Professor (W2) for Molecular Virology of Human...

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0.5 0.6 0.7 0.8 0.9 1 1.1 0.6 0.8 1 1.2 1.4 1.6 1.8 Liquid Solid Ttriple point=0.694 T ρ t=10 t=60 t=120 t=160 Growth kinetics of solid-liquid interfaces Francesco Turci 1 , Martin Oettel 2 , Tanja Schilling 1 2. Langevin dynamics of LJ particles 5. DDFT 1. Introduction 1 Theory of Soft Matter Group - Université du Luxembourg , 2 Institut für Angewandte Physik - Eberhard Karls Universität Tübingen Materials science makes extensive use of coarse-grained models for the dynamics and growth of solid and melt phases. In particular, so called Phase-Field models are used for the determination of macroscopic properties. This theory can be derived from a simplification of the Dynamical Density Functional Theory [1]. This effective approach implies that few density modes are sufficient for the description of the dynamics. We test this assumption on a simple non-equilibrium model for crystal growth, comparing numerical simulations and 3d DDFT calculations. Fig.2. Crystalline growth: perfect, frozen fcc particles (yellow), free fcc particles (green), pre-structured particles (fuchsia) and liquid (turquoise), distinguished using the locally averaged bond order parameters. Pre- structured hcp patches are concentrated at the interfaces. Planar growth of a crystal of Lennard-Jones particles. Langevin dynamics (for comparison with DDFT where Brownian motion is assumed) NVT ensemble. Fixed structured perfect fcc walls exposing the [100] orientation to the liquid. Metastable liquid such that ρ liq =ρ so l =0.9732. Fig.1 LJ phase diagram: melting line. Simple model @⇢( ~ r, t) @ t = r ( ~ r, t)r δ F δ⇢ + V ext ( ~ r ) δ F δ⇢ = β -1 (ln - Δc (2) ref + μ ref ) Deterministic evolution of the density field according to a diffusion-like equation where the chemical potential is chosen according to the Ramakrishnan- Youssouf approximation with being the direct correlation function, derived via mean field approximation from the pair potential of choice. c (2) ref 2 1.5 1 0.5 0 4 3 2 1 0 Density field Chemical Potential Real-space, discrete-time evolution provides the 3d density field and reproduces the crystal growth. We have then access to related quantities such as the free energy, the chemical potential or the grand potential. References [1] H. Emmerich et al. Advances in Physics 61, 665 (2012). [2] W. Lechner and C. Dellago, J. Chem. Phys. 129, 114707 (2008). [3] E. Marinari et al., J. Phys. A, 33, 8181 (2000). [4] M. Oettel et al, Physical Review E 86, 021404 (2012). 5 10 15 20 25 z -1 0 1 2 3 4 5 6 7 8 (z ) -15 -10 -5 0 5 10 15 k[/2a] 0 500 1000 1500 2000 5 10 15 20 25 z -1 0 1 2 3 4 5 6 7 8 (z ) -10 -5 0 5 10 k[/2a] 0 500 1000 1500 2000 A few modes are needed to determine the laterally averaged density profile, correctly matching the position of the interface (fig. 5). Fig.5. Laterally averaged density profile (yellow) and its reconstruction using low order modes (black) during growth. 4. Modes and interface width After full growth, the ABAB fcc stacking in [100] implies a defect when the walls facets are not compatible. The defect is a dislocation of all the crystalline planes. before after ABABABABABABABABABABABABABABABABABABBABABABAB t=10 t=60 t=90 3. Geometrical properties Averaged local bond order parameters [2] distinguish liquid/ solid phases (Fig.2). At the interface (Fig. 3) the particles jump from an hcp order to the fcc stacking. hcp fcc hcp fcc hcp fcc Fig.3. PDF of the averaged local bond order parameters and at different times during the growth (see fig.2 for comparison) for particles in the vicinity of the interface. ¯ q 6 ¯ q 4 Interface widths can be computed from both the density and the q6 profiles. The scaling w~t α is different for the two approaches and deviates from the KPZ growth model . From q 6 From Density Prole 0.1589x 0.71179 t 0.1161 t 0.24 , 3D KPZ width 0.5 1 2 t 5 10 20 50 Fig.6. Interface widths computed from the BOP profile and the density profile compared with KPZ predictions. Fig.4. Formation of a dislocation. We will therefore extend previous equilibrium work [4] providing a full comparison of the interface properties between the atomistic and the coarse- grained model.

Transcript of Professor (W2) for Molecular Virology of Human...

Page 1: Professor (W2) for Molecular Virology of Human …orbilu.uni.lu/bitstream/10993/16070/1/Lausanne2013Poster.pdf · Liquid Solid Ttriple point=0.694 T ... 2 Institut für Angewandte

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1

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Liquid

Solid

Ttriple point=0.694

T

ρ

t=10

t=60

t=120

t=160

Growth kinetics of solid-liquid interfacesFrancesco Turci 1, Martin Oettel 2, Tanja Schilling 1

2. Langevin dynamics of LJ particles

5. DDFT

1. Introduction

1 Theory of Soft Matter Group - Université du Luxembourg , 2 Institut für Angewandte Physik - Eberhard Karls Universität Tübingen

Materials science makes extensive use of coarse-grained models for the dynamics and growth of solid and melt phases. In particular, so called Phase-Field models are used for the determination of macroscopic properties. This theory can be derived from a simplification of the Dynamical Density Functional Theory [1].

This effective approach implies that few density modes are sufficient for the description of the dynamics. We test this assumption on a simple non-equilibrium model for crystal growth, comparing numerical simulations and 3d DDFT calculations.

Fig.2. Crystalline growth: perfect, frozen fcc particles (yellow), free fcc particles (green), pre-structured particles (fuchsia) and liquid (turquoise), distinguished using the locally averaged bond order parameters. Pre-structured hcp patches are concentrated at the interfaces.

Planar growth of a crystal of Lennard-Jones particles.

•Langevin dynamics (for comparison with DDFT where Brownian motion is assumed)

•NVT ensemble.•Fixed structured perfect fcc walls exposing the [100]

orientation to the liquid.•Metastable liquid such that ρliq=ρsol=0.9732.

Fig.1 LJ phase diagram: melting line.

Simple model

INVESTIGATING FUTURE CHALLENGES

2011 ANNUAL REPORT

The Faculty of Medicine at the Eberhard Karls Universität Tübingen and the Institute of Medical Virology and Epidemiology of Viral Diseases offer the positon of a

Professor (W2) for Molecular Virology of Human Infectious Diseases

to be filled as soon as possible.

According to § 50 (2) No. 5 Landeshochschulgesetz Baden-Württemberg the professorship is limited to a period of six years and shall be established with the objective to promote highly-qualified young scientists.

Applicants should have a proven track record of international excellence in the field of molecular virology of human infectious diseases. His/her research focus may include functional aspects of host-virus interaction, immune defense of viral diseases as well as tumor diseases and chronic diseases caused by relevant human pathogenic viruses.

He/she is expected to actively participate in the research fields of infection biology and immunotherapy as well as in existing and future DFG-projects (SFB 685). In addition the successful candidate will need to work closely with the existing German health centres „German Centre for Infection Research“ (DZIF) and „German Cancer Research Centre“ (DKTK)“. Teaching at the Faculty of Medicine in the fields of human medicine, molecular medicine and medical technology is expected, particularly in the graduate programs of the university.

Requirements for appointment are a university degree either in human medicine or in life sciences, broad experience in molecular virology, a record of excellent research activities equivalent to the German Habilitation and documented teaching skills.

Tübingen University is particularly interested in applications from female candidates for this position and therefore strongly urges women to apply.

Applications from disabled candidates will be given preference if the qualifications of these candidates are identical to those of a non-disabled candidate.

Applications including Curriculum Vitae, copies of relevant documents, a structured list of publications, listing of grants and teaching experience, results of teaching evaluations, a list of research collaborations, concepts for future research (not more than 3 pages) should be submitted twofold until March 14, 2013 to the

Dean of the Faculty of Medicine Eberhard Karls Universität Tübingen Professor Dr. med. Ingo B. Autenrieth Geissweg 5 72076 Tübingen, Germany

Please submit only copies of the relevant documents as applications can not be returned but are destroyed in conformity with data protection rules.

Please also complete the application questionnaire that can be downloaded under http://www.medizin.uni-tuebingen.de/Mitarbeiter/Karriere/Job+finden+_+Bewerben/ Jobangebote/Berufungen.html and send it to: [email protected]

@⇢(~r, t)

@t= r

⇢(~r, t)r

✓�F

�⇢+ V ext(~r)

◆�

�F

�⇢= ��1(ln ⇢��⇢ ⇤ c(2)ref + µref )

Deterministic evolution of the density field according to a diffusion-like equation

where the chemical potential is chosen according to the Ramakrishnan-Youssouf approximation

with being the direct correlation function, derived via mean field approximation from the pair potential of choice.

c(2)ref

2

1.5

1

0.5

0

4

3

2

1

0

Density field

Chemical Potential

Real-space, discrete-time evolution provides the 3d density field and reproduces the crystal growth.

We have then access to related quantities such as the free energy, the chemical potential or the grand potential.

References[1] H. Emmerich et al. Advances in Physics 61, 665 (2012).[2] W. Lechner and C. Dellago, J. Chem. Phys. 129, 114707 (2008).[3] E. Marinari et al., J. Phys. A, 33, 8181 (2000).[4] M. Oettel et al, Physical Review E 86, 021404 (2012).

5 10 15 20 25z

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0

1

2

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4

5

6

7

8

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5 10 15 20 25z

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0

1

2

3

4

5

6

7

8

⇢(z)

�10 �5 0 5 10k[⇡/2a]

0500

100015002000

A few modes are needed to determine the laterally averaged density profile, correctly matching the position of the interface (fig. 5).

Fig.5. Laterally averaged density profile (yellow) and its reconstruction using low order modes (black) during growth.

4. Modes and interface width

After full growth, the ABAB fcc stacking in [100] implies a defect when the walls facets are not compatible. The defect is a dislocation of all the crystalline planes.

before

after

ABABABABABABABABABABABABABABABABABABBABABABAB

t=10 t=60 t=90

3. Geometrical properties

Averaged local bond order parameters [2] distinguish liquid/solid phases (Fig.2). At the interface (Fig. 3) the particles jump from an hcp order to the fcc stacking.

hcp

fcc

hcp

fcc

hcp

fcc

Fig.3. PDF of the averaged local bond order parameters and at different times during the growth (see fig.2 for comparison) for particles in the vicinity of the interface.

q̄6q̄4

Interface widths can be computed from both the density and the q6 profiles. The scaling w~tα is different for the two approaches and deviates from the KPZ growth model .

From q6From Density Profile0.1589x0.71179

t0.1161

t0.24, 3D KPZ

widt

h

0.5

1

2

t5 10 20 50

Fig.6. Interface widths computed from the BOP profile and the density profile compared with KPZ predictions.

Fig.4. Formation of a dislocation.

We will therefore extend previous equilibrium work [4] providing a full comparison of the interface properties between the atomistic and the coarse-grained model.