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Biomedical subjects

B Yurke

Publications and source records attributed to B Yurke.

At least 19 recordsLinked to original sources
PubMed2000

A DNA-fuelled molecular machine made of DNA.

Molecular recognition between complementary strands of DNA allows construction on a nanometre length scale. For example, DNA tags may be used to organize the assembly of colloidal particles, and DNA templates can direct the growth of semiconductor nanocrystals and metal wires. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles, linked rings and polyhedra. The construction of active devices is also possible--for example, a nanomechanical switch, whose conformation is changed by inducing a transition in the chirality of the DNA double helix. Melting of chemically modified DNA has been induced by optical absorption, and conformational changes caused by the binding of oligonucleotides or other small groups have been shown to change the enzymatic activity of ribozymes. Here we report the construction of a DNA machine in which the DNA is used not only as a structural material, but also as 'fuel'. The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of 'fuel' DNA; each cycle produces a duplex DNA waste product.

DNA↗
PubMed1999

Article for analog vector algebra computation.

We introduce the concept of an analog neural network represented by chemical operations performed on strands of DNA. This new type of DNA computing has the advantage that it should be fault tolerant and thus more immune to DNA hybridization errors than a Boolean DNA computer. We describe a particular set of DNA operations to effect the interconversion of electrical and DNA data and to represent the Hopfield associative memory and the feed-forward neural network of Rumelhart et al. We speculate that networks containing as many as 10(9) neurons might be feasible.

Animals↗
PubMed1997

Measurement of the force-velocity relation for growing microtubules.

Forces generated by protein polymerization are important for various forms of cellular motility. Assembling microtubules, for instance, are believed to exert pushing forces on chromosomes during mitosis. The force that a single microtubule can generate was measured by attaching microtubules to a substrate at one end and causing them to push against a microfabricated rigid barrier at the other end. The subsequent buckling of the microtubules was analyzed to determine both the force on each microtubule end and the growth velocity. The growth velocity decreased from 1.2 micrometers per minute at zero force to 0.2 micrometer per minute at forces of 3 to 4 piconewtons. The force-velocity relation fits well to a decaying exponential, in agreement with theoretical models, but the rate of decay is faster than predicted.

Animals↗
PubMed1997

Assembly and positioning of microtubule asters in microfabricated chambers.

Intracellular organization depends on a variety of molecular assembly processes; while some of these have been studied in simplified cell-free systems, others depend on the confined geometry of cells and cannot be reconstructed using bulk techniques. To study the latter processes in vitro, we fabricated microscopic chambers that simulate the closed environment of cells. We used these chambers to study the positioning of microtubule asters. Microtubule assembly alone, without the action of molecular motors, is sufficient to position asters. Asters with short microtubules move toward the position expected from symmetry; however, once the microtubules become long enough to buckle, symmetry is broken. Calculations and experiments show that the bending-energy landscape has multiple minima. Microtubule dynamic instability modifies the landscape over time and allows asters to explore otherwise inaccessible configurations.

Cells↗