Is it possible to simulate ions flying through non-vacuum
conditions (i.e. ions colliding with background gas)?
Yes, a number of models can be specified for this.
First, why simulate collisions? Normally, SIMION assumes that ions fly through
perfect vacuum, and often this is a valid approximation. However, this
assumption is not always appropriate. For example, the effect is significant
in ion mobility mass spectrometry. In ion traps, ion funnels, and similar
devices, a non-negligible buffer gas is often used to kinetically cool and
How are collisions simulated? A collision model can be introduced into a
simulation via a SIMION user program. This works well in SIMION 8 though is
also supported via a lower-level programming language in 6 and 7. A number of
pre-built collision models are included as examples in SIMION 8, such as
Stokes’ Law (drag), hard-sphere (HS1), and high-pressure (SDS), but sure to
download the latest 8.0.x update. A number of models have also been described
in the literature below and can be found for version 7. If desired, you can
customize these models or program your own. The way the models work is that at
each time-step, such a user program applies an adjustment to the ion motion
(typically in other_actions or accel_adjust segment) according to some
equation or algorithm depending on the desired collision model.
Note, however, that SIMION is not a Computational Fluid Dynamics (CFD) solver.
SIMION will not in itself calculate the bulk pressure, temperature, velocity,
and density fields for gas flow from first principles (Navier-Stokes).
You may, however, input known bulk flows into the SIMION collision model either
via arrays or analytic equations.
These bulk flows could be determined by third-party CFD software (e.g. Fluent),
approximated with analytic equations
(e.g. Hagen-Poiseuille flow) in simpler cases,
or obtained by experimental measurements.
One of the SIMION distributors also has been developing a new CFD solver called
Virtual Device Hydrodynamics
which specializes in supersonic gas flow calculations (e.g. ESI) and has direct
integration with SIMION. See Computational Fluid Dynamics (CFD) for further details.
The following main types of models are typically used:
- Viscous damping
- Hard sphere collision model
The viscous damping models apply a force that is a function of the
particle velocity vector. Often, this is Stokes’ law in which the force is
proportional to ion velocity vector, particle radius, and fluid viscosity (see
Wikipedia: Stokes’ law).
The hard-sphere collision models are based on the kinetic theory of gases
in which, unlike the viscous damping models, the individual collisions between
ion and gas particles are modeled. The expected frequency of collisions,
measured as a distance (the mean-free-path) is predicted by the kinetic theory
of gases as a function of the known pressure, temperature, and collisional
cross sections of colliding particles. Collisions between ion and gas
particles result in positive and negative energy transfers as well as
scattering (deflection of ion velocity vectors), or even absorptions (e.g. in
electron-gas collisions). The energy transfers provide for the kinetic cooling
of a fast moving ion as well as the kinetic heating of a slow moving
ion. Usually, we treat the colliding particles as hard-spheres. Often we
assume that the collisions are elastic. Generally, the background gas is
non-stationary and has a Maxwell-Boltzmann distribution of velocities, which
is a function of temperature. The proposed reference model for hard sphere
elastic collisions is Collision Model HS1 (an updated version of which
is included in SIMION 8).
Some newer models are hybrids and have been successful at higher
Below are links that include SIMION code for collision models.
Combined viscous and hard-sphere, hybrid, or other collision
- Anthony D.
Appelhans, David A. Dahl. SIMION ion optics simulations at
International Journal of Mass Spectrometry,
244 (2005) 1-14. (source code is included with the electronic
version online). –”The statistical diffusion simulation (SDS) user
program avoids the computationally intensive issues of high
collision rates by employing collision statistics to simulate the
effects of millions of collisions per time step. Ion motions are
simulated by a combined viscous ion mobility and random ion jumping
approach.” (suitable for atmospheric pressures) – Note: A Lua
version of this is available and is included in SIMION 8.0.3. The
SDS model is further analyzed in
David A. Dahl, Timothy R. McJunkin and Jill R. Scott. Comparison of ion
trajectories in vacuum and viscous environments using SIMION:
Insights for instrument design.
International Journal of Mass
Spectrometry. Volume 266, Issues 1-3, 1 October 2007, Pages
156-165. and Hanh
Lai, Timothy R. McJunkin, Carla J. Miller, Jill R. Scott, José R.
Almirall. The predictive power of SIMION/SDS simulation software
for modeling ion mobility spectrometry instruments. International
Journal of Mass Spectrometry, 276 (2008) 1-8.
The SIMION “faims” example extends SDS to FAIMS.
Adrian Mariano, Wansheng Su, Samar Guharay
Effect of Space Charge on Resolving Power and Ion Loss in Ion Mobility Spectrometry repeatedly applies the
SIMION 8.1 Poisson solver during the trajectory integration of an ion mobility
system using SDS.
More SDS validation is done in
Wissdorf, W. Pohler, L. Klee, S. Müller, D. Benter, T.
“Simulation of Ion Motion at Atmospheric Pressure: Particle Tracing Versus Electrokinetic Flow”
Journal of The American Society for Mass Spectrometry.
volume 23, issue 2, year 2011, pp. 397-406.
An extension of SDS supporting chemical reaction simulations is in SIMION Example: collision_rs.
- The SIMION Example: drag (SIMION 8.1, 2016-12-19) now contains a
drag_mobility_diffusion.iob (mobilitydiffusionlib.lua), which is like SDS in that
it superimposes a Stokes’ law mobility with superimposed diffusion, except that the
diffusion is calculated from the mobility constant (with longitudinal Dl and transverse Dt
- The special
Hydrodynamics version of Virtual Device contains a collision
model for ion movement in gas plus a model of a supersonic jet, with a
detailed description of the math/physical model, tests against experiments,
and PRG code. Uses mobility and monte-carlo collisions with large
step optimization. In supersonic jet ions typically travel from ~1
atmosphere to 10 Pa. Under 1 atmosphere for length of travel 0.2 mm
(one trajectory), it takes approximately half an hour (using small
step algorithm) or only two minutes (using big step algorithm).
Collision model and model of supersonic jet is in PRG code, with
supersonic jet a semianalytical model verified from hydrodynamics
software that outputs arrays of pressure, density, temperature, adn
velocity of gas. Documentation and some results online.
- Jun Xu and William
B. Whitten. Monte Carlo simulation of ion transport in ion mobility
International Journal for Ion Mobility Spectrometry.
April 10, 2008. - Elastic collisions between ions and gas particles
and conducted for an IMS drift tube. Typical IMS parameters,
including pressure, temperature, and flow rate of the drift gas
were taken into account in the simulations.
Hard-sphere collision models
- D. Manura 2005. Collision Model HS1 - A fairly complete
hard-sphere collision model: elastic, ion-neutral, non-stationary
backgroung gas with Maxwell-Boltzmann distribution, random
collision angles, mean-free-path a function of relative velocity.
SL code. (Note: an updated version of this is included in SIMION
- D. Dahl. (dahl_drag.prg) -
Hard-sphere collision model: elastic,
ion-neutral, non-stationary backgroung gas with Maxwell-Boltzmann
distribution, random collision angles, constant mean-free-path. PRG
code. Compared to Collision Model HS1, some algorithms are less elegant,
mean-free-path is constant, and it’s implemented in PRG code.
- A. Appelhans and D. Dahl. Measurement of external ion injection and
trapping efficiency in the ion trap mass spectrometer and comparison with a
International Journal of Mass Spectrometry.
Volume 216, Issue 3, 15 May 2002, pp. 269-284 (see link in the
References/Documentation page.) - A simple hard-sphere collision
model: elastic, ion-neutral, stationary backgroung gas,
head-on/frontal collisions with random deflection angles, constant
mean-free-path. Includes a small section of PRG code. Compared to
Collision Model HS1, background gas is stationary, elastic collision
model is simpler, mean-free-path is constant, and it’s implemented
in PRG code.
- D. Dahl. _Trap example (INJECT.PRG) in SIMION 7.0 - very simple
and limited hard-sphere collision model: elastic, head-on/frontal
collisions, stationary background gas. PRG code. Simulates simple
kinetic cooling but not kinetic heating. This is much more limited
that Collision Model HS1. The SIMION 8.0 “trap” example contains
an updated Lua version.
Wu, Li-Wei Chen, and Ya-Ping Lin. Simulation of the Collisional
Cooling Effect in a Quadrupole Ion Trap Mass Spectrometer. J. Chin.
Chem. Soc., Vol. 46, No. 6, 1999. – Applies Langevin theory, whose
implementation is described in some detail.
Stoke’s Law viscosity models
- D. Dahl. “_Drag” (“drag”) example in SIMION 7.0 or 8.0. See also p.
I-29 to I-30 of the SIMION 7.0 manual. This model is based on
Stoke’s Law viscosity.
Below are links that discuss collision models in SIMION.
Hard-sphere collision models.
- Li Ding,
Michael Sudakav, Sumio Kumashiro. A simulation study of the
digital ion trap mass spectrometer. International Journal
Spectrometry, Volume 221, Issue 2, 15 November 2002, Pages 117-138.
- Hard-sphere collision model: elastic, ion-neutral, non-stationary
backgroung gas with Maxwell-Boltzmann distribution, random
collision angles, mean-free-path a function of relative velocity.
- An electrostatic
focusing ion guide for ion mobility-mass spectrometry, Kent J.
Gillig, Brandon T. Ruotolo, Earle G. Stone and David H. Russell, -
Collision model using a Maxwell-Boltzman distribution for the
collision gas energy and accomodating collisions from behind the
- M. W.
Forbes, M. Sharifi, T. Croley, Z. Lausevic, and R.E. March.
Simulation of Ion Trajectories in a Quadrupole Ion Trap: a
comparison of Three Simulation Programs.
Journal of Mass
Spectrometry, 34, 1219-1239, 1999. – Discusses collision models in
SIMION, ITSIM, ISIS, and in general, especially with respect to ion
traps. A bit dated in some aspects (limited SIMION collision
- Ling He and David M. Lubman. Simulation of External Ion Injection,
Cooling and Extraction Processes with SIMION 6.0 for the Ion
Trap/Reflectron Time-of-flight Mass Spectrometer. Rapid
Communications in Mass Spectrometry, 11, 1467-1477 (1997).
Hard-sphere collision model: elastic, ion-neutral, non-stationary
backgroung gas (without Maxwell-Boltzmann distribution?), random
but orthogonal collision angles, mean-free-path a function of
- Aleksey V.
Tolmachev, Harold R. Udseth and Richard D. Smith. Modeling the ion
density distribution in collisional cooling RF multipole ion
Journal of Mass Spectrometry. Volume 222,
Issues 1-3 , 1 January 2003, Pages 155-174.
Comparison of viscous drag and ion/neutral collision models and
- Chris M. Lock, Edward W. Dyer. Simulation of ion trajectories
through a high pressure radio frequency only quadrupole collision
cell by SIMION 6.0. Rapid
Communications in Mass Spectrometry,
Volume 13, Issue 5 , Pages 422 - 431. 1999. –”Two collision
modeling programs were designed and compared, one based on viscous
drag cooling which is applicable to ions of high m/z, and the other
on discrete ion/neutral collision phenomena for ions of low m/z.
The latter approach included an ion scattering model (the theory of
which is described here) to simulate changes in trajectory with
each binary collision.”
- S. Henry, I. Martel-Bravo, M. de Saint Simon, M. Jacotin, J.-F.
Képinski, and D. Lunney. Beam Cooling Using a Gas-Filled RFQ Ion
M.D. Lunney, R.B. Moore. Cooling of mass-separated beams using an
RFQ ion guide -
supports viscous dampening over hard-sphere
collisions for low KE.
Moore. Buffer Gas Cooling of ion Beams. January 2002
pages)–”This note summarizes the principles involved in the
containment of the motion of ions in buffer gas and in the
resultant cooling of the ion motion.”
A few posters at ASMS 2004 described use of collision models:
- Modelling Ion Trajectories in an Ion Mobility Drift Tube using
SIMION Michael M. Sakal; Robert R. Hudgins; York University ,
Toronto, ON, Canada (ion mobility, using collision model based code
from David Dahl.
- Transmission of Ions Through Conductance
Pathways from Atmospheric Pressure Ross C. Willoughby; Edward W.
Sheehan; Chem-Space Associates, Pittsburgh, PA (adapted SIMION to
include viscous flow components)
- Characterization of Higher
Order Fields in a Compensated Cylindrical Ion Trap Desmond A.
Kaplan; Gary L. Glish; The University of North Carolina, Chapel
Hill, NC Some at ASMS 2005 used collisions models too.