Auxetics at the Molecular Level: A Negative Poisson's Ratio in Molecular Rods

N. Pour et al, "Auxetics at the Molecular Level: A Negative Poisson's Ratio in Molecular Rods"

Angew. Chem. Int. Ed. 45, 5981 (2006)

Most materials become thinner when they are pulled longitudinally, and thicker when compressed. However, auxetic materials have just the opposite behavior--while this might seem counterintuitive, in fact foams, certain crystals (along special axes), and the exotic forms of matter found in white dwarfs all have this property. In this paper, the authors perform (AM1, various DFT, and MP2) calculations to demonstrate this type of behavior on the nanoscale for prismane-like rods. While more of a theoretical curiosity at this point, the authors hope this will stimulate the syntheses of these types of materials.

A Four-position Chlorophyll-a molecular switch

Violeta Iancu and Saw-Wai Hla, "Realizing a Four-Step Molecular Switch in Scanning Tunneling Microscope Manipulation of Single Chlorophyll-a Molecules"

cond-mat/0609077

This paper combines a lot of things I like reading about: chlorophyll, STM-manipulation of molecules, and semi-empirical calculations. Basically the title says it all: you can use inelastic tunneling spectroscopy (IETS) to move the phytyl tail around into 4 distinct positions. The pictures are quite nice too, thanks to the PM3 calculations.

Limitations of Quantum Simulation Examined by Simulating a Pairing Hamiltonian Using Nuclear Magnetic Resonance

Kenneth R. Brown, Robert J. Clark, and Isaac L. Chuang, "Limitations of Quantum Simulation Examined by Simulating a Pairing Hamiltonian Using Nuclear Magnetic Resonance"
PRL 97, 050504 (2006)

In this paper, my old grad school buddy Ken Brown (& co.) reports on combined theoretical and experimental (NMR) tests on the effects of control errors, fault tolerance, and error bounding for quantum-computer based simulations of pairing model Hamiltonians. Ultimately they conclude that quantum simulations may outperform classical simulations for large problems where only limited precision is desired, but in the current case find the simulations to be sensititve to systematic errors, and more importantly that current fault tolerant implementations are inefficient as compared to the "Trotterization" of the unitary evolution.

Quantum engineering: An atom-sorting machine

Miroshnychenko et al, Nature 442, 151 (2006)

Wow. Individual manipulation of neutral atoms in strings of atoms, by optical tweezers. Check out the movie in the supplementary materials.

Vinod Khosla Biofuels talk @ Google

Not being an economist, I have never understood the economic technology required to get biofuels into a larger role--this puts a good VC-face on the technology of therecent DOE and NRC reports. Despite the between-the-lines emphasis on synthetic biology and other green-tech, nanoscience can play an important role in the water-gas-shift processes that are briefly mentioned. A very enjoyable seminar.

Demonstration of a nanoparticle-based optical diode

D. Alexander et al, "Demonstration of a nanoparticle-based optical diode", Optics Lett. 31, 1957(2006)

This is a neat demonstration of an optical diode (light transmission only in one direction, using a pair of CdSe/ZnS core-shell nanocrystals with the appropriate fluorescence and absorption spectra. The diode "switching speed" is limited to about 25-33 MHz, due to the 10-20ns fluorescence lifetime of the nanocrystals. I always like a neat analogy to electronics, and this really demos a case where the systematically tunable optical properties of nanocrystals can be used to achieve something that would be nearly impossible to do using small molecules.

Possible method to determine the two-dimensional to three-dimensional crossover of gold clusters by examining their vibrational modes

Wei Fa and Jinming Dong , "Possible method to determine the two-dimensional to three-dimensional crossover of gold clusters by examining their vibrational modes", APL 89, 013117 (2006)

There has been a lot of interest lately in small metal clusters, comprised of less than 30 atoms. In particular gold is an interesting case, as Au nanoclusters display catalytic properties which are not observed in the bulk. However, the characterization of these clusters, and in particular the characterization of the relative stabilities of the different possible structures has been elusive. These guys use relativistic DFT calculations and find that the 2D and 3D geometries have distinct vibrational modes. This could be an easy way to identify them spectroscopically.

There's gold in them thar' hills!

Reith, et al, "Biomineralization of Gold: Biofilms on Bacterioform Gold"
Science 313(5784) 233-236 (2006)

Maybe it's because I live in California, and the legend of the Gold Rush of 1849 plays a part in the collective subconsious, but it's always nice to find bacteria, in this case Ralstonia metallidurans that can precipitate gold from aqueous solutions. While this serves as a defense mechanism (the aqueous Au is quite toxic to the little guys), it is suspected that this might be the origin of the small secondary gold grains found around the world. With some good biochemistry, this might be a step towards reducing the environmental impact of gold mining, which has typically relied on mercury, etc (a pollution problem still left over here from more than 150 years ago).

Photoinduced Reversible Change of Fluid Viscosity

Sakai et al, "Photoinduced Reversible Change of Fluid Viscosity"
J. Am. Chem. Soc., 127 (39), 13454, 2005.

Using a modified azobenzene molecule, the author demonstrate a fluid in which the viscosity may be switched reversibly from high viscosity to low viscosity, using visible/ultraviolet light to flip a bond from trans to cis conformations. This could form the basis for a neat science "magic" trick.

Scanning tunneling microscopy single atom/molecule manipulation and its application to nanoscience and technology

Saw-Wai Hla, "Scanning tunneling microscopy single atom/molecule manipulation and its application to nanoscience and technology"
J. Vacuum Sci. Tech B 23, 1351 (2005)

A nice introduction to the field.

Personally, I find this type of single-molecule chemistry-by-STM to be amazingly fascinating stuff. I really wanted to do something like this as a postdoc, so I read a lot of papers, etc. Some particularly cool work was done by Sylvain Martel (Montreal Polytechnic) and Ian Hunter (MIT), published in the Journal of Micromechatronics (the reference is in my lab notebook, but it was 2004, IIRC) in which they designed sugar-cube sized robots, each capable of moving around on a surface, and alternately carrying STM or AFM devices, as well as optical allignment sensors, etc. Unfortunately, Hunter didn't have any room in his lab when I applied (or at least that was his white-lie), and I never got a response from Martel (who probably looked at my laughable theoretician CV and deleted the email at once). Hla, who previously was affiliated (or at least wrote some papers) with Karlheinz Rieder, at the Free University of Berlin, did some of the pioneering work, doing classical "organic chemistry" stuff like making iodobenzene by dissociating iodine, and dragging it onto benzene(!) (this was in a PRL back in 2000, IIRC), etc. But, I can barely speak English (as you, my dedicated readers, might be able to tell), so the thought of learning German was out. And I really liked staying in the Bay Area.

So if any of you reading this is looking for a postdoc to do this type of stuff...even for a few months...

Fast Quantum Algorithm for Numerical Gradient Estimation

S. P. Jordan, "Fast Quantum Algorithm for Numerical Gradient Estimation"
PRL 95, 050501 (2005)

Gradient evaluation is an important subroutine in a wide variety of problems in quantum chemistry and nanoscience (not to mention many other "real world" problems. Classically, for a d-dimensional system, at least d+1 function calls are required in order to determine the gradient; Jordan demonstrates a quantum algorithm that can do this in only one function call, using a generalization of the Bernstein-Vazirani algorithm to continuous functions with finite precision. Now we only need to build a quantum computer...

Quantitative Mass Spectrometric Identification of Isomers Applying Coherent Laser Control

Dela Cruz et al., "Quantitative Mass Spectrometric Identification of Isomers Applying Coherent Laser Control"
J. Phys. Chem. A, 109 (38), 8447-8450 (2005)

Mass spectrometry works by breaking molecules into pieces into pieces in order to identify them. That's great, except in isomers, such as ortho, meta, and para- xylenes, in which the molecules consist of the same pieces. Dela Cruz combine Mass Spec with femtosecond laser-based dissociation; since the quantum mechanical energy levels are different, carefully controlled laser pulses can be used to selectively dissociate these molecules (and other isomeric pairs) Furthermore, as they point out, most of this technology is available "off the shelf", there is no reason this cannot be widely applied.

Simple and Surprisingly Accurate Approach to the Chemical Bond Obtained from Dimensional Scaling

Svidzinsky et al., "Simple and Surprisingly Accurate Approach to the Chemical Bond Obtained from Dimensional Scaling"
PRL 95, 080401 (2005)

Using a dimensional scaling trick borrowed from the toolbox of string theory, in which one adds an infinite number of dimensions to the problem, and then rescales back to the "right" answer, these guys get the potential energy curve of the hydrogen molecule more or less right. Interestingly, in the large-D limit, this gives a semiclassical picture, similar to a model proposed by Bohr, in which the electrons are confined to specific orbits, BUT the uncertainty principle is retained. They also apply this to some of the standard "theoretician" diatomic molecules, such as HeH, He2, and BeH, and get pretty good results.

Mechanism of a molecular electronic photoswitch

Zhuang and Erznzerhof, "Mechanism of a molecular electronic photoswitch"
PRB 72, 073104 (2005)

This is a cute theoretical paper (DFT+NEGF), on the mechanism behind a nice light-driven molecular switch that has already been experimentally demonstrated. However, as a sign of "the spirit of the age", an almost identical paper appeared less than a month ago from Kondo et al., Chem Phys Lett 412, 55 (2005) Kondo (KTY) et al submitted 4 months earlier than Zhuang and Erznzerhof (ZE), but ZE had their paper in final form a month earlier than KTY. Despite this, KTY appeared online a month earlier than ZE. Is molecular transport becoming like biology, where (if the horror stories are correct) a PI listening to a conference talk will be on the phone immediately to tell his/her army of postdocs and graduate students the details of a protocol, so that they can race to publish it a week or two before some other group?
Maybe somebody should also start a blog just to chronicle these types of incidences.

Photovoltaic effect in ideal carbon nanotube diodes

Ji Ung Lee, "Photovoltaic effect in ideal carbon nanotube diodes"
Appl Phys Lett 87, 073101 (2005)

An experimental demonstration that individual single-wall carbon nanotubes can form IDEAL p-n junction diodes, and as a result, perform well as photovoltaic devices. Lee estimates that the efficiency is greater than 5% of light absorption
(the experimentally measured value is less, due to only a small amount of the light being absorbed for various
experimental reasons. The best part is that 0.8 nm diameter SWNTs have a band gap of 1.4 eV, which is almost ideal for for a single bulk junction device at the standard solar spectrum...and additional gains could be had by using networks of tubes. The down side, is you still need a lithographically defined set of metal gates on a wafer for your source and drain, so it's not quite at the point of being a totally bottom-up self assembly.

Nanocrystal-Powered Nanomotor

Regan et al, "Nanocrystal-Powered Nanomotor"
Nano Lett. 5, 1730 (2005)


Not long ago, Zettl & co. learned that applying electric current to carbon nanotubes leads to heading, which can be used as a mass conveyor belt for indium atoms. Now they extend this effect, using the transport of the indium atoms to create the equivalent of a "frost heave"-based growth of In nanocrystals between two CNTs, in order to create a linear motor, that can be adjust from 0 to 130 nm in extension, at a rate of 1900 nm/s. Applying a reverse bias allows the arm to be retracted again. Based on this frost heave physical analogy, they estimate a force of ~ 1 nN, which is several orders of magnitude greater than known biomolecular linear motors...similarly, the volumetric power density ranges from 8 GW/m^3 to 20 MW/m^3 at full extension; biomolecular linear motors are in the range of 30 MW/m^3, and (as an amusing comparison made by the authors), a V6 car engine (assuming 3 L volume displacement), has a power density of 50 MW/m^3. They also have done similar work with cobalt, and suggest that electrocrystallizing organic materials may also function. Unfortunately there are no movies in the supplementary material, which is a shame, because I first saw this in a seminar several months ago, and was even more astounded when I saw these "in motion".

Alice Falls into a Black Hole: Entanglement in Noninertial Frames

Fuentes-Schuller and Mann, "Alice Falls into a Black Hole: Entanglement in Noninertial Frames"
PRL 95, 120404 (2005)

A maximally entangled state becomes "less entangled" when measured by two observes, one of whom is in an accelerating inertial reference frame with respect to the other. I've been thinking a bit lately about the relationship between electron correlation and entanglement, so perhaps this has some application to the problem of relativistic electrons in heavy (high-Z) atoms. Maybe not.

13C NMR Pattern of Sc3N@C80. Structural Assignment of the First Fullerene With Adjacent Pentagons

Reveles et al. "13C NMR Pattern of Sc3N@C80. Structural Assignment of the First Fullerene With Adjacent Pentagons"
JPCA 109, 7068 (2005)


Using a combination of computation and experiment, these guys have determined that the C80 cage containing Sc3N@C80 hs adjacent pentagons. Now typically there is a 70-90 kJ/mol penalty for having fused pentagons, so it's not a particularly energetically feasible configuration. This is enshrined as the "Isolated Pentagon Rule", which serves as a way of screening out a lot of the unfeasible geometries wehn trying to determine the structure. Of course, when you start putting metals inside, all bets are off, as they can have substantial interactions with the cage.

Molecular self-difussion in nanocscale cylindrical pores and classical Fick's law predictions

Molecular self-difussion in nanocscale cylindrical pores and classical Fick's law predictions
St. T. Cui
JCP 123, 054706 (2005)


Using molecular dynamics simulations of water, the author shows that
the self difussion follows the classical Fick's law, even when the pore
diameter is as small as 1.5-3.0 nm, which might be the case, e.g., in a
carbon nanotube. Which means one less thing you have to retrain your
engineers about when you decide to construct nano-fluidic devices.

"How a Frog Can Learn What Is Where in the Dark"

How a Frog Can Learn What Is WHere in the Dark
Franosch et al.
PRL 95, 078106 (2005)


An insect floundering on water produces waves. Frogs have what are
called "lateral-line" organs on their skin, which can sense local
water velocity; similar organs exist in crocodiles and fish.
Amazingly, using this information, the frogs can
distinguish wave sources of different frequencies, presented
simultaneous, at different positions on the water surface.
The authors construct a realistic, trainable neural network that can
do precisely this. I for one, welcome our new Xenopic masters.

"Flash Ignition and Initiation of Explosives-Nanotubes Mixture"

Flash Ignition and Initiation of Explosives-Nanotubes Mixture
M. Riad Manaa et al
J. Am. Chem. Soc., 127 (40), 13786 -13787, 2005.


When you tell people you are a chemist, one of the common responses
(besides, "I hated chemistry in high school") is "Do you blow things
up?" I suspect that this paper will lead people to the same type of
response when you tell them you are a nanoscientist. As prepared
nanotubes, (with ~30% metal impurities), are in fact good explosives:
even the demonstration was comparable to the common ordanance
explosive RDX, and could in fact be improved. But what is perhaps
more interesting is that the explosion could be trigger with a flash
photography bulb, of an illumination of ~17 Watts per square
centimeter: normally light-triggering of explosives require lasers or
other high-intensity sources. As a result, this could lead to safer
and less-expensive explosive bolts for space (and other) applications.

Trying something new...with some back issues...

For a few months, I have been kicking around the idea of starting a blog centered around the neat "nanoscience" journal articles that I read in my everyday life, with some funny remarks, and of course links. Some blatant self-promotion, but mostly just a kind of pointing to what I (and perhaps others) find to be "cool". Back when I first thought of this, I started compiling some of these, so I will post them tonight.

Enjoy!
--js