Mesoscale or coarse-grained modeling

Coarse Grained & Mesoscopic Modeling

This project is a very active one in our group. Most of the work as of the end of 2003 revolves around our ablation project. This situation is changing, however, as we are interested in applying mesoscopic models to ionization in SIMS and synergistic effects of UV radiation and O atom bombardment in low earth orbit. Barbara

Coarse Grained Chemical Reaction Model

A methodology for including effects of chemical reactions in coarse-grained computer simulations such as those that use the united atom approximation was developed by Yaroslava G. Yingling in our group. The new coarse-grained chemical reaction model (CGCRM) adopts the philosophy of kinetic Monte Carlos approaches and includes a probabilistic element to predicting when reactions occur, thus obviating the need for a chemically correct interaction potential. The CGCRM uses known chemical reactions along with their probabilities and exothermicities for a specific material in order to assess the effect of chemical reactions on a physical process of interest. The reaction event in the simulation is implemented by removing the reactant molecules from the simulation and replacing them with product molecules. The position of the product molecules is carefully adjusted to make sure that the total energy change of the system corresponds to the reaction exothermicity. The CGCR model has been applied to simulations of laser irradiation of chlorobenzene at fluences such that there is ablation or massive removal of material. In the photochemical simulation, the photon cleaves the C-Cl bond creating two radicals that can undergo subsequent abstraction and radical-radical recombination reactions. An overview of the CGCRM is in Ref. 249. The first reference is Ref. 213. More information on results is given on our photoablation web page.

Breathing Sphere Model

This model was developed by Leonid V. Zhigilei when he was a postdoc in our group for describing laser ablation due to thermal processes. The novel feature is an internal (or breathing) mode in the "molecule" that allows us to include a reasonable rate of energy transfer from the irradiated molecule to the remaining solid.

The first reference is Ref. 164.
An early feature article is Ref. 175.
A comprehensive study is given in Ref. 196.
Two reviews and comparisions to experimental data are given in Refs. 218 & 235.
More information including all the references is on the thermal ablation web page.

Methodology Advances

A dynamic boundary condition is developed to account for the laser induced pressure wave propagation through the boundary of the computational cell as well as for the direct laser energy deposition in the boundary region. The boundary condition allows us to focus the computational effort of the MD simulation to the region where active processes of laser induced melting, ablation and damage occur. See Fig. 14 (10K), Fig. 15 (12K), and Refs. 182 and 188.
A combined molecular dynamics - finite element method has been implemented and tested on the propagation of the laser induced pressure wave through a micrometer-sized sample. This computational approach can be useful in cases where a detailed atomic-level analysis is necessary in localized spatially separated regions of a large system. Fig. 16 (6K), Ref. 180.
A two-stage computational method combines the molecular dynamics breathing sphere model for simulation of the initial stage of laser ablation and the direct simulation Monte Carlo (DSMC) method for simulation of the multi-component ablation plume development on the time- and length-scales of a real experimental configurations. This multiscale simulation, addressing physical processes on different length- and time scales, gains a new insight into the laser ablation in the stress confinement regime. Specifically we demonstrate how to include a sparse but important cluster distribution in the plume in the DSMC calculation. Ref. 224, 231, 233 and 239.

Publications:


249.	Coarse Grained Chemical Reaction Model, Y. G. Yingling and B.J. Garrison, J. Phys. Chem. B, Feature Article, 108, 1815-1821 (2004).[full article - PDF]
248.	Evolution of a plume in laser ablation: dependence on the spot size, M. I. Zeifman, B. J. Garrison,and L. V. Zhigilei, Proceedings of the 36th AIAA Thermophysics Conference,AIAA Paper 2003-3493, (2003).[full article - PDF]
247.	The limit of overheating and the threshold behavior in laser ablation, B. J. Garrison,T. E. Itina, and L. V. Zhigilei, Physical Review E, 68, 041501-1 to 041501-4 (2003).[full article - PDF]
241.	Substrate-assisted Laser-initiated Ejection of Proteins Embedded in Water Films, Y. Dou, N. Winograd, B. J. Garrison and L. V. Zhigilei, Journal of Physical Chemistry B, 107, 2362-2365 (2003).[full article - PDF]
239.	A Hybrid MD-DSMC Model of Picosecond Laser Ablation and Desorption, M. I. Zeifman, B. J. Garrison and L. V. Zhigilei, AIP Conference Proceedings, 23rd International Symposium on Rarefied Gas Dynamics, ed. A. D. Ketsdever and E. P. Muntz, 939-946 (2003).[full article - PDF]
238.	Photochemical ablation of organic solids, Y. G. Yingling and B.J. Garrison, Nucl. Instrum. Methods B, 203, 188-194 (2003).[full article - PDF]
235.	Computer Simulation of Laser Ablation of Molecular Substrates, L. V. Zhigilei, E. Leveugle, B. J. Garrison, Y. G. Yingling, and M. I. Zeifman, Chemical Reviews, 103, 321-348 (2003).[full article - PDF]
234.	Photochemical induced effects in material ejection in laser ablation, Y. G. Yingling and B. J. Garrison, Chem. Phys. Lett., 364, 237-243 (2002).[full article - PDF]
233.	Direct Simulation Monte Carlo Calculation: Strategies for Using Complex Initial Conditions, M. I. Zeifman, B. J. Garrison, and L. V. Zhigilei, MRS Proceedings, 731, W3.8.1-W3.8.6 (2002).[full article - PDF]
231.	Combined Molecular Dynamics - Direct Simulation Monte Carlo Computational Simulation of Laser Ablation Plume Evolution, M. Zeifman, B. J. Garrison, and L. V. Zhigilei, Journal of Applied Physics, 92, 2181-2193 (2002).[full article - PDF]
226.	Big Molecule Ejection - SIMS vs. MALDI, B. J. Garrison, A. Delcorte, L. V. Zhigilei, T. E. Itina, K. D. Krantzman, Y. G. Yingling, C. M. McQuaw, E. J. Smiley and N. Winograd, SIMS-XIII Proceedings, Appl. Surf. Sci., 203-204, 69-71 (2003).[full article - PDF]
224.	Multiscale Simulation of Laser Ablation of Organic Solids: Evolution of the Plume, M. I. Zeifman, B. J. Garrison, L. V. Zhigilei, Appl. Surf. Sci., COLA'01 Proceedings, 197-198, 27-34 (2002).[full article - PDF]
221.	Pressure-transmitting boundary conditions for molecular-dynamics simulations, C. Schaefer, H. M. Urbassek, L. V. Zhigilei and B. J. Garrison, Computational Materials Science, 24, 421-429 (2002).[full article - PDF]
219.	Microscopic mechanisms of matrix assisted laser desorption of analyte molecules: Insights from molecular dynamics simulation, T. E. Itina, L. V. Zhigilei and B. J. Garrison, J. Phys. Chem B, 106, 303-310 (2002).[full article - PDF]
218.	MD Simulations of MALDesorption - Connections to Experiment, L. V. Zhigilei, Y. G. Yingling, T. E. Itina, T. A. Schoolcraft and B. J. Garrison, Int. J. Mass Spectrom. Ion Processes, Franz Hillenkamp, special issue, 226, 85-106 (2003).[full article - PDF]
216.	Laser Expulsion of an Organic Molecular Nano-jet from a Confined Domain onto a Polymer Surface, M. Goto, L. V. Zhigilei, J. Hobley, M. Kishimoto, B. J. Garrison and H. Fukumura, J. Appl. Phys.,90, 4755-4760 (2001).[full article - PDF]
215.	The role of inertial and spatial confinement in laser interaction with organic materials, L. V. Zhigilei, B. J. Garrison, M. Goto, J. Hobley, M. Kishimoto, H. Fukumura and A. G. Zhidkov, Proceedings of the 5th World Conference on Systemics, Cybernetics and Informatics,(Institute of Informatics, Orlando, Florida), 215-220 (2001)[full article - PDF]
213.	The Role of the Photochemical Fragmentation in Laser Ablation, Y. G. Yingling, L. V. Zhigilei and B. J. Garrison, J. Photochemistry and Photobiology A: Chemistry, 145, 173-181 (2001).[full article - PDF]
211.	Explosive Boiling of Water Films Adjacent to Heated Surfaces: A Microscopic Description, Y. S. Dou, L. V. Zhigilei, N. Winograd, and B. J. Garrison, J. Phys. Chem. A, Zeitschrift for William H. Miller Issue, 105, 2748-2755 (2001).[full article - PDF]
210.	Laser Ablation of Bi-component Systems: A Probe of Molecular Ejection Mechanisms, Y. G. Yingling, L. V. Zhigilei, B. J. Garrison, A. Koubenakis, J. Labrakis, and S. Georgiou, Appl. Phys. Lett., 78, 1631-1633 (2001).[full article - PDF]
209.	Molecular Dynamics Simulations of Laser Disintegration of Aerosol Particles, T. A. Schoolcraft, G. S. Constable, L. V. Zhigilei, and B. J. Garrison, Anal. Chem., Accelerated Article, 72, 5143-5150 (2000). [full article - PDF]
207.	Thickness Effects of Water Overlayer on its Explosive Evaporation at Heated Metal Surfaces, Y. Dou, L. V. Zhigilei, Z. Postawa, N. Winograd, and B. J. Garrison, Nucl. Instrum. Methods Phys. Research B, 180, 105-111 (2001).[full article - PDF]
205.	Photochemical Fragmentation Processes in Laser Ablation of Organic Solids, Y. G. Yingling, L. V. Zhigilei, and B. J. Garrison, Nucl. Instrum. Methods Phys. Research B, 180, 171-175 (2001).[full article - PDF]
204.	Matrix assisted pulsed laser evaporation of polymeric materials: molecular dynamics simulation, T. E. Itina, L. V. Zhigilei, and B. J. Garrison, Nucl. Instrum. Methods Phys. Research B, 180, 238-244 (2001).[full article - PDF]
202.	Laser ablation in a model two-phase system, G. J. Williams, L. V. Zhigilei, and B. J. Garrison, Nucl. Instrum. Methods Phys. Research B, 180, 209-215 (2001).[full article - PDF]
201.	Molecular Dynamics Simulations of Laser Disintegration of Amorphous Aerosol Particles with Spatially Nonuniform Absorption, T. A. Schoolcraft, G. S. Constable, B. Jackson, L. V. Zhigilei, and B. J. Garrison, Nucl. Instrum. Methods Phys. Research B, 180, 245-250 (2001).[full article - PDF]
196.	Microscopic Mechanisms of Laser Ablation of Organic Solids in the Thermal and Stress Confinement Irradiation Regimes, L. V. Zhigilei and Barbara J. Garrison, Journal of Applied Physics, 88, 1281-1298 (2000). [full article - PDF]
193.	Mechanisms of Laser Ablation from Molecular Dynamics Simulations: Dependence on the Initial Temperature and Pulse Duration, L. V. Zhigilei and B. J. Garrison, Appl. Phys. A, 69, S75-S80 (1999). [full article - PDF]
188.	Mesoscopic Breathing Sphere Model for Computer Simulation of Laser Ablation and Damage, L. V. Zhigilei and B.J. Garrison, Proceedings of Int'l Conf. On Modeling and Sim. Of Microsystems, Semi-conductors, Sensors and Actuators, MSM '99, 138-141 (1999). [full article - PDF]
186.	Phase Transition at Low Fluences in Laser Desorption of Organic Solids: A Molecular Dynamics Study, P. B. S. Kodali, L. V. Zhigilei and B. J. Garrison, Nucl. Intrum. Methods Phys. Research B, 153, 167-171 (1999). [full article - PDF]
182.	Pressure Waves in Microscopic Simulations of Laser Ablation, L. V. Zhigilei, B. J. Garrison, Multiscale Modelling of Materials, edited by T. Diaz de la Rubia, T. Kaxiras, V. Bulatov, N. M. Ghoniem, and R. Phillips, 491-496 (1999). [full article -PDF]
181.	Molecular Dynamics Simulation Study of the Fluence Dependence of Yield and Plume Composition in Laser Desorption and Ablation, L. V. Zhigilei and B. J. Garrison, Appl. Phys. Lett. 74, 1341-1343 (1999). [full article - PDF]
180.	A Combined Molecular Dynamics and Finite Element Method Technique Applied to Laser Induced Pressure Wave Propagation, J. A. Smirnova, L. V. Zhigilei, B. J. Garrison, Computer Physics Communications, 118, 11-16 (1999). [full article - PDF]
176.	Velocity Distributions of Analyte Molecules in Matrix-Assisted Laser Desorption from Computer Simulations, L. V. Zhigilei and B. J. Garrison, Rapid Commun. Mass Spectrom. 12, 1273-1277 (1998). [full article - PDF]
175.	A Microscopic View of Laser Ablation, L. V. Zhigilei, P. B. S. Kodali and B. J. Garrison, J. Phys. Chem. B, Feature Article, 102, 2845-2853 (1998). [full article - PDF]
173.	Microscopic Simulation of Short Pulse Laser Damage of Melanin Particles, L. V. Zhigilei, B. J. Garrison, Laser-Tissue Interaction IX, S. L. Jacques, Editor, Proc. SPIE 3254, 135-143 (1998). [full article - PDF]
172.	Computer Simulation Study of Damage and Ablation of Submicron Particles from Short Pulse Laser Irradiation, L. V. Zhigilei and B. J. Garrison, Appl. Surf. Sci., 127, 142-150 (1998). [full article - PDF]
168.	Velocity Distributions of Molecules Ejected in Laser Ablation, L. Zhigilei and B. J. Garrison, Appl. Phys. Lett. 71 551-553 (1997). [full article - PDF]
167.	On the Threshold Behavior in the Laser Ablation of Organic Solids, L. V. Zhigilei, P. B. S. Kodali and B. J. Garrison, Chem. Phys. Lett., 276, 269-273 (1997). [full article - PDF]
164.	Molecular Dynamics Model for Laser Ablation of Organic Solids, L. V. Zhigilei, P. B. S. Kodali and B. J. Garrison, J. Phys. Chem. B 101, 2028-2037 (1997). [full article - PDF]

Barbara J. Garrison - December 23, 2003