All images were created by Robert R. Johnson using Visual Molecular Dynamics and Adobe Photoshop.

I am always looking for new opportunities to communicate science through images and animations. Please contact me ( if you have a request for the design of a new scientific image or are interested in using/modifying these images for publication.

DNA-Carbon Nanotube Hybrid

Despite never encountering each other in nature, single-stranded DNA and carbon nanotubes are chemically compatible and readily self-assemble into DNA-carbon nanotube hybrids (pictured here). These materials have applications in nanoelectronics, medicine, environmental safety and homeland security. Dr. Robert R. Johnson of the University of Pennsylvania has used computer simulation to study the structure of these nanomaterials. Simulation shows that DNA spontaneously binds to carbon nanotubes by attractive interactions between the DNA bases (green hexagons) and the carbon nanotube sidewall (gray cylinder). The simulations also show that DNA can assume many conformations about the nanotube including the helical wrapping as depicted here.

Robert R. Johnson, et al. Nano Letters, 8, 69 (2008)

Translocation of Chemically Modified DNA through a Solid State Nanopore

The fundamental instructions for life are encoded in sequences of nucleotides located in an organism's DNA. However, genetic sequence is not the sole determinant of a living creature's phenotype. There exist many epigenetic (above genetic) factors that affect the traits of an organism. One of these factors is chemical modification of DNA bases. Determining the type and location of such modifications in an organism's DNA is crucial for a fundamental understanding of life. Dr. Meni Wanunu, Dr. Marija Drndic and others at the University of Pennsylvania have threaded DNA through solid state nanopores in order to gain information about chemically modified DNA. The image depicts chemically modified DNA translocating through a nanoscale pore in silicon nitride. The modified DNA bases are shown in yellow. The red and green spheres represent potassium and chloride ions that compose the electrolytic solution that maintain electric neutrality of the system.

Wanunu, et al. Journal of the American Chemical Society, (2011)

DNA-Functionalized Graphene Field Effect Transistor for Chemical Sensing

Graphene, a single layer of graphite, has remarkable electronic properties and, similar to carbon nanotubes, can be fashioned into highly sensitive chemical sensing devices that have applications in homeland security, disease diagnosis and environmental safety. Pictured here is a field effect transistor fashioned out of graphene coated with a self-assembled layer of single-stranded DNA that has been fabricated by the Dr. A.T. Charlie Johnson group of the University of Pennsylvania. Exposure to gaseous chemicals (red molecules) results in a characteristic change (shown as an orange glow on the graphene surface) in the electronic properties of the transistor. These electronic responses serve as signatures that hold the potential to uniquely identify trace amounts of a molecular substance. The presence of DNA is crucial to device functionality as it increases the sensitivity and selectivity of the device.

Lu, et al. Applied Physics Letters, 97, 083107 (2010)

DNA Translocation Through Graphene Nanopores

Determining the sequence of nucleotides that compose a DNA strand is of paramount importance in medicine and microbiology. Current techniques for DNA sequencing are complicated, error-prone, time consuming and only enable sequencing of short strands of DNA. Methods for the fast sequencing of genomic DNA are highly desired. This may be achieved in the near future by measuring the electrical properties of DNA bases as a DNA strand threads through nanoscale pores in graphene, an atomically thin, single layer of graphite. Because of their small thickness, graphene nanopores are promising materials for electronic DNA sequencing applications. Dr. Chris Merchant and Dr. Marija Drndic and others at the University of Pennsylvania are already making headway towards ultrafast DNA-sequencing using this graphene-based platform. The image here depicts the translocation of DNA through a nanopore composed of a few layers of graphene. The yellow and green spheres represent potassium and chloride ions that compose the electrolytic solution that maintain electric neutrality of the system.

Merchant, et al. Nano Letters, 10, 2915 (2010)

Blinking Semiconducting Nanorods

The image depicts several clusters of semiconducting nanorods being illuminated by blue light. The nanorods are composed of cadmum selenide. The nanorods absorb blue light, become excited and emit red light. The emission of light by individual nanorods occurs in a random fashion with the nanorod turning "on" and "off" for variable lengths of time. Clustering the nanorods together increases the length of the "on" time. Current applications of semiconducting nanorods includes fluorescent labeling of biological molecules. Increasing the nanorod "on" time will improve the functionality of these labels.

Wang, et al. Nature Communications, 2, 34 (2011)

Protein-Carbon Nanotube Hybrid for Biosensing

Many viruses initiate infection by binding to specific receptor proteins located in the membrane of a host cell. One of the goals of nanotechnology is the development of ultra-sensitive devices that detect viruses and other harmful biological agents by identifying when these binding events take place. The image depicts a nanobiosensor consisting of a carbon nanotube (gray cylinder)covalently attached to the coxsackie-adenovirus receptor (magenta). This device detects the adenovirus (the icosahedral structures in the background), one of the viruses responsible for the common cold, when Knob proteins from the virus capsid (orange) bind to the receptor (magenta). These devices were synthesized in the Dr. A.T. Charlie Johnson group at the University of Pennsylvania. Dr. Robert R. Johnson has performed computer simulations that have shed light on the physics of this nanoscale device and have provided a means to rationalize the design of similar biosensors.

Robert R. Johnson, et al. Journal of Physical Chemistry B, 113, 11589 (2009)

Detecting microRNA with Solid State Nanopores

RNA is most widely known for delivering genetic messages from DNA to ribosomes, the protein factories of cells. However, RNA carries out many other complex cellular functions. It is now known that cells use RNA to both send genetic messages as well as to cancel them. Short nucleic acids known as microRNA target specific messenger RNA sequences on their way from the cell nucleus to the ribosome and render the messenger inactive. Thus, microRNA is one way cells regulate the expression of genes. Understanding the properties of microRNA is needed in order to achieve better knowledge of microbiology and to develop RNA-based therapies. Recently, Dr. Meni Wanunu, Dr. Marija Drndic and others at the University of Pennsylvania have used solid state nanopores to study microRNA. The image here depicts how the microRNA is collected and purified for their experiments. First, target microRNA strands (blue) from living tissue are hybridized with a probe RNA sequence (red). These RNA duplexes are then collected by magnetic beads (orange spheres) that are coated with a protein called p19 (green). Each p19 protein binds the RNA duplex like a clamp. These beads are then separated from the rest of the cellular material by a magnet. The RNA duplexes are then removed from the proteins and delivered to the nanopore that probes their properties.

Wanunu, et al. Nature Nanotechnology,5, 807 (2010)

Prototype for a Nanoscale Electronic Nose

Your nose contains millions of microscopic chemical sensors called olfactory receptor proteins that bind odorant molecules and send signals to your brain whenever a scent is present. The human nose contains about 400 different types of olfactory receptors, each of which can detect a range of odorants. Mouse and dog noses, on the other hand, contain about 1000 types of receptors which is, in part, why these mammals have such an excellent sense of smell. Despite much technological progress, the mammalian sense of smell still outperforms manmade devices for detecting chemicals and explosives. In order to relieve our reliance on mammalian olfaction for chemical sensing, better technology is needed. Researchers in the Dr. A.T. Charlie Johnson group at the University of Pennsylvania have coupled olfactory receptor proteins from mice to carbon nanotubes to create a prototypical electronic nose, which is depicted in this image. Olfactory receptors (red) are embedded in nanodiscs (blue spheres and sticks wrapped by purple helices) that mimic the environment of the cell membrane that houses the receptors in vivo. Odorant molecules (yellow) bind to the receptor (red), which produces an electrical response in the carbon nanotube (gray cylinder). These devices can be systematically improved and expanded and may soon replace mammals for chemical sensing applications.

Goldsmith, et al. ACS Nano,, (2011)

Self-Assembly of Proteins on Carbon Nanotubes

There is a need for proteins that self-organzing into specific molecular superstructures on a variety of inorganic and organic surfaces. These structures can then be used to direct further assembly of other molecules, creating a rich multilayered surface functionalization. Design of such proteins can be aided by computers that predict the surface recognition and favorable intersubunit packing interactions of the proteins. This procedure is exemplified in the design of peptides that assemble into a tubular structure surrounding single-walled carbon nanotubes. The geometrically defined, virus-like coating created by these peptides converts the smooth surfaces of carbon nanotubes into highly textured assemblies with long-scale order, capable of directing the assembly of gold nanoparticles into helical arrays along the nanotube axis.

Gevorg, et al. Science, 5, 332 (2011)

Rolling up a Graphene Sheet into a Carbon Nanotube

Carbon nanotubes are cylindrical sheets of carbon atoms with diameters of about 1 nanometer. Carbon nanotubes can be thought of as a rolled up sheet of graphite. The direction of rolling is defined by the green arrow, called the chiral vector, in the animation to the right. The atomic structure of the resulting nanotube depends on the direction and length of the chiral vector as shown in the image below. While real carbon nanotubes are not synthesized in this way, this animation provides a convenient way to visualize their structure.