Research: Why do we study moving molecules?
Really simple: you (the reader) are an assembly of many Avogadro’s numbers of molecules that somehow overcame their natural tendency to diffuse away in separate directions. We can argue that through intricately controlled motions the many molecules that form your body make you somehow understand this text and make you feel excited (we hope) about what you are reading.
We start with simpler systems, in which individual molecules are programmed to perform certain tasks, such as move from point A to point B. Then we look at whether such molecules can perform additional tasks on their way, such as pick up a load at C and drop it off at D. While these tasks sound like trivial accomplishments for each individual molecule, their strength is in their numbers. We also study what happens when two or more molecules influence each other and communicate. From a computer science standpoint we can have one Turing machine moving over an endless tape in infinite time, with well-defined transitions, capable of powerful computing. Or we can have many smaller machines, each performing one simple task with very short and rapid walks, but we also have the ability to couple them together. Thus, in the long run, we are looking to explain the increase of complexity from simple, programmable, systems with moving molecules. Our work towards explaining and engineering this natural phenomenon gives rise to a new science, the chemistry of molecular robots. One day mixtures of molecules, each performing simple tasks, will repair your tissues, eliminate cancerous cells, or autonomously release insulin upon increase in glucose concentration in blood. Or they will build a device, from scratch, in front of your eyes. What you will read below is just the beginning.
- Our Movers
- Our Control Mechanisms
- Our Tools
- Who are we?
Our methods can be applied to many systems, inorganic, organic,
or biological.
However, we focus mostly on artificial DNA systems, because of the
available tools and because we know how to control them well.
As a result of Ned Seeman's research in the
precise programming of individual interactions between
molecules, or molecules and their landscapes
(
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the field of structural DNA nanotechnology was singlehandedly
created. We work to further this field in numerous ways.
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We are focused on three types of moving molecules:
1. Our currently most processive molecular movers are called spiders.
Spiders are polycatalytic assemblies that undergo a self-repelling random walk over surfaces covered with substrates. Essentially, if you release a spider on substrates, it will keep moving in the direction of new substrates, without leaving the surface, until it runs out of substrates. The spider will then switch to ordinary random walk (read Paul Krapivsky’s papers on spider theory here . You can also read the initial paper on spiders called NICKs here . Since that publication, we (Mrksich, Rudchenko, Stojanovic, Yan, Winfree) have expanded these systems to 2D surfaces and origami linear landscapes.
2. Our most powerful motor is Niles’s bioinspired DNA polymerization motor . This motor separates two points by 8 nm.
3. Our remotely controlled molecules are Ned’s and Niles’s walkers. In a convergent effort, both groups reported the ability to control DNA walkers. We hope that they will one day compete with spiders in a processivity challenge. See Niles’ new and exciting results !
Several mechanisms of control are possible, but we use mostly either Milan and Darko’s deoxyribozyme-based logic gates () or Erik’s new catalytic circuits ( ). If you are interested in early approaches to autonomous computing by self-assembly, you can look at Erik’s early work ( ) on programmable molecules, which is now really taking off.
Our projects are enabled by a general process of handling and
visualization of single molecules, and by a general process of
engineering small systems. For example we extensively use AFM
(Winfree, Yan) and fluorescence methods (Walter, Rudchenko, Pierce)
to characterize our walkers. We make landscapes
for our movers using tools of nanotechnology such as origami (Paul,
Erik, Ned, Hao), dip-pen nanollitography (Mrksich),
or nanofluidics (Lin). Our systems are designed with a help of our in-house program, NUPACK( ), which is freely available.
We are chemists, computer scientists, biophysicists, physicists, mathematicians, and there are even a few among us who call themselves nanotechnologists. One can argue that the roots of our projects are closest to chemistry, much of our thinking comes from computer science, while, by an accident of nature, our systems are the right size to take advantage of nanotechnology.
