Robust Self-Assembly Using Highly Designable Structures
Xerox Palo Alto Research Center
Palo Alto, CA 94304
*Corresponding author: email@example.com
Web page for corresponding author: http://www.parc.xerox.com/hogg
This is a draft paper for the
Foresight Conference on Molecular Nanotechnology.
The final version has been submitted
for publication in the special Conference issue of Nanotechnology.
Self-assembly creates structures through a statistical exploration of many possibilities. In some cases, these explorations give rise to a few highly designable structures that can be formed in exceptionally many ways. Using such structures for self-assembly tasks is a general approach to improving their reliability. This design principle can be applied to a variety of situations, including molecular devices and coordinated behaviors from collections of autonomous robots.
Manufacturing often builds objects from their components by directly
placing them in the necessary arrangements. Common examples include
buildings, cars and electronic circuits. This technique requires
knowledge of the precise structure needed to serve a desired function,
the ability to create the components with the necessary tolerances and
the ability to place each component in its proper location in the
When these requirements are not met, self-assembly offers
another approach to building structures from components. This method
involves a statistical exploration of many possible structures before
settling into the final one. The particular structure produced from
given components is determined by biases in the exploration, given by
component interactions. These biases arise when the strength of
interaction between components depends on their relative locations in
the structure. These interactions can reflect constraints on the
desirability of a component being near its neighbors in the final
structure. For each possible structure, the interactions combine to
give a measure of the extent to which the constraints are violated,
which can be viewed as a cost or energy for that structure.
Through the biased statistical exploration of structures, each set of
components tends to assemble into that structure with the minimum
energy for that set. In these terms, self-assembly can be viewed as a
process using a local specification, in terms of components and
their interactions, to produce a resulting global structure. The
local specification is, in effect, a set of instructions that
implicitly describes the resulting structure.
Self-assembly can be very precise in spite of the inherently
statistical nature of the process. Examples include chemical
reactions driven by diffusive mixing of the reactants, such as the
creation of polymers [32, 33],
proteins  and molecular assemblies ,
patterned mesoscale objects [3, 39] and structures
consisting of tiny robots [2, 4, 14, 45].
This technique can also automatically reconfigure structures when
their environments or task requirements change, or when a few
While self-assembly can create a wide range of structures, it has some
basic difficulties. First, the precise set of components and
interactions that will construct a given global structure can be
difficult to determine, especially if the components themselves have
manufacturing defects or the environment surrounding the components is
noisy. Second, the statistical exploration of different possibilities
provides the power of self-assembly, but can also make it difficult to
settle on a single final structure, or to resist continual
environmental noise once assembled. Third, the assembly process can
become stuck in local minima, thereby requiring a long time to
identify the final structure.
To help overcome these difficulties, this paper describes some
characteristics of the statistical distributions of self-assembled
structures. These characteristics in turn suggest a general principle
for designing self-assembly processes that minimizes these
problems. This principle relies on the fact that many choices for the
components and their interactions can produce the same end
result. While such choices are often determined by ease of component
construction, they also provide an opportunity to improve the
performance of the self-assembly process.
Self-assembly is useful for a wide range of applications. Some of
these are described in this section, giving a concrete basis for the
discussion of aggregate statistical properties in
Section 3. These examples are also used to suggest a
number of extensions to self-assembly beyond the construction of
For protein assembly, the components are amino acids arranged in a
specific sequence. The global structures are the folded
three-dimensional shapes of the proteins. The interactions between
amino acids depend on their relative locations in the folded
structure. In simple terms, the interactions can be expressed as
constraints on the relative affinities of polar and nonpolar amino
acids [24, 37]. These interactions are determined by the
chemical properties of the components, so the relevant degrees of
freedom for the local specification are the choices of the amino acids
in the sequence. Engineering applications need not be restricted to
naturally occuring amino acids, giving the possibility of using
additional components, with different interactions. Various folding
polymers offer an even larger range of possibilities for engineered
structures [32, 33].
This example suggests a general manufacturing strategy: lay out the
components connected in a simple structure, such as a chain or, more
generally, a planar graph, and then allow it to fold into the final
shape. Because the initial connected structure is much easier to
create directly than a complex three-dimensional structure, this
technique is a useful combination of directed manufacturing of a
relatively simple structure followed by self-assembly of the final,
more complex, structure. Alternatively, a nominal initial
configuration could be directly constructed while subsequent
adjustments to the actual environment or failed components takes place
through self-assembly .
A wider range of interactions is possible with manufactured particles
of various sizes. At a molecular scale, suitable interactions can
produce self-assembled structures with new properties .
At somewhat larger scales, attaching DNA to small particles allows
using the selective binding interactions of DNA to create specific
structures in response to environmental changes, which can act as
sensors . For larger particles, individual shapes
and surface properties determine the interactions and hence the
resulting structures .
The widest range of component interactions arises when the components
are complex enough to have computational capabilities, e.g.,
robots [5, 14, 22, 31, 34, 45, 46]. The
interactions between robots are determined both by their physical
properties (e.g., their weight) and the choices made in their programs
(e.g., whether to hold on to a particular neighbor). The component
robots assemble into various overall shapes, or global structures. By
disconnecting from their neighbors, collections of robots can explore
a wider range of topological possibilities than the fixed sequence of
amino acids in the protein example.
Collections of robots offer an interesting contrast between
self-assembly and direct construction. For instance, each robot could,
in principle, be instructed precisely where to go through a
predetermined program. While suitable for relatively small groups of
robots and a well-understood environment, this programming task
becomes increasingly difficult with larger numbers of robots acting in
poorly defined or unpredictably changing
environments . An alternate and more robust
approach is for the programs to specify only simple local interactions
that together produce the final desired structure through an
exploration of possibilities, i.e., through self-assembly.
As these examples show, the suitability of a global structure need not
just depend on its particular physical shape. Instead, its functional
properties may be more important for some applications. For example,
a task may require exerting particular forces, e.g., to support or
move other objects, rather than a specific shape. Thus, self-assembly
can be viewed as a technique for finding combinations of components
that satisfy some global constraints on behavior. That is,
self-assembly can solve a combinatorial optimization or a constraint
satisfaction problem  where the resulting structure
should satisfy as many of the constraints as possible. In the case of
modular robots, techniques such as simulated
annealing  and genetic
algorithms  have been applied to identify suitable
structures [34, 5]. Finally, the statistical
exploration of self-assembly is also useful in organizing purely
software systems .
As a final observation on the application of self-assembly, complex
artifacts often consist of a series of levels, where the components
used at one level of the structure are in turn formed from a smaller
set of components . In such cases, some levels could be
assembled through direct construction while self-assembly is used to
create others. Such situations give further opportunities to design
the components and levels to exploit statistical properties of
self-assembly described in Section 3.
Self-assembly can form precise structures beyond the current
capability of direct manufacturing. Choosing appropriate components
and interactions to take advantage of this capability can be
difficult. The most straightforward technique for designing
self-assembly is to examine, with a computer simulation, the neighbors
of each component in the desired global structure, and then choose the
interactions between components to encourage those neighbors to be
Unfortunately, such a design may inadvertently make some other
structure even more stable or introduce numerous local minima in the
energies leading to a slow assembly process. Furthermore, the limited
range of interactions and component types in some cases, such as for
proteins, may not be able to produce the desired interactions among
all the components. Even worse, the limited knowledge of the precise
global structure desired, environmental noise and component defects
may make it impossible to determine the best set of interactions in
the first place.
Instead, the statistical nature of self-assembly gives rise to a
variety of statistical regularities when the number of components is
large. In many cases, these regularities can be exploited to design a
robust self-assembly process. Examples of such properties are
described in the remainder of this section.
One difficulty with designing self-assembly processes is the indirect,
or emergent, connection between the interactions and the
properties of the resulting global structures. While this difficulty
connecting local behaviors with global results arises in many
different contexts, a particular consequence for self-assembly is the
possibility of errors due to defective components or environmental
noise. To help address this problem, it would be useful to arrange the
self-assembly so the desired structures can be formed in many ways,
increasing the likelihood they will be correctly constructed even with
some unexpected changes in the components or their interactions. That
is, the resulting global structure should not be too sensitive to
errors that may occur in the local specification.
This notion is formalized by the designability of global
structures. Specifically, if G is a global structure and L is a
collection of components, or the local specification, then the
interactions among the components based on their placement in the
global structure can be viewed as defining an energy E(G,L). Small
values for the energy correspond to global structures that satisfy
many of the constraints. The best global structure for a given set of
components L is the one that minimizes this energy. With a
sufficient statistical exploration of the possible global structures
the minimum energy structure will be the one eventually assembled from
L. Notationally, let denote the global structure
G is the assembled result from L. That is, among all possible
global structures, G has the minimum energy for L.
In this context, we can ask how many different component sets assemble
to the same global structure G. We refer to this count as the
designability of the structure, i.e.,
where denotes the size of a set and is the set of all component collections that assemble to G.
A given assembly process can then be characterized by a distribution
of designability, i.e., the number of global structures with various
designability values. This distribution is given by values of over a range of choices for x.
Schematic distribution of designability, i.e., the number of different
component configurations producing a given global structure. Each
point on the curve indicates the number of global structures with a
given designability. The long tail of the distribution indicates a few
global structures are highly designable, i.e., far more designable
than typical cases.
A schematic example of such a distribution is shown in
Fig. 1. Significantly, the distribution of
designability illustrated here is extremely skewed: a few structures
are much more designable than most others. These highly designable
structures can be formed in relatively many ways in response to
interactions among the component parts. Thus such structures are
relatively more tolerant of errors in the choice of components than is
typically the case, producing one form of robustness for
A simple generalization of this definition of designability is when a
variety of global structures have the same functional properties. For
instance, if the global structures are physical shapes, rotated
versions of these shapes may be functionally identical. Or in the
case of tiny robots, matching a shape to within a specific tolerance
or delivering a required force, rather than exactly matching a
specific shape, may be sufficient. In such cases, rather than
requiring a single specific resulting structure, a self-assembly
process that produces any structure with the desired behavior
can be viewed as successful. This leads to considering functionally
identical global structures as equivalent when defining
designability. That is, an equivalence relation, , can be defined on the global structures that give rise to
identical behaviors for the particular application under
consideration. Designability then becomes
Thus an additional ingredient to consider for designing self-assembly
processes is the actual performance requirement for the resulting
structure, rather than limiting attention just to forming a particular
As a final note, from the viewpoint of constraint satisfaction
problems, designability is related to studies of situations that give
rise to stable solutions , i.e., solutions that
remain solutions even with a few changes in the constraints. Failing
this, solutions should at least be easy to fix when conditions
change , corresponding to simple repairs that require
only adjusting a few components.
As self-assembly operates, the components perform a biased statistical
sampling of the possible global structures on the way to forming the
final structure. This process allows a variety of complex structures
to be formed. Unfortunately, this exploration can also lead to
continual and undesired changes in the final global structure. In
some situations it will be possible to terminate the exploration by an
explicit command (e.g., a broadcast signal sent to a collection of
tiny robots). In other cases, this will not be possible: either
because the continual changes are driven by uncontrolled environmental
noise or are needed to keep the system adaptable to further unexpected
changes, e.g., additional weight added to a group of robots supporting
Designability addresses the sensitivity of the assembly process to
errors in the local specification, or instructions, as described in
Section 3.1. Another important property is the extent
to which desired global structures can resist continual environmental
noise once formed. This property of self-assembled structures can be
formalized by their energy gap, the difference in energy, due to
interactions among the components, between the global structure with
the smallest energy for those components and that structure with the
second smallest energy:
Structures with relatively large energy gaps will be more robust with
respect to environmental noise than those with smaller gaps. One way
to characterize this value  for a given structure G is
with the average of the energy gap associated with all component
configurations that produce G, i.e.,
This average will be a useful characterization when most values
of are fairly close to the average.
Designability reflects the behavior of a given global structure with
respect to different sets of components. Thus it characterizes the
effect of errors or other changes in the set of components. By
contrast, the energy gap characterizes a given set of components with
respect to the different global structures that set could form.
Significantly, self-assembly processes with skewed distributions of
designability can also produce relatively large energy gaps for the
highly designable structures, as illustrated in Fig. 2.
This schematic example illustrates one possibility: an abrupt
transition in the energy gap as designability increases. Such a
situation would be another example of the transition phenomena
commonly found in constrained systems, both physical 
and computational . Another possibility is for a smooth
increase rather than an abrupt change.
Schematic illustration of one way robustness of global structures can vary
with their designability.
This association is easily understood since small changes in the
components will usually result in only small changes in the energies
of new configurations. This is because the overall energy E(G,L) is
usually due to the combination of interactions among pairs of
components, based on their location in the global structure. For
structures consisting of many components, changing a few components
will only modify a small fraction of the total interactions, and
typically give a relatively small shift to the energy associated with
each global structure. That is, a small change from L to L' will
usually result in corresponding small changes in energy from E(G,L)
to E(G,L'). Such shifts are illustrated in Fig. 3,
which shows the energies associated with four global structures for
L and L' as the black and gray points,
respectively. Fig. 3a shows a large energy gap so small
changes in the energies of all the global structures do not change the
one with the minimum energy. On the other hand, small changes in a
situation with a small gap are likely to change the minimum energy
structure, as illustrated in Fig. 3b. Thus large gaps
are likely to be associated with structures that are energy minima for
many different local specifications, i.e., structures that are highly
Schematic illustration of the association between large energy gaps
and high designability. Black points are energies for different global
structures for a given set of components. Gray points are the shifted
energy values due to a small change in the component set. The arrows
indicate the original energy gaps. With a small gap, the shifts are
likely to change the minimum energy structure as illustrated here.
Further insight into the possible changes in energies arises from the
nature of the constraints involved in a structure. In many cases these
constraints are somewhat frustrated, i.e., they cannot all be
simultaneously satisfied completely. For example, we may want a
structure that is light and strong. Typically in these cases a small
change to a global structure G, producing a neighbor structure
, will introduce changes in the constraints
involving just a few parts of the structure, giving rise to a change
in energy characterized by the energies involved in
just a few constraints. If G is a low-energy structure, such changes
are likely to introduce new frustrations and raise the energy, i.e.,
G has a lower energy than its neighbors and is a minimum in the
energy with respect to small changes. Adjusting to these new
frustrations will often require further changes, involving additional
parts of the structure, to again find a new structure G' with a
relatively low energy and, in particular, lower energy than its
This discussion suggests two qualitatively distinct causes of the
minimum energy gap. First, if G satisfies the constraints
particularly well, its energy will be considerably less than any
local minima, so the gap will be determined by the typical energy
scale of changes in a few constraints, . Second, if
there are several structures that adjust reasonably well to the
frustrated constraints in different ways, the energy differences among
these local minima will determine the gap, which will then be
considerably less than , as illustrated in
Schematic illustration of energies associated with various global
structures. The horizontal axis is ordered so neighboring structures,
i.e., those with similar shapes, are close together. In this case
the energy gap is determined by a local minimum shown by the solid
arrow. The gray arrow indicates the gap due to a small change in
When this distinction holds, we can expect large gaps, characterized
by , to arise when some structure can satisfy the
constraints particularly well. In other cases, the gap will be
smaller and characterized by energy differences among alternate ways
of satisfying frustrated constraints. Such situations will result
in two distinct regimes for the energy gap as illustrated in
Designability and the energy gap determine the robustness of the final
structure with respect to variations in the components, interactions
or environment. Another important question is how long self-assembly
takes. While structures can be explored rapidly, especially for
molecular sized components, the number of possible structures often
grows so rapidly with the number of components that they cannot all be
examined in any reasonable amount of time. Fortunately, the biases
introduced in the exploration by the interactions can greatly reduce
the number of structures that need to be examined.
In some cases, these interactions can also give rise to local
minima, structures with lower energy than all their neighboring
structures but still with relatively high energy. Such situations lead
to sluggish behavior in both physical  and
computational  systems because the system can remain in
a local energy minimum a long time. In such cases, the bias in the
exploration toward lower energy structures tends to keep the system in
the local minimum.
Models of protein folding suggest this need not be a severe limitation
for simple interactions . More generally, the extent to
which local minima are a problem depends on several factors. First,
for some applications a structure corresponding to a local minimum may
be quite adequate, even though it does not satisfy the constraints as
well as the true minimum. Second, the number of initial structures
leading to the true minimum may be much larger than those leading to
local minima. This is often the case when the true minimum is
associated with a large energy gap and the individual constraints are
relatively weak. Third, if the system allows a fine degree of control
over the component behaviors, as with modular robots, it may be
possible to explicitly plan a sequence of motions to avoid local
minima . Finally, local minima may be fairly rare.
One way to reduce the number of local minima is through another
statistical property of systems with many components: with a
sufficient number of ways to change a structure, i.e., a sufficiently
high dimensional space of configurations, there is likely to be at
least one direction in the space allowing the energy to decrease.
This observation can be formalized by examining the statistical
distribution of stability, particularly the existence of energy
minima, in the space of configurations. Specifically, the stability is
determined by the eigenvalues of the matrix of derivatives (the
Jacobian) of the forces acting on the system, e.g., due to component
interactions. Generally, increases in the size of such matrices or
the variation in their values lead to instabilities, i.e., the local
minimum becomes a saddle point with at least one direction of change
giving lower energy [11, 17, 27, 28]. In this
case, the variation in the matrix values could arise from a diversity
of interactions among the components, e.g., due to a large number of
relatively weak constraints rather than a few strong ones. These
mathematical properties of large matrices involve systems that can
change continuously, which will apply to self-assembly tasks where
components can move continuously. For systems with discrete
positions, with a sufficiently large number of components the behavior
in many cases will be similar to that of a continuous system. For
other cases, extensions of these techniques to discrete dynamical
systems will be necessary .
Finally, if local minima are a problem, it will be necessary to reduce
the bias in the exploration to make changes that temporarily increase
the energy more likely. This can be done through an annealing process
of slowly cooling the system from a relatively high temperature or,
for programmable interactions among robots, using the software
equivalent: simulated annealing . However, by
requiring the system wait to find a series of improving changes by
chance, such techniques can still be quite slow. When the components
are fairly sophisticated, e.g., with programmable robots, a more
powerful alternative is the use of computational
markets  that allow the system to exploit locally
coordinated groups of changes that move around the energy
The nature of designability and energy gap distributions affect the
robustness of self-assembly. Particularly favorable cases occur when
highly designable structures are associated with large energy gaps.
While such distributions are seen in models of protein
folding , an important practical question is how widespread
such distributions are.
While the full extent of this question remains to be explored, a
particularly simple case is when the system decomposes into several
independent parts. That is, suppose the local specification consists
of parts and the global structure consists of
corresponding parts . Independence means the
energy is the sum of that from the independent parts, i.e.,
With this decomposition, if G is the minimum energy global structure
for L, then each part must be the minimum for , otherwise
another choice for the jth structure will reduce the energy
further. This observation means the number of local structures L for
which G is the minimum energy configuration, i.e., the designability
d(G) of G, is just the product of the designability of the
On the other hand, the smallest energy gap would be due to a change in
just one of the parts, since changes in any other parts will increase
the energy further. Thus
These relations result in enhanced tails for the distributions of
designability and the gap. In particular, for a wide range of
distributions for the individual parts, the product in Eq. (6)
gives rise to a lognormal distribution [1, 7] for
d(G). This distribution has a particularly long tail, giving a few
highly designable cases as illustrated schematically in
Similarly, will be governed by the extreme value
distribution , again with a relatively extended
tail. Significantly these relations can also act to enhance the
relation between those cases with high designability and relatively
large energy gap. This is because G will be highly designable when
most of the parts are so. Further, to have a relatively large
gap, the gaps associated with all of the parts
must be large. Thus if designability
and gap size are somewhat correlated for the parts, these values can
become even more related at the high end of the distributions for the
Of course interesting self-assembled structures will not have
completely independent parts. Nevertheless, this example provides
insight into structures with some dependence between the parts, i.e.,
situations where the energy is nearly decomposable into a sum of
contributions from different parts. In such cases Eq. (6)
and (7) will be approximately correct and still lead to
distributions with long tails. This extension to nearly decomposable
structures is significant because many structures, both natural and
engineered, are nearly decomposable . That is, they
consist of a set of parts with relatively strong interactions within
each part and weaker ones between them. The example of independent
parts is the extreme case where there are no interactions between
parts. Furthermore, this near decomposability often extends through a
series of levels in the structure, giving hierarchical structures
where interaction strengths decrease with the distance between
components in the hierarchy, i.e., the number of levels up the
hierarchy required to find a common ancestor of the components. At
each level in such a hierarchy, Eq. (6) and (7) will
apply approximately, leading to distributions with enhanced tails, at
least provided the interactions between parts are relatively
weak. This argument suggests highly designable structures will occur
in a variety of self-assembly processes.
Self-assembly of highly designable structures is particularly robust,
both with respect to errors in the specification of the components and
environmental noise. Thus we have a general design principle for
robust self-assembly: select the components, interactions and possible
global structures so the types of structures desired for a particular
application are highly designable.
Applying this principle requires two capabilities. The first is
finding processes leading to highly designable structures of the
desired forms. That is, even when a few highly designable structures
exist, there remains the question of identifying those structures so
as to make use of them for particular applications. Or conversely,
finding choices of components and interactions for which desired
global structures are highly designable. Identifying such processes
uses properties of the tails of statistical distributions, which are
more difficult to characterize than those of their central parts.
However, some specific examples have been identified, e.g.,
lattice-based models of protein folding  and analyses of
the genetic code , that suggest evolution has taken
advantage of this design principle. Whether or not such simplified
models accurately capture the behavior of natural protein folding,
they show such distributions exist in systems with fairly simple
interactions and components. Furthermore, this framework is
well-suited for genetic algorithms  to find
appropriate processes where possible local specifications and global
structures correspond to genotypes and phenotypes, respectively.
The second requirement for applying this design principle is the
ability to create the necessary interactions among the components.
For simple components, the range of possible interactions may be
fairly limited and hence further restrict the search for suitable
processes. More complex components, such as tiny robots, can have
arbitrary interactions programmed into the components, subject only to
restrictions on the timely availability of required information, which
tends to enforce the use of local interactions. For example, the
interactions could include negotiation among the
components  or arbitrage opportunities in market-based
systems [6, 29]. The ability to program desired
interactions is particularly significant in allowing designed systems
to more accurately reflect simplifications in the models than would be
the case for describing naturally existing assembly situations. Thus,
like the development of computational ecologies ,
designed self-assembly provides an example of how prescriptive use of
simple models relating global to local behaviors can result in more
accurate analyses than their approximate descriptive use for naturally
existing systems. Moreover, the flexibility of programmed interactions
makes this design principle particularly applicable to collections of
Achieving a general understanding of the conditions that give rise to
highly designable structures is largely a computational problem that
can be addressed before actual implementations become possible. Thus,
developing this principle for self-assembly design is particularly
appropriate in situations where explorations of design possibilities
takes place well ahead of the necessary technological
capabilities . Even after the development of precise
fabrication technologies, principles of robust self-assembly will
remain useful for designing and programming structures that robustly
adjust to changes in their environments or task requirements.
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