h andan arkın 1,2 , w olfhard janke 1
DESCRIPTION
Thermodynamics of a p olymer c hain in an a ttractive spherical cage. H andan Arkın 1,2 , W olfhard Janke 1. 1 Institut f ü r Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany 2 Department of Physics Engineering, Faculty of Engineering, - PowerPoint PPT PresentationTRANSCRIPT
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Handan Arkın1,2, Wolfhard Janke1
1 Institut für Theoretische Physik, Universität Leipzig,Postfach 100 920, D-04009 Leipzig, Germany
2 Department of Physics Engineering, Faculty of Engineering,Ankara University Tandogan, 06100 Ankara, Turkey
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Outline
■ Motivation
■ Model: Off-lattice Polymer inside an Attractive Sphere
■ Multicanonical Monte Carlo Method
■ Some Simulation results
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Motivation
Investigating basis structure formation mechanisms of biomolecules at different interfaces is one of the major challenges of modern interdisciplinary research and possible application in nanotechnology
Applications: Polymer adhesion to metals, semiconductors biomedical implants and biosensors, smart drugs etc.
Due to the complexity introduced by the huge amount of possible substrate structures and sequence variations this problem is not trivial.
Therefore the theoretical treatment of the adsorption of macromolecules within the framework of minimalistic coarse-grained polymer models in statistical mechanics has been a longstanding problem.
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The polymer Model
2
1 2612
2
1
114cos1
4
1 N
i
N
ij ijij
N
kip
rrE
Bending energyLennard-Jones
potential
Interaction energy:
■ Coarse-grained off-lattice
■ Semi-flexible
■ Three-dimensional
Adjacent monomers are connected by rigid covalent bonds and the distance between them is fixed and set to unityThe position vector of the ith monomer is ir
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Polymer Chain inside an Attractice Sphere Potential
■ The interaction of polymer monomers and the attractive sphere is of van der Walls type, modeled by LJ 12-6
We integrate this potential over the entire sphere inner surface
Where the surface element in spherical coordinates is
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Polymer Chain inside an Attractice Sphere Potential
icicicicr
rrRrRrRrR
RVi
ccs
441010
25
14)(
cR The radius of the sphere
ir The distance of a monomer to the origin
c Set to unity
Varied during simulation
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Polymer Chain inside an Attractice Sphere Potential
2
1 2612
2
1
114cos1
4
1 N
i
N
ij ijij
N
kip
rrE
icicicic rRrRrRrRV
N
i iccs rRr
441010
125
114)(
20N
20cR4.11.0
Simulations in Generalized Ensembles
• Idea: choose ensemble that allows better sampling
• Example: Multicanonical Ensemble • General Procedure: Determine the weight factors Large scale simulation Calculate expectation values for desired temperatures
• Problem: Find good estimators for the weights
• Advantages: Any energy barrier can be crossed. The probability of finding the global minimum is enhanced. Thermodynamic quantities for a range of temperatures
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Multicanonical Monte Carlo Method
• The canonical ensemble samples with the Boltzmann probability density
where x labels the configuration. The probability of the
energy E is
where n(E) is the density of states.
• The Muca ensemble is based on a probability function in which the different energies are equally probable:
where w(E) are multicanonical weight factors.
ZTkExP Bx
B //exp
ZTkEEnEP B
B
T //exp
.constEwEnEPMU
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Observables
Specific Heat:2
22
)(NT
TCEE
V
Radius of gyration:
Mean number of adsorbed monomers to the inner wall of the sphere:
We define a monomer i is being adsorbed if
and this can be expressed as .
N
i
N
j jicmi
N
ig NrrNrrR1 1
222
1
2 2/)(/)(
2.1 cic rrR
N
i ics rrN1
)(
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Observables
■ Gyration Tensor
Transformation to principal axis system diagonalizes S
Where the eigenvalues are sorted in descending order
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Observables
■ The first invariant of Gyration Tensor
The second invariant shape descriptor is Shape Anisotropy (reflects both symmetry and dimensionality)
Where
The last shape desciptor is the asphericity parameter
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Results: Pseudo Phase Diagram
D : Desorbed
A: Adsorbed
E: Extended
G: Globular
C:Compact
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Results: Specific -Heat
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Results: Radius of Gyration
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Results: The mean number of adsorbed monomers
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Results: Relative Shape Anisotropy
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Results: The eigenvalues of the Gyration tensor
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Results: Fluctuations of the Observables
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Results: Low Energy Conformations
1.0 4.0 7.0 0.1
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Acknowlegments
Thanks to ...
CQT Team, Institute of Theoretical Physics, Leipzig
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Results: The ratio of the greatest eigenvalue to the smallest