Self Assembly

Self Assembly

 Definition.
 Characterization.

Examples and Applications

...to go.

© JP Carbajal 05. 2008 1

Self Assembly: Definition
 Q&A: what is self-assembly.


Answers from the experts
 “...refers to aggregation of particles into an organized structure
without external assistance”. D. J. Campbell 2002.
 “...we limit the term to processes that involve pre-existing com-
ponents, are reversible, and can be controlled by the proper design
of the components”. G. M. Whitesides 2002.
 “...is the ubiquitous process by which objects autonomously as-
semble into complexes”. C. Aggarwal 2005.
 “...we limit SA to the spontaneous formation of organized structures
from many discrete components that interact with one another dir-
ectly and/or indirectly through their environment. In addition, the
assembling components may also be subject to various global poten-
tials such as externally imposed electromagnetic field or chemical
potentials”. B. A. Grzybowski 2006.



Self-assembly refers to spontaneous formation of organized
structures through a stochastic process that involves pre-ex-
isting components, are reversible, and can be controlled by
the proper design of the components, the environment, and
the driving force. Ilya Prigogine Video
 Static SA refers to that subclass of self-assembly processes
that leads to structures in local or global equilibrium.

Dynamic SA refers to that subclass of self-assembly processes
that leads to stable non-equilibrium structures. These struc-
tures persist only as long as the system is dissipating energy.
 Programmable SA refers to that subclass of self-assembly pro-
cesses where the components of the system carry informa-
tion about the final desired structures or its function.
from: J. A. Pelesko. Self Assembly: The science of things that put themselves
together. Chapman & Hall / CRC. 2007


Self Assembly: Examples
 Snow crystals & Amphiphilic molecules. (static
SA. Lyotropic)


Graph Grammar SA.

Diffusion-limited aggregation & Flumini's tiles.

Protein folding & Chain Tribolon.

Magnetofluids (dynamic)


Snow Crystals

snowcrystals.com

Amphiphilic molecules


Amphiphilic molecules. Lyotropic liquid crystals

Lyotropic states


Self Assembly: Potential Applications

V. P. Torchilin (2007). Micellar Nanocarriers: Pharmaceutical Perspectives.
Pharmaceutical Research, vol 24, no. 1, pp 1-16.
N. Maurer et al. (2001).Developments in liposomal drug delivery systems.
Expert Opinion on Biological Therapy, v. 1, no. 6, pp 923-947.

Self Assembly

 Definition.
 Characterization.

Examples and Applications

...to go.


Self Assembly: Characterization
The four essential features of SA
 Units.

 Interaction.

Environment.

Driving Forces.

The mechanism of SA
 Energy minimization.


Thermodynamic hypothesis.
 Folding funnel theory.


Units

Simple or structured particles.
 The internal structure, that may be changed by external
stimuli is called conformation of the unit.
 Passive or active conformational changes.

Actuation intensity


Interaction
Force field - driven interaction: the energy is
provided by the interaction mechanism itself.
Electromagnetic interaction, gravitational interaction,
surface tension interaction, ...

Information-based interaction: the information is the
trigger of physical/chemical processes, but has no
relationship with the energy or energy flows needed by
the latter to unfold. Chemical signals, signal on waves
(EM or mechanical), electric signals, ...

J. G. Roederer, “Information, life and brains”, in J. Chela-Flores, G. Lemarchand and J. Oró, eds.,
Astrobiology (Kluwer Acad, Publ., Dordrecht, The Netherlands, 2000), pp. 179-194.

Self Assembly: Unit + Interaction
D. Fazio, C. Mongin, B. Donnio, Y. Galerne, D. Guillon, and D. W. Bruce J. Mater. Chem 11

Curvature arising from a large head group
(A) and a small head group (B).

Unit “shape” defines structure

Carbohydrate liquid crystals designed to
show particular phases. A large head group
example (A,C) and a small head group case
(B,D).


 Snow crystals & Amphiphilic molecules.

Graph Grammar SA.(information-based. Programmable SA)





Graph Grammar SA

E. Klavins (2007). Programmable self-assembly.
IEEE control systems vol. 27, no 4, pp. 3 -56

Graph Grammar SA


Graph Grammar SA


Set of rules, transitions.


Uniqueness given by natural dynamics.


Environment

Static or dynamic environments

Provides a way to control the system.
Isign model applet

J. Bishop, E. Klavins (2006). Collective Sensing with Self-Organizing Robots.
Proc. 45th IEEE Conf. on Decision & Control.



Graph Grammar SA.
 Diffusion-limited aggregation & Flumini's tiles.
(Environment, external fields. Passive conformational switches)





Self Assembly: Examples (Reminder)


DLA
Cluster grown from a copper sulfate
solution in an electrodeposition cell.

Simulated 3D DLA with external fields.
DLA movie
http://www.andylomas.com/


Flumini's tiles

Shaking table movie


Flumini's tiles

➔ Can we obtain the
phase diagram?
➔ What are the
parameters to
study?


Driving Forces

Could be induced by the interaction.

Independent of the system to avoid clamping.

natural dynamics


Thermodynamic Hypothesis

Proposed in relation to protein folding: A protein as-
sumes a particular conformation because that state
is thermodynamically the most favorable. The con-
formation is a global minimum of the free energy of
the system. The protein samples the energy space,
eventually winding up at a global minimum. Random
conformational search

Critics ... Stochastic assembly


Folding Pathway Hypothesis
 Time needed to explore the possibilities
is astronomical, “Levinthal paradox”.
The folding sequence is “predefined” in
the dynamics of structure.
C. Levinthal (1968). quot;Are there pathways for protein folding?quot;.
J. Chimie Phys. Phys.-Chimie Biol. 65: 44-45

Folding Funnel Hypothesis

The energy minimum is extremely deep and
with steep walls.


Folding Funnel Hypothesis
Conformational entropy is the entropy associated with the geometrical
arrangement of a chain of units. The concept is most commonly ap-
plied to biological macromolecules such as proteins and RNA. To cal-
culate the conformational entropy, the possible conformations as-
sumed by the chain may be discretized into a finite number of states,
usually characterized by unique combinations of certain structural
parameters, each of which has been assigned an energy level. The
conformational entropy associated with a particular conformation is
then dependent on the probability associated with the system taking
that state, as determined by the sum of the energies associated with
the parameters describing the state.



Graph Grammar SA.


Protein folding & Chain Tribolon.(search space)



Protein Folding

A given amino acid takes on roughly the same route and pro-
ceeds through roughly the same intermediates and transition
states.
 Alpha helices and beta sheets then tertiary structure. Forma-
tion of quaternary structure usually involves the assembly of
subunits that have already folded.
 The amino acid sequence of each protein contains the inform-
ation that specifies both the native structure and the pathway
to attain that state.

Conformations differ based on environmental factors.


Chain Tribolon
Conformational entropy

... ~ 242


Graph Grammar SA.



Ferrofluids. (dynamic SA)


Ferrofluids

Ferrofluid demostration

K. Butter et al. (2003). Direct observation of dipolar chains in iron ferrofluids by cryogenic
electron microscopy. Nature Materials no. 2, pp 88 - 91.

Self Assembly: Potential Applications
Self-repair /self-healing: Reconstruction of skin from a
suspension of skin cells from a 15-day embryonic mouse.

(B) t=0 (D) Migration

(E) t=72 hr
(A) intact embryonic skin

(C) t=24 hr self-healing robot

Monroy, A. and A. A. Moscona. Introductory Concepts in Developmental Biology.
University of Chicago Press, Chicago. 1979.


Self Assembly: ...to go

 Functionality

How to endow our engineered systems with func-
tionality?

Theory
 What are the underlying principles of SA?

Can we generalize to different scales?


Self Assembly: Questions?

the end...?


Self Assembly

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Self Assembly