Soft Matter Soft matter does not exhibit the crystalline order (Lect. 7b, Slides 1,2) that is characteristic of most hard matter (except amorphous solids). Nevertheless, some order remains. Soft matter lends itself to self-assembly which produces a large variety of nanostructures. Pierre-Gilles de Gennes received the 1991 Physics Nobel Prize for bringing order into soft matter, particularly liquid crystals and polymers.

Liqid Crystals Translational order is partially lost, but orientational order remains.

Nematic Liqid Crystals Example: Pairs of molecules with a hydrophilic and a hydrophobic end 8CB dimer: Nematic liquid crystals behave like a quadrupole (+--+), not like a dipole (+-).

Liquid Crystal Display (LCD) A nematic liquid crystal is forced into a twisted structure by oriented polymers at the top and bottom plates. The thickness is adjusted such that the twist rotates the polarization of light by 90 0, i.e. light is transmitted between crossed polarizers. A voltage applied between top and bottom straightens out the nematic molecules. The polarization remains unchanged and light is blocked by the crossed polarizers.

Micelles and Inverse Micelles Surfactant: Hydrophilic HeadExample: Phospholipid + Hydrophobic Tail Micelle: Inverse Micelle: Heads outside, Water outsideHeads inside, Water inside

Bilayer Structures, Vesicle Part of a Cell Wall

Drug Delivery via Liposomes

Supramolecular Assemblies

Polymers Monomer:A Oligomer:A-A-A-A Homopolymer:A-A-A-A-A-A-A-A-A-A-A-A-A- … Heteropolymer = Copolymer:A-B-B-A-B-A-B-A-B-A-A-B-A-B- … Block Copolymer:A-A-A-A-A-A-A-A-A—B-B-B-B The volume ratio of the A- and B- blocks, plus the strength of the interaction between A and B (hydrophilic, phobic) determines their phase diagram (next).

A Hydrophilic-Hydrophobic Block Copolymer PMMA  PS (polymethylmethacrylate) (polystyrene) Negative charge on the Neutral hydrocarbons oxygen makes it hydrophilic. make it hydrophobic.

Identify Polymers by their Molecular Orbitals

Phase Diagram of a Diblock Copolymer Hydrophilic + Hydrophobic Volume Fraction Interaction Strength Theory Data

Triblock Copolymers: Even more Options

Cylinders (or vertical sheets) Spheres (or vertical cylinders) Various Block Copolymer Phases

N Biopolymers: Proteins The Peptide Bond between Amino Acids in a Protein Two amino acids react. N forms the bridge. covalent + (zwitter)-ionic N O See the  * orbital of this double bond in X-ray absorption

See the peptide bond with X-ray absorption spectroscopy at the N 1s edge The  * orbital of the peptide bond is the largest N 1s peak. Xiaosong Liu et al., (2006) h (eV) Need a dimer to establish the peptide bond orbital. Gordon et al. (2003)

Protein Folding Hierarchy

Hemoglobin

Protein Folding Patterns  -helix Pleated sheet Random coil Hydrogen bonds play a large role.

J. Lipkowski, U. Guelph, Canada Amide vibrational modes: Amide I, C=O stretch secondary structure  -helix: cm -1  -sheet: cm -1 Amide II, N-H bend tertiary structure H  D exchange: 1550  1450 cm -1 oxygen Protein Infrared Spectroscopy Vibrations reveal the secondary and tertiary structure.

Biopolymers: DNA Adenine Thymine Guanine Cytosine Base pairing via hydrogen bonds :

While cells are typically  m in size, their interior contains many nanometer-sized objects. Cells

The basement membrane is a thin sheet of fibers that underlies the epithelium, which lines the organs, or the endothelium, which lines the interior of blood vessels. Most cells need a basement membrane as support (except blood cells). The basement membrane contains structures on the 100 nm scale. The Basement Membrane

Neurons Is there a way to tap into the electrical signal of a single neuron to figure out how the brain works ?

Connecting Neurons to an Electronic Circuit Fromherz group One can poke a micropipette into a neuron, but the neuron does not live very long after that. It is better to grow neurons on a transistor and transmit electrical signals via a capacitor (both input and output).

Growing Neurons on a Biocompatible Microchip

Wiring up a Neuron

Communication between a Network of Neurons and a Computer

Transmitting Electrical Signals between Transistor and Neuron