Monday, February 21, 2011

Molecular Machinery: A Brief Overview

Functional molecular devices have been designed and fabricated for several years now:
Gold nanorotor

Such nano versions of macroscopic machines are in part inspired by the visionary physicist Richard Feynman 50 years ago.  Also, fabrication and synthesis technologies has advanced enough to initialize and perpetuate the quest to miniaturize machinery in the current science and engineering disciplines. 

One of the most advanced current fabrication meths, the "top-down approach to miniturization in the semiconductor industry, is approaching the limits in scaling. For example, the band structure of silicon disappears when silicon layers are just a few atoms thick.  What about photolithography?  Well, its operational wavelengths are too limited for making nanomachines with moving parts.  

Recently, organic chemists in Rice University realized they can synthesize 3 × 4 nm nanocars in 100 mL laboratory reaction flasks–30 mg worth (that translates into 3 × 10¹⁸ nanocars–far exceeding the number of automobiles made in the history of the world.).  30 nanocars, side by side, can span the 90 nm width of a small in line in the most advanced logic chip being made today.  Tiny objects with many moving parts like nanocars have to be made differently, from the "bottom-up".  This follows more naturally in line with Darwinian evolution at the biochemical level, although we're nowhere near the sophistication of Nature's handiwork.  Consequently, molecular scientists have turned their attention to much simpler systems, where the machinery may be easier to construct and understand, perhaps serving as a base for eventual progression toward sophisticated and useful nanomachines.  

Most of the molecular machines shown above were designed and synthesized to operate in the liquid phase because of the abundant tools available to analyze products in solution.  However, useful nanomachines with mechanical functions require eventual integration into devices that interface surrounding systems (likely to operate in the solid phase).  For example, the biological nanomachine ATPase is anchored in a biological membrane in order to connect with its surroundings.  Overcoming this interface problem ranks among the most intractable of problems in nanomachine design.  

Nevertheless, there are several viable designs that (1) work in a crystalline solid, or (2) be mounted on and operated on surface, or (3) move around and operate on a surface.  
Machines operating in crystalline solid state
UCLA researchers have made considerable progress in the formulation, design, and preparation of crystalline molecular machines.  Examples of their work include molecular compasses and gyroscopes.  

The center component of the molecule above (red) has a magnetic moment that responds via rotation to external magnetic fields.  The plot qualitatively indicates the energy required for the rotation to occur. 

 Conventional crystalline materials have their molecular components tightly bonded and restricts their motion, which contrasts to another class of materials known as amphidynamic crystals.  These exotic crystals possess rigid lattices connected to moving parts (See pic below).   
Example of an amphidynamic crystal

Successful utilization of such crystals will lead to photonics materials whose components  stem from the bulk (not from solution or thin films), which increases the density, which leads to greater advances.  

Machines mounted and operating on a surface

Molecular machines heavily depend on positioning to be to pump, push, lift materials, or other useful work.  Examples of such machines already produced in the lab are: (see captions of following pictures)
cyclodextrin necklaces. 
J. Am. Chem. Soc. 2000, 122, 5411-5412
Molecular Shuttles,
Light powered molecular motor.  The absorption of sunlight by one of the two stoppers, a light-harvesting one, causes the transfer of one electron to station A, which is deactivated as far as wanting the ring to encircle it. As a consequence, the ring moves to its second port of call, station B. Station A is subsequently reactivated by the return of the transferred electron to the light-harvesting stopper, and the ring moves back to this station. Copyright © UCLA
Machines moving and operating on a surface
As if mounting nanomachines on a surface weren't hard enough, people are also trying to make them move and do stuff.  That may call for zealous usage of scanning probes such as the scanning tunneling microscope (STM).  In fact, the STM has been used to push these molecules on a surface laterally, with atomic scale precision.  Perhaps the most famous molecule used for this purpose is the molecular wheelbarrow:

(a) macroscopic wheelbarrow.  Its colors correspond to the chemical structure in (b).  (c) shows the molecule in the gas phase. 
Mechanical interactions between molecule and surface determines the molecule's motion on a variety of surfaces.  For macroscopic objects, the theory and basic rules for the design of machinery is well-known and justly exploited.  Skiing works for snow, but not for asphalt.  On water, wheels only float on their own if they're made of rubber; recommended solution, get a sailboat.  These situations don't require much brainpower to imagine, but rigorous mathematical and physical theories are necessary to explain them.  But on the atomic level, the rules are different, and therefore the normal human intuitions for working machinery do not apply.  Movement on surfaces might not follow Newtonian physics, but rather quantum mechanics.  Quantum calculations are notoriously difficult and computationally costly to obtain exact answers with the currently available tools.  For now, the development of molecular machinery depends mostly on dogged trial-and-error.  

Friday, February 18, 2011

DNA Robospider

The nanites are here, and they're made of DNA.  Well, not really, but researchers at 4 institutions across the country have created and programmed DNA spider-bots that walk independently across a a nano-scale track.  A baby step (spider step?), but also a milestone, in the nascent fields of molecular computing and and robotics.  Eric Drexler had long envisioned molecular robots in his seminal book Engines of Creation, now manifesting into reality. 
Normally, a robot would have a set of instructions to follow specific tasks repeatedly, from vacuuming carpets to welding cars, but programming biomolecules?  Not a simple task, and requires researchers from many disciplines (CS, chemistry, engineering, biology) to collaborate, which did occur.  The result are DNA walkers with 'legs' that allow them to briefly walk autonomously on a fabricated 2D landscape.  They can begin and continue walking, turn, then stop.  Rinse and repeat.  The walkers are only ~ 4 nm in diameter, and walk very slowly, covering 100 nm in 30 minutes to an hour by only 100 steps.   Compare that to previous walkers took that long to walk only 3 nm.
Researchers have created and observed a molecular robot capable of many steps, and of making decisions where to step and how long to stay. As the robot walks on the substrate, it changes each piece by cleaving off a part. If it touches a spot that has been cleaved already, it does not linger as long. The end of the track glows red and captures the robot, letting the researchers know when it has completed its walk. The robot glows green, allowing for the researchers to see it better. Credit: Zina Deretsky, National Science Foundation

This shows high promise for the emerging nanomedicine field, which promises localized cancer treatment.  Imagine a time when we can look back and consider chemotherapy to be barbaric and inhumane.  Nanomedicine could be our ticket to that future.