Computational approach
In the proposed computational study two types of molecular dynamics models will be
used to address different aspects of cluster impact phenomenon. First, a mesoscopic
description based on the breathing sphere model will be used to investigate the processes
of cluster disintegration under different experimental conditions realized in IDEC.
Second, an atomic-level description of the analyte and solvent molecules and will be used
to obtain more detailed quantitative information on the energy redistribution during the
cluster impact. Below we give a short description of the models.
The mesoscopic breathing sphere model [1,2] will be used to simulate the cluster
impact phenomenon and to obtain the parameters of the disintegration process. In this
model, each molecule (or group of molecules) is represented by a single particle and the
intermolecular interaction is defined by the distance between the edges of the particles
rather than their centers. The parameters within the model are chosen to reproduce the
properties of the simulated organic material. The main advantage of the breathing sphere
model is the ability to study the dynamics of the system at the mesoscopic length scale, a
regime that is not accessible neither with atomistic nor continuum computational methods
[3,4,5]. The length scale of the simulation is defined by the size of the dynamic elements
for which equations of motion are solved. The dynamic elements in the breathing sphere
model are significantly larger than individual atoms and the size of the computational cell
can be much larger than the one in atomistic simulations. The time-step in the numerical
integration controls the total time that can be simulated and the fastest motion in the
system dictates the time-step. Since explicit atomic vibrations, especially H atom
vibrations, are not followed in the meso-scale model, the time-step of integration can be
increased by several orders of magnitude. Of relevance to the proposed study is the
demonstrated ability of the breathing sphere model to provide microscopic information
on the thermal and mechanical (induced by the pressure waves) processes leading to
disintegration of molecular clusters [6,7,8].
In order to examine the conditions and events leading to fragmentation of analyte
molecules embedded in a molecular cluster, a combination of the breathing sphere model
for solvent molecules with a bead-and-spring model for polymer analyte molecules
[9,10,11] will be used. Each bead in the bead-and-spring model represents a functional
group of the molecule, the chains are assumed to be flexible with an interaction potential
that is appropriate for chemical bond strengths. Most importantly, the bonds between
beads can dissociate if the energy imparted to the molecule is sufficiently large. The use
of coarse-grained models for both molecular matrix and larger analyte molecules will
allow us to perform simulations at the experimental time and length-scales
Atomistic modeling will be used to examine the atomic-level processes under specific
conditions realized in the cluster during or following the collision with the substrate. The
events and conditions leading to fragmentation of the analyte molecules will be studied
by performing a series of simulations at a range of conditions realized at different times
during the cluster impact. The conditions for atomistic simulations will be provided by a
coarse-grained breathing sphere model described above.
Two types of interaction potentials will be used in the atomic-level simulations. The first
is the many-body CH potential of Brenner [12] for hydrocarbons that allows simulation
of reactions including dissociation. In order to use this potential for simulation of the
shock wave induced disintegration of a molecular cluster we will add a long range van
der Waals potential to the original Brenner potential. We will use the approach proposed
by Stuart et al. [13] that takes into account the saturation of the chemical bonds within the
interacting molecules. Of relevance to the present study is the tested ability of the
reactive Brenner potential to reproduce the shock-induced chemistry in molecular solids
[14,15].
The potentials of the second type we will use in the proposed study are the ones
developed for biological simulations. These potentials can be used to describe a variety
of organic molecules and ions but do not allows reactions or bond cleavage to occur. As
a starting point in using these potentials, because of the potential importance of H2O in
IDEC experiments, we will perform simulations of water clusters [16]. The interaction
potentials available for MD simulations of H2O are sufficiently reliable such that a
quantitative analysis of the simulation results can be directly related to the
thermodynamic parameters of water [17,18]. Coding a potential for a biological
molecule is a laborious task due to the extensive bookkeeping required for all the
interactions and configurations. Therefore, we will develop our own code for pure water
only and will use existing commercial or public domain codes for biomolecules. Two
codes that are readily available and allow us to have the source code are Tinker [19] and
Amber [20].
In all the simulations the metal target will be simulated using the embedded-atom method
[21,22] that provides a computationally simple but rather realistic description of bonding
in metallic systems.
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[3]
L. V. Zhigilei and B. J. Garrison, Microscopic mechanisms of laser ablation of organic solids in the
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L. V. Zhigilei and B. J. Garrison, Molecular dynamics simulation study of the fluence dependence of
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[8]
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particles from short pulse laser irradiation, Applied Surface Science 127-129, 142-150 (1998).
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[12]
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S. J. Stuart, A. B. Tutein, and J. A. Harrison, A reactive potential for hydrocarbons with
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interface of SPC/E water, J. Phys. Chem. B 100, 11720-11725 (1996).
[19]
Tinker was developed by
/dasher.uwastl.edu/tinker/.
[20]
Amber was developed by the P. A. Kollman group and is available for $400 to non-profit
organizations from /www.amber.ucsf.edu/amber/.
[21]
M. S. Daw, S. M. Foiles, and M. I. Baskes, The embedded-atom method: a review of theory and
applications, Mat. Sci. Rep. 9, 251-310 (1993).
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