Erik Winfree | |
---|---|
Born | September 26, 1969 |
Nationality | American |
Alma mater | |
Scientific career | |
Fields | Computer science Bioengineering |
Institutions | California Institute of Technology |
Thesis | Algorithmic self-assembly of DNA (1998) |
Doctoral advisor | John J. Hopfield |
Erik Winfree (born September 26, 1969 [1] ) is an American applied computer scientist, bioengineer, and professor at California Institute of Technology. [2] He is a leading researcher into DNA computing and DNA nanotechnology. [3] [4] [5]
In 1998, Winfree in collaboration with Nadrian Seeman published the creation of two-dimensional lattices of DNA tiles using the "double crossover" motif. These tile-based structures provided the capability to implement DNA computing, which was demonstrated by Winfree and Paul Rothemund in 2004, and for which they shared the 2006 Feynman Prize in Nanotechnology. [3] [6]
In 1999, he was named to the MIT Technology Review TR100 as one of the top 100 innovators in the world under the age of 35. [7]
He received a Bachelor of Science from the University of Chicago in 1991 and a Doctor of Philosophy from the California Institute of Technology in 1998. [8] For his doctoral studies, he enrolled in the Computation and Neural Systems program at Caltech under advisors John Hopfield and Al Barr. [9] He was a Lewis Thomas Postdoctoral Fellow in Molecular Biology at Princeton University. [10] He was a 2000 MacArthur Fellow. His father Arthur Winfree, a theoretical biologist, was also a MacArthur Fellow.
In computability theory, a system of data-manipulation rules is said to be Turing-complete or computationally universal if it can be used to simulate any Turing machine. This means that this system is able to recognize or decode other data-manipulation rule sets. Turing completeness is used as a way to express the power of such a data-manipulation rule set. Virtually all programming languages today are Turing-complete.
Wang tiles, first proposed by mathematician, logician, and philosopher Hao Wang in 1961, is a class of formal systems. They are modeled visually by square tiles with a color on each side. A set of such tiles is selected, and copies of the tiles are arranged side by side with matching colors, without rotating or reflecting them.
Peter Williston Shor is an American theoretical computer scientist known for his work on quantum computation, in particular for devising Shor's algorithm, a quantum algorithm for factoring exponentially faster than the best currently-known algorithm running on a classical computer. He has been a professor of applied mathematics at the Massachusetts Institute of Technology (MIT) since 2003.
DNA computing is an emerging branch of unconventional computing which uses DNA, biochemistry, and molecular biology hardware, instead of the traditional electronic computing. Research and development in this area concerns theory, experiments, and applications of DNA computing. Although the field originally started with the demonstration of a computing application by Len Adleman in 1994, it has now been expanded to several other avenues such as the development of storage technologies, nanoscale imaging modalities, synthetic controllers and reaction networks, etc.
Shlomi Dolev is a Rita Altura Trust Chair Professor in Computer Science at Ben-Gurion University of the Negev (BGU) and the head of the BGU Negev Hi-Tech Faculty Startup Accelerator.
DNA origami is the nanoscale folding of DNA to create arbitrary two- and three-dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs make DNA a useful construction material, through design of its base sequences. DNA is a well-understood material that is suitable for creating scaffolds that hold other molecules in place or to create structures all on its own.
Paul Wilhelm Karl Rothemund is a research professor at the Computation and Neural Systems department at Caltech. He has become known in the fields of DNA nanotechnology and synthetic biology for his pioneering work with DNA origami. He shared both categories of the 2006 Feynman Prize in Nanotechnology with Erik Winfree for their work in creating DNA nanotubes, algorithmic molecular self-assembly of DNA tile structures, and their theoretical work on DNA computing. Rothemund is also a 2007 recipient of the MacArthur Fellowship.
A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after Robin Holliday, the molecular biologist who proposed its existence in 1964.
Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing. It is necessary because there are many possible sequences of nucleic acid strands that will fold into a given secondary structure, but many of these sequences will have undesired additional interactions which must be avoided. In addition, there are many tertiary structure considerations which affect the choice of a secondary structure for a given design.
Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. These representations include closely packed spheres made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Grzegorz Rozenberg is a Polish and Dutch computer scientist.
DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. Researchers in the field have created static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes, and functional devices such as molecular machines and DNA computers. The field is beginning to be used as a tool to solve basic science problems in structural biology and biophysics, including applications in X-ray crystallography and nuclear magnetic resonance spectroscopy of proteins to determine structures. Potential applications in molecular scale electronics and nanomedicine are also being investigated.
Natural computing, also called natural computation, is a terminology introduced to encompass three classes of methods: 1) those that take inspiration from nature for the development of novel problem-solving techniques; 2) those that are based on the use of computers to synthesize natural phenomena; and 3) those that employ natural materials to compute. The main fields of research that compose these three branches are artificial neural networks, evolutionary algorithms, swarm intelligence, artificial immune systems, fractal geometry, artificial life, DNA computing, and quantum computing, among others.
Nadrian C. "Ned" Seeman was an American nanotechnologist and crystallographer known for inventing the field of DNA nanotechnology.
The International Society for Nanoscale Science, Computation, and Engineering is a scientific society specializing in nanotechnology and DNA computing. It was started in 2004 by Nadrian Seeman, founder of the field of DNA nanotechnology. According to the society, its purpose is "to promote the study of the control of the arrangement of the atoms in matter, examine the principles that lead to such control, to develop tools and methods to increase such control, and to investigate the use of these principles for molecular computation, and for engineering on the finest possible scales."
Donald M. Eigler is an American physicist associated with the IBM Almaden Research Center, who is noted for his achievements in nanotechnology.
Georg Seelig is a Swiss computer scientist, bioengineer, and synthetic biologist. He is an associate professor of Electrical Engineering and Computer Science & Engineering at the University of Washington. He is a researcher in the field of DNA nanotechnology.
Leonard J. Y. Schulman is professor of computer science in the Computing and Mathematical Sciences Department at the California Institute of Technology. He is known for work on algorithms, information theory, coding theory, and quantum computation.
Nataša Jonoska is a Macedonian mathematician and professor at the University of South Florida known for her work in DNA computing. Her research is about how biology performs computation, "in particular using formal models such as cellular or other finite types of automata, formal language theory symbolic dynamics, and topological graph theory to describe molecular computation".
Lulu Qian is a Chinese-American biochemist who is a professor at the California Institute of Technology. Her research uses DNA-like molecules to build artificial machines.