ESC-483 Simulation and Design of Nanostructures

Prof. Melik C. Demirel

demirel@psu.edu

melikdemirel@gmail.com

Examples from Literature

• MD simulations

• MC simulations

• Correlations/Physical Properties

• Condensed Matter Simulations (grain boundary, nanotube, etc)

• Soft Matter Simulations (proteins, lipids, etc..)

• Molecular Mechanics (nanobearing, liquid crystals, and self-assembly)

Studies in Molecular Dynamics.

1. what are the limitations in MD simulations? Name 3. (boundaries, phase transitions, time for reaching equilibrium)2. what is the time scale of MD simulations (i.e. iteration of each step)? (1 fs)3. what is the advantage of using periodic boundary condition for MD? (minimizes the surface effect)

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Anisotropic self-assembly of spherical polymer-grafted nanoparticles

1. what is the criteria to reach equilibrium in monte carlo simulations? (Multiple initial seed –energy position)2. what is the metropolis monte carlo simulation? (Energy function is involved)3. how does the MC simulation can help design new materials for assembly? (Transition states for assembly but still stochastic)

Correlations in the motion of atoms in liquid argon

1. what is the correlation function used to obtain diffusion value? (time independent correlation)2. Why argon is chosen for the simulation? (chemically inert)3. Why did they chose ~800 atoms for the liquid Argon simulation (vander walls potential for liquid phase simulation)

New pressure-induced structural transformations in silica obtained by

computer simulations

1. How does NPT algorithm (constant pressure) works? (Berendson volume scaling)2. What is the criteria for choosing the unit cell for silica phases? (symmetry)3. What is the limit of MD simulations in solid state calculations? (accuracy of force field and empirical parameters)

Dislocation processes in the deformation of nanocrystalline aluminum by molecular-

dynamics simulation1. what is the size limitation in MD simulations for dislocations? Speed of the dislocations in the nanocrystalline system2. why do we need molecular dynamics simulations for the dislocations? (details of the deformation)3. what are the application of dislocation dynamics? Computational shear strength and compare it with theoretical/experimental values

Computing the mobility of grain boundaries

1. what is the experimental challenge for grain boundary simulations? (Flat boundaries, large misorientation)2. what determined the size of grain for the simulation (e.g. The paper selected 26,000 atoms and a range between 14,000 and 150,000 was used for the runs) curvature, computational cost, surface area3. what is the application of this simulation in terms of grain boundary engineering? (Optical, electronic and mechanical properties)

The stress-strain behavior of polymer-nanotube composites from molecular dynamics simulation

1. why do we use MD for polymer-nanotube composites? mechanical properties (knowledge of structure and energetics)2. what is the application of this simulation? (aerospace light weight high strength)3. how is the interface modeled? Why is it important? Vanderwallsinteraction—directional dependent response due to weak interface properties

Molecular dynamics simulations in biology

1. How do we obtain force parameters for MD simulations (1. QD or 2. Experiments)2. What are the limitations MD for protein folding? (computational power, experimental parameters, MD)3. what do we care about MD simulations in biology? (equilibrium systems such as myoglobin heme and photosyntheis)

Molecular Dynamics Simulation of a Phospholipid Micelle

1. What determined the size of the micelle calculation? (The geometric constraint of the repeating unit)2. Why do we see micelle to spherical structure transition? (packing of the repeat unit)3. why do we need molecular dynamics simulations in addition to experiments for micelles? (transition states)•

Large-scale molecular dynamics simulation of self-assembling systems

1. what is the maximum size of simulation for MD simulation? (1 million coarse grained particles and 100 ns currently)2. how does physical properties could be obtained from MD simulations (correlation function)3. what is the applications of coarse grained simulations? (micelle and vesicle—large scale macromolecular systems)

Deformation and failure of protein materials in physiologically extreme conditions and disease

1. what is the difference between continuum experiments (MEMS) and molecular experiments (AFM)? Ensemble v.s. single molecule2. What are the challenges in linking simulation and experiments (different in length scales and can’t use single molecule measurement to determine larger scale properties of materials)3. how does the molecular simulation can help solve protein disease problems? Understanding the formation of amyloid plaques by coarse graining or structure of amyloid proteins will help to solve the problem.

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MEMS testing

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Tomography

X-ray

diffraction

NMR

Transmission elct ron

microscopy (e.g. cryo)

Optical/ magnetic tweezers

Atomic force microscopy

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Collagen fibril

Molecular Dynamics simulation of the ice nucleation and growth process leading to water freezing

1. what is the h-bonding? Electrostatic interaction between two delocalized electrons; the electronegative atoms (e.g. N,S,O) share one H-atom 2. why is the water difficult to simulate? Water is an anomalous liquid Density Maximum in the liquid state (i.e. ice floats!) Growth of Isothermal compressibility on cooling, Cp (cold water is more "squeezable"

than warm water) Formation of Hydrogen bond networks3. what are the applications of understanding ice nucleation and growth? (ice formation on on any machinery, e.g. airplane wings)

Liquid Crystals: More than Display Fillings

1. What is molecular mechanics? It is the energy minimization based on a force field. 2. What is the molecular mechanics is useful for? It can simulate final state of the structures based on conformation and rigidity, for example self assembly of colloids (unlike MD, it doesn’t care about actual changes as a function of time) 3. What is the application of liquid crystals? Display (conventional), electro-optical devices (future)

618 NATURE MATERIALS | VOL 8 | AUGUST 2009 | www.nature.com/naturematerials

news & views

et al.

n

Ralf Stannarius is at the Institute of Experimental

Physics, Otto von Guericke University Magdeburg,

D-39016 Magdeburg, Germany.

e-mail: ralf.stannarius@physik.uni-magdeburg.de

ReferencesESF Exploratory Workshop on Frontiers in European Research

on Liquid Crystalline So Matter

Science

275,

et al. Phys. Rev. Lett. 99,

et al. Phys. Rev. Lett. 100,

et al. Phys. Rev. E 77,

So Matter

4,

et al. So Matter 5,

et al. Angew. Chem. Int. Ed. 47,

Farad. Discuss.

ChemPhysChem 10,

J. Phys. II

2,

Proc. Natl Acad. Sci. USA

106,

Plenty of Room at the Bottom

+ +

Figure 1 | Entangled colloidal particles in a

nematic LC. The top image shows the equilibrium

structure of six 4.5- m microspheres bound by a

disclination loop. In the central image, two laser

traps (red crosses) are used to stretch the chain.

The bottom image is a computer simulation; the

red line marks the low-order-parameter region

around the disclination. The images are courtesy

of Igor Muševič.

nmat_N&V_AUG09.indd 618 10/7/09 12:23:16

Particle self assembly on soft elastic shells

1. what is self assembly? disordered system of pre-existing components forms an organized structure2. Why is fopply-von karman number is important for the particles? (sphericity of the shape)3. what are the applications of self-assembly of soft shells? Nanodrug delivery

Rotation of a Single Molecule within a supramolecular bearing

1. how do we obtain computational force parameters for cupper interacting with HPCQ molecule? a calculation from first principles (Quantum Mechanics) of simulated scanning probe microscopy images together with a standard molecular mechanics (MM2) routine, to optimize the structural rigidity and conformations of the molecules2. Why copper is selected for the substrate?–Metallic surface is required for surface tunneling microscopy measurements

-organic molecules adsorbed on a metallic substrate extend over a considerable number of sites, and adapt to surface chemistry, geometry and corrugation, and it can be expected a priori that their internal configurations will vary––sometimes substantially––as a result of the interaction.3. what are the application ? (molecular bearing, molecular electronics)

observations indicate that, given sufficient

space at sites of low symmetry, the molecule

rotates at speeds higher than the scan rate

used for imaging. This results in a time-

averaged image, which reduces the six lobes

to a toroidal form.

Two other possibilities exist for the obser-

vation of toroidal structures, both of which

can be discounted. It is possible that the torus

is not a molecule or is a decomposed mole-

cule (8), or that the molecular structure is

smeared to a torus by lateral diffusion. Figure

3 shows a sequence of images of a toroidal

structure, which was observed to exist in one

of two states involving a lateral translation of

0.26 nm. A toroidal structure was observed

when the molecular rotor was located at a

low-symmetry site with respect to the sur-

rounding molecules (Fig. 3, B and D). After

lateral translation of the same molecule into a

higher-symmetry site (Fig. 3, A and C), the

six lobes of the immobilized molecule in its

engaged state could be clearly observed. This

observation supports the conclusion that an

intact molecule exists in a rotational (disen-

gaged) state or immobilized (engaged) state.

If the molecule were to exhibit a very rapid

translational oscillatory motion, then the di-

mensions of the toroidal structure would be

larger than those of the molecular image in its

immobilized state. We confirmed that the

overall dimensions of the torus and the six-

lobed structures were identical, which al-

lowed us to eliminate this possibility.

These observations permit us to make

some statements concerning the nature of the

molecular rotor. First, rotation should occur

at low-symmetry sites and is controlled by

supramolecular interactions of the molecular

rotor with a bearing formed by the surround-

ing molecules. Second, the rotation appears

to be driven by thermal energy. Using ESQC

coupled with molecular mechanics calcula-

tions (ESQC-MM2), we computed the me-

chanics of the molecular bearing. We consid-

ered the supramolecular bearing with the mo-

lecular coordinates first extracted from the

STM images in Fig. 3, A and B before opti-

mizing the bearing (Fig. 4, A and B). Then,

the full atomic conformation of each of the

six molecules forming the rotor and bearing

was optimized, and the central propeller was

rotated by 1° steps in both the engaged and

the disengaged state. In the engaged state, a

rotational barrier of 117 kJ/mol was obtained.

Here, the central HB-DC forms a ratchet in

the cavity and, hence, has no significant ro-

tational degree of freedom at room tempera-

ture. In the disengaged state, the rotor is first

shifted 0.26 nm out of registry with the mo-

lecular lattice (Fig. 3). This is sufficient to

lower its rotation barrier to 29 kJ/mol, and the

central HB-DC is now free to rotate. This is

in excellent agreement with our observations.

As HB-DC was rotated, the conformation of

the t-butyl groups in contact was observed to

reorient. In addition, we calculated a transla-

tion-energy barrier to move the HB-DC from

the engaged to the disengaged position of

42 kJ/mol. This is consistent with our ob-

servation of a low rate of lateral shuttle action

driven by kT as observed in Fig. 3 when the

molecule moves from the engaged to the

disengaged state.

Compared to many proposed or synthe-

sized molecular mechanisms (11–14), our

molecular rotor works in a dry state and

appears to be wearless. Its transition from the

fixed to the rotating states can be controlled

locally by STM tip manipulation (8). The

mass of the rotor is only 1.33 10–24 kg,

leading to negligible inertia, and the rotor

will stop instantaneously when the external

drive is stopped. To examine the time scale of

the rotation, we also recorded the tunnel cur-

rent and its Fourier components up to 30

kHz, for both their fixed and rotating states.

The tunnel-current noise displays a 1/f noise

characteristic similar to the immobilized mol-

ecule, indicating that the motion occurs on a

shorter time scale.

The potential energy profile shown in Fig.

4C is highly asymmetric, but periodic in the

engaged state. Chemically driven protein mo-

tors (15) and unimolecular ratchets (16) also

have asymmetric rotational potentials. These

potentials are reminiscent of Feynman’s

“ratchet and pawl” devised to show that it is

not possible to extract unidirectional rotation-

al work from the background thermal noise

(17). Similar to Maxwell’s demon (18), the

second law of thermodynamics cannot be

violated by such macroscopic devices, be-

cause work cannot be extracted from back-

ground (white) noise (17). It has nevertheless

been proposed that work can be extracted,

using an asymmetric periodic potential, if a

secondary colored noise is applied and there-

fore rectified by the system (14). In the spirit

Fig. 3. Sequence of STM images of an atomi-cally clean Cu(100) surface after exposure to acoverage just below one complete monolayerof HB-DC measured in UHV at room tempera-ture. In (B) and (D) the molecule is imaged as atorus and is in a location where it is not inphase with the overall 2D molecular overlayer(disengaged state). In (A) and (C), the samemolecule is translated by 0.26 nm and imagedas a six-lobed structure in registry with thesurrounding molecular layer. Image area is 5.75nm by 5.75 nm, recorded with a tunnel voltageof Vt 0.35 V and a tunnel current of it 90pA.

Fig. 4. Model of the molecular mechanicssimulation used to determine the rotationalbarrier for HB-DC in (A) the engaged and (B)the disengaged state using coordinates fromFig. 3, A and B. In the simulation, the centralmolecule is incrementally rotated, and theatoms of each molecule are allowed to relaxto a minimum energy configuration to cal-culate total energy of the system. As themolecule is rotated, the conformation of thelegs is allowed to adapt in response to vander Waals interactions. (C) Rotational energybarrier computed for rotation of the mole-cule in the engaged (solid curve) and disen-gaged (dashed curve) state as a function of rotation angle.

R E P O R T S

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