The document describes a new language for modeling biological processes that accounts for spatial information. The language extends the SPiM language to place mobile processes in 3D space where they can only interact if within communication distance of each other. This allows for more accurate modeling of reactions not occurring in a homogeneous mixture. The language is being applied to model a drug delivery nano-system in collaboration with professors from CCBBME. Ongoing work includes adding new features like shapes, validating the correctness of simulations, improving simulation performance, and using the language to model a specific drug delivery system through controlled experiments.

1. ddd
Stochas*c,
Spa*al
and
Concurrent
Biological
Processes
Modeling
Yifei
Bao,
Philippe
Bidinger,
Eduardo
Bonelli,
Vishakha
Sharma,
Jus*n
Sousa,
and
Peter
Zafonte
Advisor:
Adriana
B.
Compagnoni
Department
of
Computer
Science,
Schaefer
School
of
Engineering
and
Science,
Stevens
Ins*tute
of
Technology,
Hoboken,
NJ
07030
Introduc*on
We
define
and
implement
a
language
for
the
stochas*c
simula*on
of
biological
processes
with
spa*al
informa*on,
which
is
an
extension
of
the
SPiM
(Stochas*c
Pi
Machine)
language.
Simula*ons
in
SPiM
assume
that
all
processes
are
uniformly
distributed
in
space,
and
interac*ons
between
processes
are
scheduled
randomly
based
on
concentra*ons
and
reac*on
rates.
Consequently,
it
cannot
accurately
model
reac*ons
that
do
not
occur
in
a
homogeneous
mixture.
In
order
to
address
this
limita*on,
our
new
language
places
mobile
processes
in
3D
space,
where
processes
can
interact
only
if
they
are
within
communica*on
distance.
We
apply
our
language
to
modeling
a
drug
delivery
nano-­‐system
in
collabora*on
with
Prof.
Libera
and
Prof.
Sukhishvili
From
CCBBME.
Drug
Delivery
System
Modeling
1.
Drug
Delivery
System
2.
Our
Language
-­‐-­‐
Simula*on
Background
 Stochas*c
Pi
Machine
(SPiM)
Our
Language
 New
Spa*al
Features
• Process
state
includes
spa*al
informa*on
– Each
process
has
a
posi*on
and
three
vectors
that
define
its
local
system
of
coordinates
• This
state
can
be
modified
by
applica*on
of
affine
maps
(transla*on,
rota*on..)
– Simula*on
of
movement
(transla*on,
rota*ons)
• Interac*ons
may
be
condi*oned
by
the
distance
between
two
molecules
Graduate Student Research
Conference
October 6, 2010
Ongoing
work
1.
New
features
(shapes)
2.
Valida*on
(correctness
of
simula*on)
3.
Improved
performance
of
simula*on
algorithm
4.
Drug
delivery
system
modeling
(controlled
experiments)