of films of sphere-forming block copolymers (BCP) assembled

on a striped chemical pattern, by means of the cell dynamics simulation technique (CDS) [4]. Along the lines of the

experimental work by Park et. al. [5], films of thickness comparable to the molecular size are considered. The pattern

periodicity Ls is set to values slightly below and above of the natural period of the domains in bulk L0. When the

spheres assemble on a chemically homogeneous surface, a single layer with a hexagonal arrangement is obtained

without long-range order. Contrarily, when the sphere-forming BCP assembles on a striped pattern with a

commensurate width with the period L0, a highly ordered six-fold array of spherical domains is obtained. Fast Fourier

transform and Voronoi diagram show the arrangement of six nearest-neighbors for the spherical domains with some

detected defects. For the structures assembled on the homogeneous surface a greater number of defects are observed

and grain boundaries are identified. For the structures on the striped pattern surface the percentage of defects reduces

significantly, from 14% to 4%. We conclude that the CDS results qualitatively agree with the experimental work [5].

Using this technique, the competing effect of the substrate and the natural morphology of the BCP can reveal new

morphologies with important practical implications.

[1] I.W. Hamley, Prog. Polym. Sci., 34, 1161 (2009)

[2] M. Pinna, A.V. Zvelindovsky, Eur. Phys. J. B, 85, 210 (2012)

[3] M.J. Fasolka, A.M. Mayes, Ann.Rev.Mat.Res, 31, 323 (2001)

[4] Y. Oono, S. Puri, Phys. Rev. Lett., 58, 836 (1987)

[5] S.M. Park, G.S.W. Craig, et.al, Macromolecules, 41, 9124 (2008)

————

Cell dynamics simulations of cylinder-forming diblock copolymers in thin films on topographical and

chemically patterned substrates.

Roberta Dessí *, Marco Pinna, and Andrei V. Zvelindovsky

Computational Physics Group and Institute for Nanotechnology and Bioengineering, University of Central Lancashire, Preston,

PR1 2HE, UK

Using 3-dimensional cell dynamics simulation, we demonstrate that the tetragonal phase of cylinder forming diblock

copolymers can be induced on both topographical and chemical patterned substrates. The results quantitatively describe

the different effect of both substrates on the degree of imperfection in the tetragonal phase observed in recent

experiments [1]. Comparative analysis of the structural evolution for different thermal noise level in square, rectangular

and diamond-shape lateral confinements is performed.

[1] J. Xu, T. P. Russel, B. M. Ocko, A. Checco, Soft Matter, 7 (2011) 3915

————


21

Large scale multiscale simulation of a thermoplastic elastomer

T. Honda

ZEON Corporation, Japan

One method of soft material simulation to evaluate physical properties is the coarse-grained molecular dynamics

simulation; it has been researched hardly by using the Kremer-Grest model [1]. Thermoplastic elastomer （TPE） is one of the targets to use this method. We simulated ideal ABA TPE with BCC sphere micro-phase separated structure

with the node density biased Monte Carlo (NDBMC) method which is the multiscale method to generate bead-spring

(BS) polymer structure from the segment density profiles obtained by the SCFT [2]. However real TPE has complicated

micro-phase structure, thus large scale simulation is needed to improve the physical properties. We have modified the

NDBMC method and it has been succeeded to get a BS model directory from a large scale SCFT simulation using

many CPUs with the MPI library. The figure shows a BS polymer model of a real TPE: styrene-isoprene-styrene (SIS)

triblock copolymer. The structure consists of 1.8 million polymers and 114 million beads. Blue beads are S, and green

beads are I. This research used computational resources of the HPCI system provided by Earth Simulator in JAMSTEC,

TSUBAME2.0 in Tokyo Tech., SR1600M/1 in Hokkaido-Univ., and K-supercomputer in RIKEN in Japan.

[1] K. Kremer, G.S. Grest, J. Chem. Phys. 29 (1990) 2057

[2] T. Aoyagi, T. Honda, M. Doi, J. Chem. Phys. 117 (2002) 8153

————

Morphologies of a diblock copolymer droplet in a homogeneous polymer mixture

Dung Ly

School of Engineering and Design, Brunel University, London, UK

Different morphologies of a diblock copolymer droplet confined inside a homogeneous polymer mixture were obtained

by using a static self-consistent field theory method. We started with a mixture of diblock copolymer droplet

surrounded by a homogeneous polymer. Upon changing temperature, chain length of the diblock copolymer and density

of the diblock copolymer droplet, different morphologies of the droplet were observed. Our calculation provided a new

method of creating/controlling structures of droplets polymer in solvents.

————

Gibbs’ criterion for completely wetting volatile liquids

M. Galvagno (1*), Y. Tsoumpas (2), P. Colinet (2), U. Thiele (1,3)


(2) TIPs-Fluid Physics, Universite Libre de Bruxelles, Belgium


We study the profile of evaporating liquid drops on substrates with a corner. A continuous influx allows to study steady

drops of different volume even in this non-equilibrium situation. Experimental results are qualitatively reproduced

employing a 2d long-wave mesoscopic hydrodynamic description that incorporates wettability via a Derjaguin

(disjoining) pressure. In particular, we study (i) the dependence of the evaporation-induced apparent contact angle on

the position of the contact line and (ii) the pinning and depinning of a droplet at a corner - that is for non-volatile liquids

well described by Gibbs’ criterion. Our results suggest that for volatile liquids, a simple modification of Gibbs’ criterion

is valid: replacing the equilibrium contact angle by the evaporation-caused apparent contact angle. Most importantly,

the calculations confirm the experimental observation, that there exists a dynamically produced critical angle for

depinning that increases with the evaporation rate.

————


22

Collapsed heteroclinic snaking near a heteroclinic chain in drawn meniscus problems

M. Galvagno (1*), D. Tseluiko (1), U. Thiele (1,2)



We study the deposition of a non-volatile liquid film onto a flat heated inclined plate extracted from a bath at constant

speed. We analyse steady-state meniscus solutions of a 2d long-wave mesoscopic hydrodynamic description that

incorporates wettability via a Derjaguin (disjoining) pressure as the plate velocity is changed. We observe snaking

behaviour when the plate inclination angle is above a certain critical value. Otherwise, the bifurcation curve is

monotonic. The solutions along these curves are characterised by a foot-like structure [1] formed close to the meniscus.

The foot is preceded by a thin precursor film further up the plate. We show that the collapsed snaking is related to the

existence of infinitely many heteroclinic orbits close to a heteroclinic chain in an appropriate 3d phase space connecting

the fixed points of the system [2].

[1] A. Muench, P.L. Evans, Phys. D 209, 2005.

[2] D. Tseluiko, M. Galvagno, U. Thiele, Eur. Phys. J. E 37, 2014.

————

DFT calculations of processes in early stage graphene growth

H. Tetlow (1*), J. Posthuma deBoer (2), D. Vvedensky (2), I. Ford (3), A. Baraldi (4,5), L. Kantorovich (1)

(1) Physics department, King's College London, Strand, London, WC2R 2LS

(2) The Blackett Laboratory, Imperial College London, London, SW7 2AZ

(3) Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London

WC1E 6BT, United Kingdom

(4) Physics Department and Center of Excellence for Nanostructured Materials, University of Trieste, Via Valerio 2, I-34127 Trieste,

Italy

(5) Istituto Officina dei Materiali IOM-CNR Laboratorio TASC, AREA Science Park, S.S. 14 Km 163.5, 34012 Trieste, Italy

Graphene has attracted a large amount of interest due to its properties that make it suitable for a variety of applications.

For many of these potential uses the graphene needs to be produced in large quantities and with high quality. This may

be possible using epitaxial growth, where graphene is grown on a transition metal surface by depositing hydrocarbon

molecules at high temperatures (>1000K). One particular method of epitaxial graphene growth, temperature

programmed growth (TPG), has successfully been used to grow graphene islands [1]. In this method hydrocarbon

molecules are deposited onto a transition metal surface at room temperature and then the temperature is increased in

order to facilitate the thermal decomposition of the hydrocarbons and lead to the formation of graphene flakes. It is

widely believed that during the thermal decomposition the molecules lose their H atoms to form carbon species on the

surface which act as the precursors for graphene growth [2]. However the mechanism behind this including whether

there is any dependence on the initial species is not understood. To investigate this we have examined the reaction

processes when ethylene is adsorbed onto an Ir(111) surface using DFT-based nudged elastic band calculations. All

possible dehydrogenation, hydrogenation and isomeristion reactions involved in the decomposition of the initial

molecule to form adsorbed carbon were included in this scheme. In addition breaking of the carbon-carbon bond was

considered. The energy barriers for each reaction have been used in rate equations to determine the species evolution on

the surface. This evolution is in complete agreement with the species identified during recent XPS experiments. Our

results, coupled with the new experimental insight, suggest that the decomposition process is not as originally thought

[2], during which the carbon-carbon bond is broken, leading to the production of C monomers.

[1] J. Coraux, A. T. N’Diaye, M. Engler, C. Busse, D. Wall, N. Buckanie, F. J. M. zu Heringdorf, R. van Gastel, B.

Poelsema, T. Michely, Growth of graphene on Ir(111), New J. Phys. 11 (2009) 023006.

[2] S. Lizzit, A. Baraldi, High-resolution fast X-ray photoelectron spectroscopy study of ethylene interaction with

Ir(111): From chemisorption to dissociation and graphene formation, Catalysis Today 154 (2010) 68 – 74.

————


23

Surface phase transition driven by deprotonation reaction

C. Paris *, A. Floris, L. Kantorovich

Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom

Molecular self-assembly on surfaces is of great interest due to large number of applications such as catalysis [1] and

fabrication of new functional materials [2,3]. Up to now, a great effort has been given mainly to metallic surfaces [4,5],

while comparatively little is known about molecule-surface interaction and chemical reactivity of organic molecules on

insulating surfaces. However, for many applications such as molecular electronics, phase-supported organic catalysis or

molecular optics, the replacement of metallic materials with insulators may improve the performance of such devices or

be even crucial in some cases (e.g. to eliminate leaking currents). In collaboration with the experimental group of Prof.

A. Kuhnle at Mainz University, we aim to understand the reactivity of 2,5-dihydroxybenzoic acid (DHBA), an organic

molecule deposited on a insulating substrate of calcite. Non-contact AFM experiments show that DHBA molecules

deposited at room temperature initially form two different molecular structures: (i) a striped phase, which consists of

hydrogen-bonded molecular dimers and (ii) a dense, highly packed phase of de-hydrogenated molecules covalently

bonded to the calcite surface. Interestingly, after several hours of observation the striped phase gradually transforms

into the dense one, which then remains the only one present [6]. We have investigated this phase transition by

performing ab-initio calculations in conjunction with kinetics modelling. In particular, we have studied the adsorption

configurations, diffusion and de-hydrogenation mechanisms of a monomer on the surface. In the present

communication, we will show our recent results and compare them with the experimental measurements.

[1] Nilius N., Risse T., Schauermann S., Shaikhutdinov S., Sterrer M., Freund H., J. Top.Catal. 54 (2011) 4–12.

[2] Forrest S. R., Chem. Rev. 97 (1997) 1793–1896.

[3] Umbach E., Glockler K., Sokolowsk, Surf. Sci. 402-404 (1998) 20–31.

[4] Rosei F., Schunack M., Naitoh Y., Jiang P., Gourdon A., Lægsgaard E., Stensgaard I., Joachim C., Besenbacher F.,

Prog., Surf. Sci. 71 (2003) 95–146.

[5] Barth J. V., Surf. Sci. Rep. 40 (2000) 75–149.

[6] Kittelmann M., Rahe P., Gourdon A., Kuhnle, ACS NANO 6 (2012) 7406-7411.

————

The influence of heterogeneous media on the collective behavior of self-propelled particles for

different cases of their alignment rule

O. Chepizhko (1,2*), F. Peruani(1)

(1) Universite de Nice Sophia Antipolis, Nice, France

(2) Odessa National University, Odessa, Ukraine

The study of self-propelled motion in heterogeneous media is an important task of modern active matter physics. The

collective motion in nature usually happens in non-uniform environment, so the modeling of such systems is an

important step from the modeling of the systems in the homogeneous media. We use obstacles, randomly distributed in

space, to model heterogeneous environment. It is shown that for the Vicsek-like alignment an optimal noise exists that

maximizes the collective motion [1]. For the non-aligning particles it is shown how the obstacles change transport

properties of the active particles [2]. The diffusion coefficient shows non-trivial behavior as the density of obstacles is

increased and trapping of active moving particles happens at some values of parameters. Also, the nematic type of

alignment is considered.

[1] O. Chepizhko, E. Altmann, F. Peruani, PRL 110 (2013) 238101

[2] O. Chepizhko, F. Peruani, PRL 111 (2013) 160604

————


24

Theory of liquid crystals

C. L. Stokes *, A. Masters

School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom

Liquid crystals are states of matter that lie between the classical liquid and solid states. What defines a liquid crystal is

long-range orientational order, as in a solid, combined with positional disorder in one or more dimensions. There are

numerous types of liquid crystal, each with their own unique properties. Two commonly known liquid crystalline

phases are nematics, which have a common orientation but no positional ordering, and smectics, which have a common

orientation and positional ordering in one direction and random orientation in the other directions. Due to the physical

and optical properties, liquid crystals have been used in technology such as liquid crystal displays of TVs and

computers. The nematic phase is normally unixial – i.e. there is just one distinct optical axis. In such a phase one set of

molecular axes are aligned but the other axes are orientationally disordered. In 1970, however, Freiser showed that a

biaxial nematic phase was theoretically possible, in which all three molecular axes are aligned. This phase has since

been observed experimentally, predicted to exist theoretically for various particle models and has been seen in

simulation studies. Such a phase would have three distinct optical axis and there are possible applications to liquid

crystal displays. The project objective is to investigate theoretically the phase transitions of bent core molecules using

Onsager’s theory [1]. The theory allows the transition from isotropic to nematic phase to be treated as a virial

expansion. Using a Monte Carlo algorithm to calculate the excluded volume, virial coefficients are calculated in order

to determine parameters relating to the phase transitions. In the poster presentation, the results of a single component

system model consisting of a chain spheres tangentially aligned is being studied where an approximate equation for the

excluded volume has already been derived [2].

[1] Onsager L, Phys. Rev., 62 (1942)

[2] Williamson and Jackson, Mol. Phys., 86 (1995)

————

Analysing molecular dynamics trajectories with Markov Chain Monte Carlo (MCMC) method

Changqiong Wang *, Richard Everitt, Alexei Likhtman

School of Mathematical and Physical Sciences, University of Reading, UK

The polymer melts are materials with complicated stress relaxation and flow behaviour, so the equations describing this

phenomenon are usually stochastic and include many parameters. This renders it challenging to obtain the model

parameters from molecular dynamics trajectories. Our aim is to investigate novel and efficient method to estimate the

parameters of these complicated stochastic models. We want to apply time series analysis (maximum likelihood

estimation via the Kalman filter) combined with MCMC methods to a given molecular dynamics trajectory. We first

verify our method by analysing the trajectory of one monomer of a Rouse chain with unknown beads frictions and

spring constant. Computer simulations indicate that the algorithm perform very well when the trajectory is long enough.

It allows us to achieve the posterior distribution of model parameters and uncertainty assessment. We then apply this

method to molecular dynamics trajectory of the centre of mass of polymer chain to extract its parameters of Generalized

Langevin Equation model which is able to describe it.

————


25

Simulations of colloidal and polymeric gels

G. Chivot *, A. Lemaitre

Navier Laboratory, University of Paris-Est, 2 allée Kepler, Champs-sur-Marne, France

We implement molecular dynamics simulations of patchy particles, that is Brownian particles which present attractive

patches on their surfaces. The interaction potential combines a repulsive potential between particle cores and several

anisotropic attractive contributions between patches. Patches can be initially fixed on the surfaces of particles, or can be

formed dynamically when two particles come within interaction range. We study in details the connection between the

potential parameters and the mechanical properties of rods or strings formed using such particles and show how a

variety of systems, ranging from attractive colloids to polymeric gels, can be built. For example, we can reproduce the

mechanical response of rods formed by sticking together ~1μm PMMA spheres, as studied by Pantina and Furst. Or

using long strings of sticky particles we can recover the behaviour of linear semi-flexible polymers and relate the

bending coefficient and persistence length to the interaction properties.

————

Fast lattice Monte Carlo simulations of polymers

Q. Wang

Department of Chemical and Biological Engineering, Colorado State University, USA

The recently proposed fast lattice Monte Carlo (FLMC) simulations, which use multiple occupancy of lattice sites

(MOL ) and Kronecker δ-function interactions, give much faster/better sampling of configuration space than both off-

lattice molecular simulations (with pair-potential calculations) and conventional lattice Monte Carlo simulations (with

self- and mutual-avoiding walk and nearest-neighbor interactions) of polymers.[1] Quantitative coarse graining of

polymeric systems can also be performed using lattice models with MOLS.[2] Here we use several model systems,

including polymer melts, solutions, blends, as well as confined and/or grafted polymers, to demonstrate the great

advantages of FLMC simulations in the study of equilibrium properties of polymers.

[1] Q. Wang, Soft Matter, 5 (2009) 4564; 6 (2010) 6206.

[2] P. Zhang and Q. Wang, Soft Matter, 9 (2013) 11183.

————


List of participants

Josep Bonet Avalos University Rovira i Virgili, Tarragona, Spain [email protected]

Dick Bedeaux Norwegian University of Science and

Technology, Trondheim, Norway

[email protected]

Oleksandr Chepizhko Universite de Nice Sophia Antipolis, France [email protected]

Guillaume Chivot University of Paris-Est, France [email protected]

Luciano Colombo University of Cagliary, Italy [email protected]

Kostas Daoulas Max Planck Institute for Polymer Research,

Mainz, Germany

[email protected]

Roberta Dessi University of Central Lancashire, UK [email protected]

Hossein Eslami Technische Universität Darmstadt, Germany [email protected]. tu-darmstadt.de

Daan Frenkel University of Cambridge, UK [email protected]

Mariano Galvagno Loughborough University, UK [email protected]

Takashi Honda ZEON Corporation, Japan [email protected]

Lev Kantorovich King’s College London, K [email protected]

Toshihiro Kawakatsu Tohoku University, Japan [email protected]

Sanliang Ling University College London, UK [email protected]

Dung Ly Brunel University, London, UK [email protected]

Andrew Masters University of Manchester, UK [email protected]

Mark Matsen University of Waterloo, Canada [email protected]

Philip Moriarty University of Nottingham, UK [email protected]

Marcus Müller Georg-August University, Göttingen,

Germany

[email protected].

uni-goenttigen.de

Manuela Mura University of Central Lancashire, UK [email protected]

Taku Ozawa JSOL, Japan [email protected]

Ignacio Pagonabarraga University of Barcelon,Spain [email protected]

Chiara Paris King’s College London, UK [email protected]

Fernando Peruani Universite de Nice Sophia Antipolis, France [email protected]

Marco Pinna University of Lincoln, UK [email protected]

Andela Saric University of Cambridge, UK [email protected]

Maria Serral Serra University Rovira i Virgili, Tarragona, Spain [email protected]

Agur Sevink Leiden University, The Netherlands [email protected]

Christine Stokes University of Manchester, UK christine.stokes@postgrad. manchester.ac.uk

Holly Tetlow King’s College London, K [email protected]

Lianheng Tong King’s College London, K [email protected]

Tom Underwood University of Edinburgh, Edinburgh, UK [email protected]

Attilio Vittorio Vargiu University of Cagliary, Italy [email protected]

Changqiong Wang University of Reading, UK Changqiong.Wang@student. reading.ac.uk

Qiang Wang Colorado State University, USA [email protected]

Ryoichi Yamamoto Kyoto University, Japan [email protected]

Andrei Zvelindovsky University of Lincoln, UK [email protected]






Shore at St. Bees, near Whitehaven (image is a courtesy of Dave Wilson, Cumbria).

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