Abdelkader Kara University of Central Florida Molecular Dynamics Simulations Applied to Materials Science Fes 25-26/12-08
Cancer Therapy: Photodynamic cancer therapy based on the destruction of cancer cells by laser generated atomic oxygen. A greater quantity of special dye that is used to generate the atomic oxygen is taken in by cancer cells, only cancer cells are destroyed, but the remaining dye molecules migrate to the skin and the eyes and make patient sensitive to daylight. To avoid this, the dye molecule is enclosed inside a porous nanoparticle and it did not spread to the other part of the body.
Imaging with gold Nanorods BIOPHOTONICS, December 2005 One main obstacle in biological imaging is that light does not pass through tissues very well. Researchers have shown a new imaging agent that shines 60 times brighter through tissues than conventional fluorescent dyes. The agent may offer a new tool for biological imaging. The nanorods pump electrons from their excited state and leave a hole in the ground state. This electron-hole recombination results in luminescence. They are dumbbell Shaped and almost pure gold, they produce unusually strong two photon signal (it is surface plasmon resonance effect). They can be used tumor and brain imaging in the near future. Ji-Xin Cheng
Nature, vol439, 9 February 2006 Chameleon-like nanoparticles of gold can be used to indicate the presence of various biomolecules. Adding aptamers-DNA strands that bind only to specific Molecues-to the mix open up further possibilities.
The never ending quest for New Materials FUNCTION PROPERTIES Towards Tailored Materials Atom by atom fashion?
time ELECTRONS ATOMS GRAINS GRIDS hours minutes seconds microsec nanosec picosec femtosec Continuum MESO KMC MD QM distance Å nm micron mm cm meters Material's Simulations Continuum simulations of real devices and materials Micromechanical modeling Deformation and Failure (dislocations, cracks, etc.) Transport properties (diffusion, thermal transport, etc.) New generation reactive force fields based purely on first principles For metals, oxides, organics. Describes: mechanical properties, chemistry, charge transfer, etc. Accurate calculations for bulk phases and molecules
“Dare I use the word nanostructure? But that is really what you want. You want almost every NiMo or CoMo sulfide-active site to be on the surface so you can maximize the activity. That has been a big challenge” -W. Shiflett Criterion Catalysis
The Beginning Xenon on Nickel (110) Stadium Corral Iron on Copper (111) Quantum Corral Iron on Copper (111) Carbon Monoxide Man Carbon Monoxide on Platinum (111) Iron on Copper (111) http://www.almaden.ibm.com/vis/stm/atomo.html
Molecular Dynamics Atom manipulation Lattice Dynamics Multi-scale & Multi-disciplinary Research chemistry computer science Chemisorption Data Mining Machine Learning Artificial Intelligence Reactivity SL-KMC Structure Ab initio Robust Model Potentials Dynamics physics Magnetic properties Optical properties Bio-inspired materials biology Functional Materials by Computer Assisted Design
Total energy minimization Searching minimum
Manipulation on flat, stepped and kinked surfaces
Experimental work Detailed tip height measurements during manipulation of single atoms, molecules, and dimers on a Cu(211) surface reveal different manipulation modes depending on tunneling parameters. Both attractive (Cu, Pb, Pb dimers) and repulsive manipulation (CO) are identified. Using attractive forces, discontinuous hopping of Cu and Pb atoms from one adsorption site to the next can be induced (“pulling”). Pb dimers can be pulled with repeated single, double, and triple hops. Pb atoms can also be “slid” continuously. The occurrence of different movement patterns is shown to be a sensitive probe for surface defects. L. Bartels, G. Meyer, and K.-H. Rieder, Phys. Rev. Lett. 79, 697 (1997)
1. G. Meyer, L. Bartels, S. Zöphel, E. Henze, and K.-H. RiederPhys. Rev. Lett. 78, 1512 (1997) • 2. G. Meyer, J. Repp, S. Zöphel, K.-F. Braun, S. W. Hla, S. Fölsch, L. Bartels, F. Moresco, K.-H.RiederSingle Molecules 1, 79 (2000) • 3. Saw-Wai Hla, Ludwig Bartels, Gerhard Meyer, and Karl-Heinz Rieder, Phys. Rev. Lett. 85, 2777 (2000) • J. Repp, F. Moresco, G. Meyer, K.-H. Rieder, P. Hyldgaard, and M. Persson, Phys. Rev. Lett. 85, 2981 (2000) • L. Bartels, G. Meyer, and K.-H. Rieder, Phys. Rev. Lett. 79, 697 (1997)
Manipulation modes: Manipulation types: • Lateral • Vertical • Pulling • Pushing • dragging
Lateral Manipulation Process attractive force(Pulling Mode) repulsive force(Pushing Mode) Movies are obtained from www.physik.fu-berlin.de
Lateral Manipulation in the pulling modeC. Ghosh, A. Kara, and T.S. RahmanTheoretical aspects of vertical and lateral manipulation of atoms, Surf. Sci. 502-503, 519, (2002).
Lateral Manipulation Model System • The model consists of 8 layers of atoms with 10 x 12 atoms per layer. • The stepped surface is created by removing 1/2 the atoms of the top layer. • The sharp tip consists of 35 atoms, both for the (100) and the (111) geometry. • The blunt tip consists of 34 atoms in each case (4 apex atoms for the (100) and 3 apex atoms for the (111)).
We useEmbedded Atom Method (EAM)as interaction potential Ei=internal Energy i=total electron density at position i due to the rest of the atoms Fi(fi)=the energy to embed atom i into electron density ρi. fij=two body central potential between atom i and j. Empirical Interaction Potential
Bridge Eb Hollow 1 Hollow 2 Illustration of shift in saddle point
Results 61.7 meV
Comparison of energy barriers for lateral manipulation at a tip height of 2.75Åabove step edge.
Vertical Manipulation C. Ghosh, A. Kara, T. S. RahmanComparative study of adatom manipulation on several fcc metal surfaces, J. of Nanoscience and Nanotechnology, 6, 1068 (2006).
Theoretical Details • The tip is placed at a certain height above the adatom. • For this height of the tip, the adatom is slowly raised in small steps from surface to tip apex. • At each step, the total energy of the system is minimized. • The above procedure is performed for several tip heights and for all three kinds of systems, viz. Flat, Stepped and Kinked systems. • A blunt (100) tip is used for all vertical manipulation calculations.
Experimental work G. Dujardin, A. Mayne, O. Robert, F. Rose, C. Joachim, and H. Tang, Phys. Rev. Lett. 80, 3085 (1998).
Model System Flat • The model consists of 8 layers of atoms with 10 x 12 atoms per layer. • The stepped surface is created by removing ½ the atoms of the top layer. • The flat surface has 7 layers. • The kinked surface is created by removing ½ the atoms from the step edge chain of the stepped system. Stepped Kinked
Atom extraction and island manipulation
A. Deshpande, H. Yildirim, A. Kara D. P. Acharya, J. Vaughn, T. S. Rahman, S.-W. Hla Phys. Rev. Lett. 98, 028304 (2007)
Model System sharp tip (35 atom) • adatom is placed in the 3-fold site on top of the 3- atom cluster. tip apex adatom • 3D island= 2D pad (25 atoms) on top of which a 3-atom cluster is adsorbed. cluster 3D island substrate • substrate= 6 atomic layers in fcc (111) orientation and 8x10 atoms in each layer
Details of the MD Simulations We monitor the time evolution of the position of each atom in the system. Our simulations are done at relatively low temperature (100 K). Simulations for several tip heights are performed for 200 ps each. The tip was given a constant lateral velocity of 10 m/s. • At relatively high positions of the tip (tip-adatom separations higher than 2.43 Å)the adatom interacts weakly with the tipand can not be extracted !!! • For the tip height 2.43 Å, when the tip is a few angstrom in front of the adatom, attractive forces between the tip and the adatom are so strong that the tip pulls and extracts the adatom !!!
Ag(111) system adatom manipulation/extraction using a sharp tip
Set-up of the calculations Energy landscapes in the absence of tip In this case, hopping down from a mound, the adatom encounters barrier of 0.3 eV (A to B: Hopping down) Once the adatom reaches B, the adatom could climb up to A after overcoming the same barrier of 0.3 eV (B to A: Climbing up). possible path for the extraction of the adatom
Energy barrier of adatom for lateral manipulation WITHOUT tip: A to B. Hopping down Energy barrier of adatom for vertical manipulation WITHOUT tip: B to A. Climbing up
Activation barriers in the presence of the tip (lateral and vertical manipulation processes with sharp/blunt tip) Table I. The activation energy barriers for Ag(111) system in case of lateral and vertical manipulation mode.
Cu adatom manipulation/extraction using a sharp tip Handan Yildirim, Abdelkader Kara, and Talat S. Rahman Phys. Rev. B 75, 205409 (2007)
Conclusions • Manipulation and extraction of atoms using an STM tip is possible due to a dramatic change in the energy landscape due to the presence of the tip in the vicinity of the adatom (island). • Extraction of Ag atom from a Ag mound is found to be done through the pulling mode • For Cu system, we found that extraction was achieved through dragging mode. • The difference between the cohesive energies and bond length for Cu and Ag are the main reasons for the two extraction modes.
Acknowledgement Talat S. Rahman Ahlam Al-Rawi Sondan Durukanoglu Weibin Fei Chandana Ghosh Sampyo Hong Altaf Karim Ulrike Kurpick Faisal Mehmood John Spangler Pavlin Staikov Sergey Stolbov Handan Yildirim Klaus-Peter Bohnen Joachim Ernst Thomas Greber Claude Henry Ricardo Ferrando