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Links 1 through 10 of 69 by Steve Koch tagged toread

Stock G, Ghosh K, Dill KA.
We show how to apply a general theoretical approach to nonequilibrium statistical mechanics, called Maximum Caliber, originally suggested by E. T. Jaynes [Annu. Rev. Phys. Chem. 31, 579 (1980)], to a problem of two-state dynamics. Maximum Caliber is a variational principle for dynamics in the same spirit that Maximum Entropy is a variational principle for equilibrium statistical mechanics. The central idea is to compute a dynamical partition function, a sum of weights over all microscopic paths, rather than over microstates. We illustrate the method on the simple problem of two-state dynamics, A<-->B, first for a single particle, then for M particles. Maximum Caliber gives a unified framework for deriving all the relevant dynamical properties, including the microtrajectories and all the moments of the time-dependent probability density. While it can readily be used to derive the traditional master equation ...

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Fazio T, Visnapuu ML, Wind S, Greene EC. Single molecule visualization of protein-DNA complexes can reveal details of reaction mechanisms and macromolecular dynamics inaccessible to traditional biochemical assays. However, these techniques are often limited by the inherent difficulty of collecting statistically relevant information from experiments explicitly designed to look at single events. New approaches that increase throughput capacity of single molecule methods have the potential for making these techniques more readily applicable to a variety of biological questions involving different types of DNA transactions. Here we show that nanofabricated chromium barriers, which are located at strategic positions on a fused silica slide otherwise coated with a supported lipid bilayer, can be used to organize DNA molecules into molecular curtains. The DNA that makes up the curtains is visualized by total internal reflection fluorescence microscopy (TIRFM)

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Jim Werner sent this "eigen worms" paper to me, since it is possibly very relevant to our microtubule tracking software. He's right that our microtubules share many similarities with the shapes of these worms. At this point, I'm thinking we should read and cite this paper as a "future work" aspect...and definitely shouldn't try to implement eigenworms yet.

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"amylome" via Pawel on twitter, "freesci @phylogenomics Your quest will never end. Amylome: proteins that are capable of forming amyloid-like fibrils " http://twitter.com/freesci/status/8948777801

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The motor protein kinesin has two heads and walks along microtubules processively using energy derived from ATP. However, how kinesin heads are coordinated to generate processive movement remains elusive. Here we created a hybrid nanomachine (DNA-kinesin) using DNA as the skeletal structure and kinesin as the functional module. Single molecule imaging of DNA-kinesin hybrid allowed us to evaluate the effects of both connect position of the heads (N, C-terminal or Mid position) and sub-nanometer changes in the distance between the two heads on motility. Our results show that although the native structure of kinesin is not essential for processive movement, it is the most efficient. Furthermore, forward bias by the power stroke of the neck linker, a 13-amino-acid chain positioned at the C-terminus of the head, and internal strain applied to the rear of the head through the neck linker are crucial for the processive movement. Results also show that the internal strain coordinates both ...

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Show ability to cut a specific, single region of human genome. Probably an incredibly useful technology, related to what Cameron was telling us about last week. Linked to me by F1000 and reviewed there by Scott K Silverman

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Lewis writes, "Sir: Even before I had succeeded in concentrating the isotope of hydrogen, I predicted that H2H2O [D2O] would not support life and would be lethal to higher organisms. As soon as heavy water became available experiments to test this idea were begun, but it was necessary to choose an experiment which would require the minimum of biological technique and also very small quantities of water. The minute seeds of tobacco..."

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Phys Rev Lett. 2008 Aug 8;101(6):065502. Epub 2008 Aug 6. Soper AK, Benmore CJ. The structures of heavy and light water at ambient conditions are investigated with the combined techniques of x-ray diffraction, neutron diffraction, and computer simulation. It is found that heavy water is a more structured liquid than light water. We find the OH bond length in H2O is approximately 3% longer than the OD bond length in D2O. This is a much larger change than current predictions. Corresponding to this, the hydrogen bond in light water is approximately 4% shorter than in heavy water, while the intermolecular HH distance is approximately 2% longer.

PMID: 18764471

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Cited by the 2008 Fernandez single-molecule D2O paper. Sheu SY, Schlag EW, Selzle HL, Yang DY. "... Furthermore, water produces a very large change in the entropy of activation due to the hydrogen bond breakage, which affects the rate by as much as 2 orders of magnitude. We also observe that there is an entire ensemble of H-bond structures, rather than a single transition state, all of which contribute to this H-bond. Here the model is tested by changing to D2O as the surrounding medium resulting in a substantial solvent isotope effect. This demonstrates the important influence of the environment on the individual hydrogen bond."

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