Enzymind Labs

Engineering and constructing meso-scale redundant materials

How is it posssible to rationally design and make materials that have highly organized micro-structure?

Periodic and pseudo random structure occurs in many naturally formed materials, but not necessarily at the desired scale, or with a specific repeated unit or material. Non-periodic but deterministic structure is less common in non-living physical systems, but is the rule for living systems.

Growth and form are often locally rule based in living systems and globally rule based in non-living systems.

7/9/08 Feather structure, from micro to macro. Do photos of diffraction and meso-structure. See "Fossil feather" reference below.

6/5/08 Thue-Morse micro-pillar optical bandgap materials (get reference).

6/4/08 Negative index of refraction: H. Lezec, CIT, "layered metals perforated by nanoscale channels".

5/23/08

- optical mirroring window

- imprint patterning

- nanoimprint lithography

In a standard T-NIL process, a thin layer of imprint resist (thermoplastic polymer) is spin coated onto the sample substrate. Then the mold, which has predefined topological patterns, is brought into contact with the sample and they are pressed together under certain pressure. When heated up above the glass transition temperature of the polymer, the pattern on the mold is pressed into the melt polymer film. After being cooled down, the mold is separated from the sample and the pattern resist is left on the substrate. A pattern transfer process (reactive ion etching, normally) can be used to transfer the pattern in the resist to the underneath substrate.^[1]

In photo nanoimprint lithography (P-NIL), a photo(UV) curable liquid resist is applied to the sample substrate and the mold is normally made of transparent material like fused silica. After the mold and the substrate are pressed together, the resist is cured in UV light and becomes solid. After mold separation, a similar pattern transfer process can be used to transfer the pattern in resist onto the underneath material.

A key benefit of nanoimprint lithography is its sheer simplicity. The single greatest cost associated with chip fabrication is optical lithography tool used to print the circuit patterns. Optical lithography requires high powered excimer lasers and immense stacks of precision ground lens elements to achieve nanometer scale resolution. There is no need for complex optics or high-energy radiation sources with a nanoimprint tool. There is no need for finely tailored photoresists designed for both resolution and sensitivity at a given wavelength. The simplified requirements of the technology lead to its low cost.

Imprint lithography is inherently a three-dimensional patterning process. Imprint molds can be fabricated with multiple layers of topography stacked vertically. Resulting imprints replicate both layers with a single imprint step, which allows chip manufactures to reduce chip fabrication costs and improve product throughput. As mentioned above, the imprint material does not need to be finely tuned for high resolution and sensitivity. A broader range of materials with varying properties are available for use with imprint lithography. The increased material variability gives chemists the freedom to design new functional materials rather than sacrificial etch resistant polymers.^[4] A functional material may be imprinted directly to form a layer in a chip with no need for pattern transfer into underlying materials.

- [To Do: Biological material imprinting examples.]

- opto-chemical patterning

- photolithography

New Laser Method Reproduces Art Masterworks To Protein Patterns

"Using laser-assisted protein adsorption by photobleaching (LAPAP), the scientific team bound fluorescently-tagged molecules to a glass slides and created patterns of proteins similar to those of the human body."

- Biological examples

- irridescent green beetle example
- Buttefly scales example
- Feathers

- Molecular machines

- From Wikipedia Molecular machine:

(Also see Brownian motor )

A molecular machine has been defined as a discrete number of molecular components that have been designed to perform mechanical-like movements (output) in response to specific stimuli (input).^[1] It is often applied more generally to molecules that simply mimic functions at the macroscopic level. The term is also common in nanotechnology, and a number of highly complex molecular machines have been proposed towards the goal of constructing a molecular assembler. Molecular machines can be divided into two broad categories: synthetic and biological.

...

Unlike macroscopic motion, molecular systems are constantly undergoing significant dynamic motions subject to the laws of Brownian mechanics (or Brownian motion), and as such, harnessing molecular motion is a far more difficult process. At the macroscopic level, many machines operate in the gas phase, and often, air resistance is neglected, as it is insignificant, but analogously for a molecular system in a Brownian environment, molecular motion is similar "to walking in a hurricane, or swimming in molasses." The phenomenon of Brownian motion (observed by Robert Brown (botanist), 1827) was later explained by Albert Einstein in 1905. Einstein found that Brownian motion is a consequence of scale and not the nature of the surroundings. As long as thermal energy is applied to a molecule, it will undergo Brownian motion with the kinetic energy appropriate to that temperature. Therefore, like Feynman's strategy, when designing a molecular machine, it seems sensible to utilize Brownian motion rather than attempt to fight against it.

Like macroscopic machines, molecular machines typically have movable parts. However, while the macroscopic machines we encounter in everyday life may provide inspiration for molecular machines, it is misleading to draw analogies between their design strategy; the dynamics of large and small length scales are simply too different. Harnessing Brownian motion and making molecular level machines is regulated by the second law of thermodynamics, with its often counter-intuitive consequences, and as such, we need another inspiration.

Although it is a challenging process to harness Brownian motion, nature has provided us with several blueprints for molecular motion performing useful work. Nature has created many useful structures for compartmentalizing molecular systems, hence creating distinct non-equilibrium distributions; the cell membrane is an excellent example. Lipophilic barriers make use of a number of different mechanisms to power motion from one compartment to another.

- From Wikipedia Molecular motor:

Molecular motors are biological molecular machines that are the essential agents of movement in living organisms. Generally speaking, a motor may be defined as a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work ^[1]. In terms of energetic efficiency, these types of motors can be superior to currently available man-made motors. One important difference between molecular motors and macroscopic motors is that molecular motors operate in the thermal bath, an environment where the fluctuations due to thermal noise are significant.

...

Recently, chemists and those involved in nanotechnology have begun to explore the possibility of creating molecular motors de novo. These synthetic molecular motors currently suffer many limitations that confine their use to the research laboratory. However, many of these limitations may be overcome as our understanding of chemistry and physics at the nanoscale increases. Systems like the nanocars, while not technically motors, are illustrative of recent efforts towards synthetic nanoscale motors.

...

Viral DNA packaging motors inject viral genomic DNA into capsids as part of their replication cycle, packing it very tightly. ^[5]

- From Wikipedia Motor protien:

Motor proteins are a class of molecular motors that are able to move along the surface of a suitable substrate. They are powered by the hydrolysis of ATP and convert chemical energy into mechanical work.

The most prominent example of a motor protein is the muscle protein myosin which "motors" the contraction of muscle fibers in animals. Motor proteins are the driving force behind most active transport of proteins and vesicles in the cytoplasm. Kinesins and dyneins play essential roles in intracellular transport such as axonal transport and in the formation of the spindle apparatus and the separation of the chromosomes during mitosis and meiosis. Dynein is found in flagella and is crucial to cell motility, for example in spermatozoa.

Also see DNA packaging molecular motors

[To Do: Ameoba chemotaxis]

WEHI-TV DNA Molecular Animations

Very nice short animated clips showing various enzymes operating on DNA/RNA.

Biologists Discover Motor Protein That Rewinds DNA

ScienceDaily (Nov. 2, 2008)

[HARP (HepA-related protein) and other "annealing helicases"]

Two biologists at the University of California, San Diego have discovered the first of a new class of cellular motor proteins that “rewind” sections of the double-stranded DNA molecule that become unwound, like the tangled ribbons from a cassette tape, in “bubbles” that prevent critical genes from being expressed.

...

...this motor protein burns energy in the same way as enzymes called helicases and, like helicases, attached to the dividing sections of DNA. But while helicases use their energy to separate two annealed nucleic acid strands—such as two strands of DNA, two strands of RNA or the strands of a RNA-DNA hybrid— the scientists found to their surprise that this protein did the opposite; that is, it rewinds sections of defective DNA and thus seals the two strands together again.

DNA Repair: Structure Of The Mre11 Protein Bound To DNA

"Repairing breaks in the two strands of the DNA double helix is critical for avoiding cancer. In humans and other organisms, a molecular machine called the MRN complex is responsible for finding and signaling double-strand breaks (DSBs), then launching the error-free method of DNA repair called homologous recombination.

...

Prompt and accurate DNA repair is so essential to life that many of the molecular machines that perform DNA repair have changed little throughout the long course of evolution; today these machines show remarkable similarity in organisms as diverse as archaea, yeast, frogs, and human beings."

Small-angle x-ray scattering confirmed the U-shape of the Mre11 dimer (gray envelope) in solution. Although of lower resolution than crystallography, SAXS was used to establish the orientation of the dimer's components, as shown in ribbon format. (Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory)

 

 Come one, come all, and witness the molecular MACHINE

Alex Palazzo

"... So how are secreated and membrane bound proteins translocated through the translocon?

...and this requires the SecA pump. So how does SecA work?

Well in the latest issue of Nature the machine has been unveiled - and it looks cool. From the structure of the SecA-SecY complex, and the accompaning biochemistry paper, it becomes clear how a molecular pump could work. The part of SecA that holds on to the peptide becomes obvious and acts like a "clamp", in previous structures the clamp was open (an not obvious), but oin the complex the clamp closes. Just like a tightening fist, the SecA clamp has a cleft that is continuous with the chanel's pore. In addition SecA and SecY both have a lateral opening to allow membrane bound proteins to exit sideways and thus partition into the membrane, and yes both lateral exits are contiguous. Finally the SecY pore was seen to be plugged by a short alpha-helix - but when SecA binds to the translocon, the SecY's configuration changes so that the plug moves (although not enough to allow a clear passage across the channel) and the chanel widens. But there's more, SecA plunges two of it's alpha-helices into the chanel itself to help open the pore. These two helices (or helix finger) resemble peptide pushing loops present in many polypeptide pumps such as the 19S subunit of the proteasome and ClpX."

 

 

- Active and passive transport, processes that organize by chemical and physical processes

Transport by diffusion (directed?), blood flow, exocytosis, and unspecified "migration". Active transport across membrane? Shape, weak bonding and adsorpsion.
 

- Revenge of the clones: the immunology movie by Sandra Porter

October 20, 2008

What happens when a group of streptococci stick to cells in your throat and start to make toxins?

About clonal selection, introducing this short animation:

Fighting Infection by Clonal Selection

- Using biologically constructed material as a template

- virus capsids

- Qian Wang, Tianwei Lin, Liang Tang, John E. Johnson & M.G. Finn (2002) Icosahedral virus particles as addressable, self-organizing nanoblocks. Angewandte Chemie International Edition 41, 459-462.

- DNA

Assembling Materials with DNA as the Guide

Faisal A. Aldaye, Alison L. Palmer,  Hanadi F. Sleiman

Science 26 September 2008:
Vol. 321. no. 5897, pp. 1795 - 1799

DNA's remarkable molecular recognition properties and structural features make it one of the most promising templates to pattern materials with nanoscale precision. The emerging field of DNA nanotechnology strips this molecule from any preconceived biological role and exploits its simple code to generate addressable nanostructures in one, two, and three dimensions. These structures have been used to precisely position proteins, nanoparticles, transition metals, and other functional components into deliberately designed patterns. They can also act as templates for the growth of nanowires, aid in the structural determination of proteins, and provide new platforms for genomics applications. The field of DNA nanotechnology is growing in a number of directions, carrying with it the promise to substantially affect materials science and biology.

 

 - viruses

Virus As Nano-building Block: Extreme Nature Helps Scientists Design Nano Materials

"A team from the UK’s John Innes Centre, the Scripps Research Institute in California and the Institut Pasteur in Paris have identified a stable, modifiable virus that could be used as a nanobuilding block.

Viral nanoparticles (VNPs) are ideally sized, can be produced in large quantities, and are very stable and robust. They can self-assemble with very high precision, but are also amenable to modification by chemical means or genetic engineering.

...depending on the chemistry used, modifications could be targeted specifically to the ends of the virus particle, to its body, or both. This spatially controlled modification is unique to this VNP, and opens up new possibilities when the nanobuilding blocks are built up into arrays or layers. Since the virus body and ends can be selectively labelled it is expected that arrays with different physical properties can be fabricated, for example by aligning particles body-to-body versus self-assembly end-to-end. This option is not possible with other rod-shaped VNPs."

 SIRV2 nanoparticle. (Credit: Image courtesy of John Innes Centre)

 

MIT engineers work toward cell-sized batteries

"First, on a clear, rubbery material the team used a common technique called soft lithography to create a pattern of tiny posts either four or eight millionths of a meter in diameter. On top of these posts, they then deposited several layers of two polymers that together act as the solid electrolyte and battery separator.

Next came viruses that preferentially self-assemble atop the polymer layers on the posts, ultimately forming the anode. In 2006, Hammond, Belcher, Chiang and colleagues reported in Science how to do this. Specifically, they altered the virus's genes so it makes protein coats that collect molecules of cobalt oxide to form ultrathin wires -- together, the anode.

The final result: a stamp of tiny posts, each covered with layers of electrolyte and the cobalt oxide anode. "Then we turn the stamp over and transfer the electrolyte and anode to a platinum structure" that, together with lithium foil, is used for testing, Hammond said."

- Patterned self-assembly

- buckytube growth from substrate
- magnetic sphere chain tube generation
- other examples and paradigms

Evolution of Block Copolymer Lithography to Highly Ordered Square Arrays

Chuanbing Tang, Erin M. Lennon, Glenn H. Fredrickson, Edward J. Kramer, Craig J. Hawker

Science 17 October 2008:
Vol. 322. no. 5900, pp. 429 - 432

"The manufacture of smaller, faster, more efficient microelectronic components is a major scientific and technological challenge, driven in part by a constant need for smaller lithographically defined features and patterns. Traditional self-assembling approaches based on block copolymer lithography spontaneously yield nanometer-sized hexagonal structures, but these features are not consistent with the industry-standard rectilinear coordinate system. We present a modular and hierarchical self-assembly strategy, combining supramolecular assembly of hydrogen-bonding units with controlled phase separation of diblock copolymers, for the generation of nanoscale square patterns. These square arrays will enable simplified addressability and circuit interconnection in integrated circuit manufacturing and nanotechnology."

 

 

- Virion structure and mechanics

- P22 electron microscopy, proposed hinged trigger mechanism, dsDNA packing, dsDNA insertion mechanism, procapsid assembly, etc.

P22 virion data and renderings

- [To Do: Fix up and redo virion structure animation.]

P22 virion structure, EMD-1220 rendering notes

Test renderings of the P22 virion EMD-1220 data set

Virus structure and mechanics information and references

- cellular architecture
- microtubules and self-assembly
- sphere packing

"Much more than chance was operating on those swirling compounds in earth's primordial seas: there were also natural laws of physics and chemistry. Spill a bag of beans on a table top and it is unlikely that they will form a pattern with regular hexagonal symmetry. But we know that when water freezes during a snowstorm the molecules form such hexagonal patterns by the millions. The reason is, of course, that electrical forces of attraction and repulsion are operating between the molecules in such a way as to make such striking patterns not only possible but extremely probable." Martin Gardner , "The Ambidextrous Universe: Left, Right and the Fall of Parity", 1964, 1969, pg. 136-137.

1964 The Ambidextrous Universe: Mirror Asymmetry and Time-Reversed Worlds (updated 1990, to be re-released with updates June 9, 2005 as The New Ambidextrous Universe: Symmetry and Asymmetry from Mirror Reflections to Superstrings: Revised Edition, Dover; ISBN 0-486-44244-6)

- inflate to make dodecahedra

Self-assembling Polymer Arrays Improve Data Storage Potential

"The method builds on existing approaches by combining the lithography techniques traditionally used to pattern microelectronics with novel self-assembling materials called block copolymers. When added to a lithographically patterned surface, the copolymers' long molecular chains spontaneously assemble into the designated arrangements."

Researchers from the University of Wisconsin-Madison and Hitachi Global Storage Technologies have reported a way to improve the quality and resolution of patterned templates such as those used to manufacture hard drives and other data storage devices. When added to lithographically patterned surfaces such as those shown in the upper left panel of this composite image, specially designed materials called block copolymers self-assemble into structures, shown in the upper right panel, with improved quality and resolution over the original patterns. These structures can be used to make templates with nanoscale elements like the silicon pillars shown in the bottom panel, which may be useful for manufacturing higher capacity hard disk drives. (Credit: Courtesy of Paul Nealey)

Fossil Feathers Preserve Evidence Of Color

"The traces of organic material found in fossil feathers are remnants of pigments that once gave birds their color, according to Yale scientists whose paper in Biology Letters opens up the potential to depict the original coloration of fossilized birds and their ancestors, the dinosaurs.

Striped fossil feather and recent woodpecker feather. Under the scanning electron microscope there are melanosomes in the dark but not the light areas (left arrows) of the fossil. For comparison, melanosomes from a broken black feather and a white feather are shown (right arrows). (Credit: J.Vinther/Yale)

In 'Novel Playground,' Metals Self-assemble Into Porous Nanostructures

"The method involves coating metal nanoparticles -- about 2 nanometers (nm) in diameter -- with an organic material known as a ligand that allows the particles to be dissolved in a liquid, then mixed with a block co-polymer (a material made up of two different chemicals whose molecules link together to solidify in a predictable pattern). When the polymer and ligand are removed, the metal particles fuse into a solid metal structure."

Computer simulation, left, shows how platinum nanoparticles will fuse into a structure with tiny pores after the polymers that guide them into position are removed. Right, electron microscope photo of the actual structure. (Credit: Wiesner Lab)

 

New Process Creates 3-D Nanostructures With Magnetic Materials

Working in the trenches: Transmission electron microscopy image of a thin cross section of 160 nanometer trenches shows deposited nickel completely filling the features without voids. (Color added for clarity.) (Credit: NIST)

Image copywrite Fred Eiserling, from Bacteriophage Ecology Group (BEG) News (015):

"Above is an updated (circa late 2002) of the classic drawing of the bacteriophage T4 virion, kindly brought to us by Fred Eiserling (who is also responsible for the original). Fred would like us to employ these watermarked images far and wide, so please feel free to copy and use them. An unwatermarked version is due to be published in the upcoming The Bacteriophages edition 2 (Oxford University Press). ... Fred can be contacted at frede@college.ucla.edu . "