Simulation of the active Brownian motion of a microswimmer

Giorgio Volpe, Sylvain Gigan, and Giovanni Volpe

Citation: American Journal of Physics 82, 659 (2014); doi: 10.1119/1.4870398

View online: http://dx.doi.org/10.1119/1.4870398
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 Simulation of the active Brownian motion of a microswimmer
Giorgio Volpe and Sylvain Gigan
Institut Langevin, ESPCI ParisTech, CNRS UMR7587, 1 rue Jussieu, 75005 Paris, France
Giovanni Volpea)
Physics Department, Bilkent University, Cankaya, 06800 Ankara, Turkey
(Received 19 December 2013; accepted 24 March 2014)
Unlike passive Brownian particles, active Brownian particles, also known as microswimmers,
propel themselves with directed motion and thus drive themselves out of equilibrium.
Understanding their motion can provide insight into out-of-equilibrium phenomena associated with
biological examples such as bacteria, as well as with artificial microswimmers. We discuss how to
mathematically model their motion using a set of stochastic differential equations and how to
numerically simulate it using the corresponding set of finite difference equations both in
homogenous and complex environments. In particular, we show how active Brownian particles do
not follow the Maxwell-Boltzmann distribution—a clear signature of their out-of-equilibrium
nature—and how, unlike passive Brownian particles, microswimmers can be funneled, trapped,
and sorted. VC 2014 American Association of Physics Teachers.
[http://dx.doi.org/10.1119/1.4870398]

I. INTRODUCTION we illustrate how to simulate the motion of an active particle

in a complex environment where several obstacles are pres-
In recent years, active Brownian motion has attracted a lot ent using reflective boundary conditions. Unlike passive
of interest from the biology and physics communities.1,2 Brownian particles, we observe that microswimmers can be
While the motion of passive Brownian particles is driven by funneled, trapped, and sorted by using the out-of-equilibrium
equilibrium thermal fluctuations, active Brownian particles, nature of their motion. We provide the MATLAB programs
often referred to as microswimmers, are able to propel them- used for these simulations as an online supplement;22 these
selves, exhibiting an interplay between random fluctuations programs can be straightforwardly adapted to the freeware
and active swimming that drives them into an out-of-equilib- SciLab23 or GNU Octave.24
rium status.3,4 Several types of microscopic biological enti-
ties perform active Brownian motion; a paradigmatic
II. MATHEMATICAL MODEL
example is the swimming behavior of bacteria such as
Escherichia coli.5 In addition, artificial active particles hold In a two-dimensional homogeneous environment, the
tremendous potential as autonomous agents to localize, pick motion of an active particle can be modeled as the combined
up, and deliver nanoscopic objects, e.g., in bioremediation, action of three different processes:25,26 a random diffusion pro-
drug delivery, and gene therapy.6–8 Such artificial active cess, an internal self-propelling force, and, in the case of chiral
Brownian particles propel themselves by several mecha- active particles, a torque. In particular, the position ½xðtÞ; yðtÞ
nisms, such as by a periodic deformation of their shape or by of a spherical microscopic particle with radius R undergoes
phoresis in, e.g., an electric field or a chemotactic or temper- Brownian diffusion with translational diffusion coefficient
ature gradient.9–19
Studying and comparing passive and active Brownian kB T
DT ¼ ; (1)
motion can provide insight into out-of-equilibrium phenom- 6pgR
ena. On the one hand, passive Brownian particles are often
used to study random phenomena because their thermally- where kB is the Boltzmann constant, T the temperature, and g
driven motion is due to random collisions with the surround- the fluid viscosity. The particle self-propulsion results in a
ing fluid molecules; this provides a well-defined noisy directed component of the motion with speed v we will
background dependent on the temperature and the fluid vis- assume to be constant and with a direction that depends on
cosity.20 On the other hand, the motion of active particles the particle orientation uðtÞ, as illustrated in Fig. 1(a).
takes them out of equilibrium.21 In order to start acquiring Finally, uðtÞ undergoes rotational diffusion with rotational
some first-hand experience with these phenomena, a good diffusion coefficient
didactical approach is to perform numerical experiments,
which have the advantage of being inexpensive and within kB T
DR ¼ : (2)
the reach of every student with access to a computational de- 8pgR3
vice. Numerical experiments can also be used to introduce
and complement real experiments. For a chiral active particle, uðtÞ also rotates with angular
In this article, we explain step by step how to model the velocity X as a consequence of a torque acting on the parti-
motion of an active Brownian particle in homogenous and cle;27 in the presence of a propulsion speed v > 0, this reor-
complex environments. First, we introduce the basic mathe- ientation of the particle translates into a rotation around an
matical model of the motion of an active Brownian particle effective external axis, as shown in Fig. 1(b). The sign of X
in a two-dimensional homogeneous environment in terms of determines the chirality of the particles. In the most general
stochastic differential equations, and solve the equations case, the resulting set of Langevin equations28 describing
numerically using a simple finite-difference algorithm. Then, this motion in two dimensions is

659 Am. J. Phys. 82 (7), July 2014 http://aapt.org/ajp C 2014 American Association of Physics Teachers
V 659

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 d pffiffiffiffiffiffiffiffiffi be obtained from Eqs. (3)–(5) by carrying out the
uðtÞ ¼ X þ 2DR Wu ; (3)
dt substitutions
d pffiffiffiffiffiffiffiffiffi uðtÞ ! ui ; xðtÞ ! xi ; yðtÞ ! yi ; (6)
xðtÞ ¼ v cos uðtÞ þ 2DT Wx ; (4)
dt
d u  ui1 d xi  xi1
d pffiffiffiffiffiffiffiffiffi uðtÞ ! i ; xðtÞ ! ;
yðtÞ ¼ v sin uðtÞ þ 2DT Wy ; (5) dt Dt dt Dt
dt d yi  yi1
yðtÞ ! ; (7)
where Wu , Wx, and Wy represent independent white noise dt Dt
processes. Inertial effects are neglected because typically wu;i wx;i wy;i
Wu ! pffiffiffiffiffi ; Wx ! pffiffiffiffiffi ; Wy ! pffiffiffiffiffi : (8)
microscopic active particles move in a low Reynolds number Dt Dt Dt
regime.29 In the following, we will always consider a particle
with radius R ¼ 1 lm at temperature T ¼ 300 K immersed in Here wu;i , wx;i , and wy;i are uncorrelated sequences of ran-
a liquid with viscosity g ¼ 0:001 N s=m2 (such as water); dom numbers taken from a Gaussian distribution with zero
the corresponding translational diffusion coefficient is mean and standard deviation 1. Many programming lan-
DT  0:22 lm2 =s and the corresponding rotational diffusion guages have built-in functions that directly generate such
coefficient is DR  0:16 rad2 =s. random sequences. Alternatively, it is possible to generate
Gaussian random numbers from uniform random numbers
between 0 and 1 using various techniques such as the Box-
III. FINITE DIFFERENCE EQUATIONS M€uller algorithm or the Marsaglia polar algorithm.31 The
numerical solution is then obtained by solving the resulting
The continuous-time solution ½uðtÞ; xðtÞ; yðtÞ to the set finite difference equation recursively for ½ui ; xi ; yi  using
of stochastic differential equations given by Eqs. (3)–(5) the values ½ui1 ; xi1 ; yi1  obtained from the previous
can be approximated by a discrete-time sequence ½ui ; xi ; yi  iteration:
 ½uðti Þ; xðti Þ; yðti Þ that is the solution of the corresponding pffiffiffiffiffiffiffiffiffiffiffiffiffi
set of finite difference equations evaluated at regular time ui ¼ ui1 þ XDt þ 2DR Dt wu;i ; (9)
steps ti ¼ iDt, where Dt is a sufficiently small time step. In pffiffiffiffiffiffiffiffiffiffiffiffiffi
order to derive the set of finite difference equations, the xi ¼ xi1 þ v cos ui1 Dt þ 2DT Dt wx;i ; (10)
white noise factors in Eqs. (3)–(5) must be dealt with care- pffiffiffiffiffiffiffiffiffiffiffiffiffi
fully, for example, by following the procedure described in yi ¼ yi1 þ v sin ui1 Dt þ 2DT Dt wy;i : (11)
Ref. 30. Explicitly, the set of finite difference equations can
We note that this is a first-order integration method that gen-
eralizes the Euler method to stochastic differential equations;
higher-order algorithms can also be employed to obtain
faster convergence of the solution.31

IV. HOMOGENEOUS ENVIRONMENT

We start by considering non-chiral (X ¼ 0) active
Brownian particles. When the self-propulsion speed v is
zero, the particle’s motion is purely diffusive with diffusion
constant DT ; some examples of the corresponding trajecto-
ries are illustrated in Fig. 1(c). As v increases we obtain
active trajectories that are characterized by directed motion
on short time scales, as shown in Figs. 1(d)–1(f). However,
while on short time scales, the motion is dominated by their
directed self-propulsion, over long time scales the orientation
of the particle is randomized by the rotational diffusion. The
Fig. 1. (Color online) Active Brownian particles in two dimensions. (a) An time scale of the rotational diffusion is given by sR ¼ 1=DR
active Brownian particle placed at ½xðtÞ; yðtÞ is characterized by an orienta-  6:25 s for the particles we consider in this article. These
tion uðtÞ along which it propels itself with speed v while it undergoes
Brownian motion in both its position and orientation. (b) A chiral active
qualitative considerations can be made more precise by cal-
Brownian particle also has a deterministic angular velocity X that, if the par- culating the mean square displacement MSDðsÞ of the par-
ticle’s speed v > 0, translates into a rotation around an effective external ticle’s motion. The MSDðsÞ quantifies how a particle moves
axis. Trajectories of active particles are shown at right for (c) v ¼ 0, from its initial position, and can be calculated from a trajec-
(d) v ¼ 1 lm=s, (e) v ¼ 2 lm=s, and (f) v ¼ 3 lm=s, all for X ¼ 0. With tory as
increasing v, the particles move longer distances before the direction of their
motion is randomized; four different 10-s trajectories are shown for each
velocity. Trajectories for chiral active particles are shown in (g) and (h),
MSDðsÞ ¼ h½ xðt þ sÞ  xðtÞ2 þ ½ yðt þ sÞ  yðtÞ2 i :
with v ¼ 31 lm=s and X ¼ 63:14 rad=s, starting at the position indicated by (12)
the cross and lasting 10 s; the sign of X causes the trajectory to bend either
(g) clockwise or (h) counterclockwise. The particles have radius R ¼ 1 lm, Numerically, the MSD can be calculated from a trajectory
are at temperature T ¼ 300 K, and are immersed in a liquid with viscosity ½xn ; yn  sampled at discrete times tn with a time step Dt as30
g ¼ 0:001 N s=m2 ; the corresponding translational diffusion coefficient is
DT  0:22 lm2 =s and the rotational diffusion coefficient is
DR  0:16 rad2 =s. MSDðmDtÞ ¼ hðxnþm  xn Þ2 þ ðynþm  yn Þ2 i: (13)

660 Am. J. Phys., Vol. 82, No. 7, July 2014 Volpe, Gigan, and Volpe 660

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 For ballistic motion MSDðsÞ is proportional to s2 while for
diffusive motion it is proportional to s. As can be seen in
Fig. 2(a), when v 6¼ 0 the MSDðsÞ deviates from a diffusive
behavior on short time scales and exhibits an enhanced effec-
tive diffusion over long time scales.
The theoretical value of MSDðsÞ is given by the
formula12,32
  v2 s2R ½ 2s=sR
MSDðsÞ ¼ 4DT þ v2 sR s þ e  1; (14) Fig. 3. Implementation of reflective boundary conditions. At each time step,
2 the algorithm (a) checks whether a particle has moved inside an obstacle; if
so: (b) the boundary of the obstacle is approximated by its tangent l at the
which is essentially the Ornstein-Uhlenbeck formula for the point p where the particle entered the obstacle, and (c) the particle position
MSD of a Brownian particle with inertia,33 describing the is reflected on this line.
transition from the ballistic regime to the diffusive regime
although at a much shorter time scale than for active V. COMPLEX ENVIRONMENTS
particles.30 From Eq. (14), we find that for s  sR the effec-
tive particle diffusion is Deff ¼ DT þ v2 sR =4, and for s  sR A. Reflective boundaries
the particle motion is ballistic with MSDðsÞ / v2 s2 . The So far we have considered particles that move only in a
theoretical MSDðsÞ calculated using Eq. (14) is shown as the homogeneous environment. However, self-propelled par-
solid lines in Fig. 2(b). While the features of the MSD of a ticles often move in patterned environments, e.g., inside the
microswimmer are well captured by Eq. (14), there can be intestinal tract, which provides the natural habitat of E. coli,5
deviations due to the microscopic dynamics of the or through porous polluted soils, where chemotactic bacteria
microswimmer.12 spread during bioremediation.7 In a similar fashion, artificial
We now consider the case of chiral active Brownian par- microswimmers must also reliably perform their tasks in
ticles. There are many natural examples of chiral micro- complex surroundings, e.g., inside lab-on-a-chip devices or
swimmers. For example, E. coli bacteria and spermatozoa in living organisms.38 When self-propelled particles move
undergo helicoidal motion, which becomes two-dimensional through a patterned environment, frequent encounters with
chiral active Brownian motion when moving near obstacles will occur. Whenever an active particle contacts an
boundaries.34–37 Figure 1(g) shows the simulated trajectory obstacle, it slides along the obstacle until its orientation
of a chiral particle with X ¼ þ3:14 rad=s and v ¼ 31 lm=s; points away from it. Numerically, this process can be mod-
it bends clockwise, tracking almost circular trajectories that eled using reflective boundaries, as shown in Fig. 3.
are modified by Brownian fluctuations. Changing the chiral- The concrete implementation of the reflective boundary
ity sign (X ¼ 3:14 rad=s) results in similar trajectories that condition is realized by updating at each time step the parti-
bend counterclockwise [Fig. 1(h)]. cle position from ri1 ¼ ½xi1 ; yi1  to ri ¼ ½xi ; yi  according
to the following algorithm:
1. tentatively update the particle position to r~i ¼ ½x~i ; y~i 
according to Eqs. (9)–(11);
2. if ~r i is not inside any obstacle, set ri ¼ ~r i and move on to
the next time step;
3. otherwise, if ~r i is inside some obstacle, as depicted in
Fig. 3(a):

Fig. 2. (Color online) (a) Numerically calculated and (b) theoretical mean Fig. 4. (Color online) Trajectories over a 10-s time period of Brownian
square displacement for active Brownian particles with self-propulsion particles moving within a circular pore (diameter 40 lm) with reflective
velocity v ¼ 0 (circles), v ¼ 1 lm=s (triangles), v ¼ 2 lm=s (squares), and boundaries at self-propulsion velocity (a) v ¼ 0, (b) v ¼ 5 lm=s, and
v ¼ 3 lm=s (diamonds); in all cases, X ¼ 0. For passive Brownian particles (c) v ¼ 10 lm=s, all for X ¼ 0. The histograms on the bottom show the
(v ¼ 0) the motion is always diffusive (MSDðsÞ / s), while for active probability distribution along a diameter of the circular pore. While the
Brownian particles the motion is ballistic on short time scales probability is uniform across the whole pore for passive Brownian particles,
(MSDðsÞ / s2 for s  sR ) and then becomes diffusive on long time scales the probability increases towards the walls for active Brownian particles as v
(MSDðsÞ / s for s  sR ) with an enhanced diffusion constant. increases.

661 Am. J. Phys., Vol. 82, No. 7, July 2014 Volpe, Gigan, and Volpe 661

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 Fig. 5. (Color online) Rectification of active Brownian motion in an asymmetric ratchet-like microchannel. A segment of the channel, whose dent is 10-lm
long, is represented by the grey structure in the inset of (a); the walls of the channel are infinitely extended. The distributions of passive (black histograms) and
active (gray/colored histograms) Brownian particles released at time t ¼ 0 from position x ¼ 0 are plotted at times (a) t ¼ 100 s, (b) t ¼ 500 s and
(c) t ¼ 1000 s. The x-axis gives the distance from the fixed, constant starting position of the particles. The higher the self-propulsion velocity, the farther the
active particles travel along the channel. Each histogram is calculated using 1000 particle trajectories.

(a) calculate the intersection point p ¼ ½xp ; yp  between Brownian particles (v ¼ 0), which are seen to explore the
the boundary and the line from ri1 to ~r i ; configuration space within the pore uniformly. By contrast,
(b) calculate the straight line l tangent to the obstacle at p active Brownian particles, shown in Figs. 4(b) (v ¼ 5 lm=s)
with tangent unit vector ^t and normal unit vector n ^ and 4(c) (v ¼ 10 lm=s), tend to spend more time at the pore
(outgoing from the obstacle), as shown in Fig. 3(b); boundaries. When a microswimmer encounters a boundary,
(c) calculate ri by reflecting ~r i on l so that it keeps on pushing against the boundary and diffusing along
the cavity perimeter until the rotational diffusion orients the
ri ¼ ~ ^ n
r i  2½ð~r i  pÞ  n ^; (15) propulsion of the particle towards the interior of the pore.
The chance that the active particle encounters the pore
where ð~ ^ is the distance between ~r i and l.
r i  pÞ  n boundary in one of its straight runs increases as its velocity
The crucial prerequisite for this numerical approach to work increases. These observations can be made more quantitative
is that the average spatial increment of a simulated trajectory by using the particle probability distribution. The histograms
is small compared to the characteristic length scale of the at the bottom of Fig. 4 each show a section of this probability
obstacles. This condition permits one to consider only one distribution along a diameter of the pore. We see that the
boundary at a time and also to approximate the boundary with probability of finding the particle at the boundaries increases
its tangent straight line. If the time step Dt is too large, this with the particle’s self-propulsion velocity.
approach can lead to some numerical instability around sharp That active Brownian particles tend to accumulate at the
corners in the boundaries, where multiple reflections may take boundaries of a pore is a sign of the fact that active particles
place, or on an obstacle wall that is too thin, where the par- are out of equilibrium. For a passive Brownian particle in
ticle’s trajectory could unnaturally pass through the obstacle. thermal equilibrium with its environment, the probability of
finding the particle at a given position in the pore pðx; yÞ is
connected to the Boltzmann potential Vðx; yÞ by the
B. Non-Boltzmann probability distribution in a pore Maxwell-Boltzmann relation pðx; yÞ / exp½Vðx; yÞ=ðkB TÞ.
In the case presented in Fig. 4, there are no external forces
As a first example of a complex environment, we consider acting on the particle and, therefore, Vðx; yÞ and the corre-
a microswimmer confined within a circular pore, as shown in sponding Maxwell-Boltzmann distribution are constant, as
Fig. 4. Figure 4(a) shows four 10-s trajectories of passive seen in Fig. 4(a). However, the fact that the distributions in

Fig. 6. Segregation of active particles (v ¼ 10 lm=s) using a series of wedges (dark structures), whose walls are 2 lm thick. (a) At t ¼ 0, the active particles
(black dots) are uniformly distributed across the square; (b) at t ¼ 100 s, most of the active particles have concentrated to the right of the wedges.
(c) Percentage of the total particles on the right of the wedges (dots) as a function of time; the percentage stabilizes at around 80% (black dashed line) after the
first 100 s.

662 Am. J. Phys., Vol. 82, No. 7, July 2014 Volpe, Gigan, and Volpe 662

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 Fig. 7. (Color online) Sorting of chiral microswimmers (v ¼ 31 lm=s and X ¼ 63:14 rad=s) with chiral “flowers” (gray rectangles, thickness 2 lm). (a) At
t ¼ 0 a balanced mixture of active particles with opposite chiralities is released inside two chiral flowers with opposite chirality. As time progresses, shown in
(b) and (c), the active particles rotating counterclockwise (darker squares) are trapped in the left chiral flower, while the particles rotating clockwise (lighter
circles) are trapped in the right chiral flower.

Figs. 4(b) and 4(c) are not constant, despite the constant chiral propellers, sorting the resulting chiral microswimmers,
potentials, is a clear deviation from the Maxwell-Boltzmann and finally detaching the propellers. Such techniques could
distribution, thus indicating the out-of-equilibrium nature of be applied in the biochemical and pharmaceutical industry
active Brownian particles. where often only one specific chirality is desired.42 Figure 7
shows a possible approach to sorting active particles based
C. Motion rectification in a microchannel on the sign of their motion chirality in the presence of some
chiral patterns in the environment, such as an arrangement of
The motion of active particles can be rectified by a pat- tilted rectangles along a circle forming a chiral “flower.” We
terned microchannel. For example, the inset of Fig. 5(a) use two of these flowers with opposite chiralities enclosed in
shows an example of such a microchannel, decorated with a a 100-lm-side box where the particles can move freely.
series of asymmetric dents on both its walls. A group of pas- We start at time t ¼ 0 with a balanced mixture of active par-
sive Brownian particles released at time t ¼ 0 from position ticles with opposite chiralities placed inside each flower
x ¼ 0 diffuses symmetrically around the initial position [Fig. 7(a)]. As time passes, most of the microswimmers
(black histograms in Fig. 5). By contrast, a group of active rotating counterclockwise (clockwise) escape the right (left)
Brownian particles is funneled by the channel in such a way chiral flower, while those with the opposite chirality remain
that an average directed motion is imposed on the particles, trapped. At t ¼ 1 000 s most of the microswimmers are sta-
as can be seen in the colored histograms in Fig. 5. The recti- bly trapped, as shown in Fig. 7(c).
fication is more pronounced when the self-propulsion velo-
city is higher. This and similar effects have been proposed
VI. FURTHER NUMERICAL EXPERIMENTS
to sort microswimmers on the basis of their velocity,26 to
trap microswimmers in moving edges,39 and to deliver mi- The approach described in this article can be generalized
croscopic cargoes to a given location.19 to more complex situations. In particular, it is interesting to
consider the case of an active spherical particle moving in
D. Trapping by asymmetric barriers three dimensions, where the particle position is described by
three coordinates and its orientation by two angles.43
Because active particles are not in thermal equilibrium with Another interesting generalization is to non-spherical active
their environment, it is possible to use the features of the envi- particles; for example, rods are a more accurate model for
ronment to perform complex tasks on active particles such as bacteria. This generalization requires the use of diffusion
separating, trapping, or sorting them on the basis of their swim- matrices instead of diffusion coefficients, as described in
ming properties. For example, Fig. 6 shows the segregation of Ref. 44. Finally, it is also interesting to consider the case of
active particles within a 100-lm-side square box divided into multiple particles interacting with each other, for example,
two parts by a series of wedges; this situation was first pro- by Yukawa or Lennard-Jones potentials. This can be imple-
posed in Ref. 40. At t ¼ 0, the active particles are homogene- mented using molecular dynamics algorithms.45
ously distributed in the box [Fig. 6(a)], while after 100 s most
of the active particles concentrate in the right portion of the ACKNOWLEDGMENTS
box [Fig. 6(b)]. The selectivity of this process depends on the
system parameters, such as the size and shape of the wedges This work was partially funded by the European Research
and the drift velocity of the microswimmers.39,40 Figure 6(c) Council (Grant No. 278025), by the Scientific and
shows the percentage of active particles in the right portion of Technological Research Council of Turkey (TUBITAK)
the box as a function of time; with our system parameters, the under Grant Nos. 112T235 and 113Z556, COST Actions
distribution quickly approaches a plateau of around 80%. MP1205 and IC1208, and Marie Curie Career Integration
Grant (MC-CIG) under Grant No. PCIG11 GA-2012-321726.
E. Chiral particle separation
a)
Electronic mail: giovanni.volpe@fen.bilkent.edu.tr
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W. C. K. Poon, “From Clarkia to Escherichia and Janus: The physics of
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