Self Assembly

05. 2008© JP Carbajal 1

Self Assembly

Definition.Definition. Characterization.

Examples and Applications ...to go.


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


Self Assembly: Definition

“...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.

Answers from the experts


Self Assembly: Definition 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

http://www.youtube.com/watch?v=2NCdpMlYJxQ


Self Assembly: Examples Snow crystals & Amphiphilic molecules.Snow crystals & Amphiphilic molecules. (static

SA. Lyotropic)

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


Self Assembly: ExamplesSnow Crystals

snowcrystals.com


Self Assembly: ExamplesSnow Crystals

snowcrystals.com


Self Assembly: ExamplesAmphiphilic molecules


Self Assembly: ExamplesAmphiphilic molecules. Lyotropic liquid crystals

Lyotropic states


Self Assembly: Potential Applications

N. Maurer et al. (2001).Developments in liposomal drug delivery systems. Expert Opinion on Biological Therapy, v. 1, no. 6, pp 923-947.

V. P. Torchilin (2007). Micellar Nanocarriers: Pharmaceutical Perspectives. Pharmaceutical Research, vol 24, no. 1, pp 1-16.


Self Assembly

Definition. Characterization.Characterization.

Examples and Applications ...to go.


Self Assembly: Characterization

Units. Interaction. Environment. Driving Forces.

The four essential features of SA

Energy minimization. Thermodynamic hypothesis. Folding funnel theory.

The mechanism of SA


Self Assembly: CharacterizationUnits

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


Self Assembly: CharacterizationInteraction

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

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

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

D. Fazio, C. Mongin, B. Donnio, Y. Galerne, D. Guillon, and D. W. Bruce J. Mater. Chem 11

Unit “shape” defines structure


Self Assembly: Examples Snow crystals & Amphiphilic molecules. Graph Grammar SA.Graph Grammar SA.(information-based. Programmable SA)

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


Self Assembly: ExamplesGraph Grammar SA

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







Set of rules, transitions.

Uniqueness given by natural dynamics.


Self Assembly: CharacterizationEnvironment

Isign model applet

Static or dynamic environments Provides a way to control the system.

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

http://www2.truman.edu/~velasco/ising.html


Self Assembly: Examples Snow crystals & Amphiphilic molecules. Graph Grammar SA. Diffusion-limited aggregation & Flumini's tiles.Diffusion-limited aggregation & Flumini's tiles.

(Environment, external fields. Passive conformational switches)

Protein folding & Chain Tribolon. Magnetofluids (dynamic)


Self Assembly: Examples (Reminder)


Self Assembly: ExamplesDLA

DLA moviehttp://www.andylomas.com/

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

Simulated 3D DLA with external fields.


Self Assembly: ExamplesFlumini's tiles

Shaking table movie


Self Assembly: ExamplesFlumini's tiles

➔ Can we obtain the phase diagram?

➔ What are the parameters to study?


Self Assembly: CharacterizationDriving Forces Could be induced by the interaction. Independent of the system to avoid clamping.

natural dynamics


Self Assembly: CharacterizationThermodynamic Hypothesis

Stochastic assembly

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 ...


Self Assembly: CharacterizationFolding Pathway Hypothesis Time needed to explore the possibilities

is astronomical, “Levinthal paradox”. The folding sequence is “predefined” in the dynamics of structure.

Folding Funnel Hypothesis The energy minimum is extremely deep and

with steep walls.

C. Levinthal (1968). "Are there pathways for protein folding?". J. Chimie Phys. Phys.-Chimie Biol. 65: 44-45


Self Assembly: CharacterizationFolding Funnel HypothesisConformational 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.


Self Assembly: Examples Snow crystals & Amphiphilic molecules. Graph Grammar SA. Diffusion-limited aggregation & Flumini's tiles. Protein folding & Chain Tribolon.Protein folding & Chain Tribolon.(search space)

Magnetofluids (dynamic)


Self Assembly: ExamplesProtein 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.


Self Assembly: ExamplesChain TribolonConformational entropy

... ~ 242


Self Assembly: Examples Snow crystals & Amphiphilic molecules. Graph Grammar SA. Diffusion-limited aggregation & Flumini's tiles. Protein folding & Chain Tribolon. Ferrofluids.Ferrofluids. (dynamic SA)(dynamic SA)


Self Assembly: ExamplesFerrofluids

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

Ferrofluid demostration

http://www.youtube.com/watch?v=A5OhZ9wT568


Self Assembly: Potential ApplicationsSelf-repair /self-healing: Reconstruction of skin from a

suspension of skin cells from a 15-day embryonic mouse.

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

(A) intact embryonic skin

(B) t=0

(C) t=24 hr

(D) Migration

(E) t=72 hr

self-healing robot

http://www.youtube.com/watch?v=uIn-sMq8-Ls


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...the end...??

Self Assembly

Technology

self assembly definition

dynamic sa

programmable sa

definition qa

discrete components

isting components

assembling components

lyotropic graph grammar