Analytic procedures for determining dimensional redundancies in electronic devices

Methods for ascertaining dimensional redundancies in mathematical functions related to electronic phenomena and for removal of redundancies are presented. Two computer programs, one to determine a complete B-matrix and the other to optimize the matrix, are discussed. Three subroutines are analyzed

Modeling integrated circuits for computing

Integrated circuit models for computer analysis and desig

An open source LABVIEW platform for simulating image series of fluorescent microtubules in gliding assays

We describe an open-source LabVIEW software platform for generating simulated images of microtubules in gliding motility assays. We describe how the software works and how to obtain the software

Effect of 2-H and 18-O water isotopes in kinesin-1 gliding assay

We show here the effects of heavy-hydrogen water (^2^H~2~O) and heavy-oxygen water (H~2~^18^O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for biomolecular devices incorporating molecular motors

Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.

The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargos inside cells.

During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules. Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and unbinding rates for kinesin and thus offers a tool to specifically probe those steps. We will report the effects of different osmolytes on microtubule speed and other observables in the gliding motility assay.

Kinesin’s kinetic core cycle hydrolyzes ATP with the help of a water molecule. Any modification to the water molecules the kinesin is in will change how ATP hydrolyzes and will ultimately affect how kinesin moves along microtubules. We will report preliminary results showing how kinesin is affected when the solvent it is in is changed from light water to heavy water.
 
When used in a surface assay or in devices, the kinesin and microtubule system is also dependent on substrate passivation. Kinesin motor domains do not transport microtubules in the gliding motility assay if kinesin is added to a glass microscope slide that has not been functionalized. Functionalization of the glass slides and slips is typically performed with bovine milk proteins called caseins. Bovine casein is a globular protein that can be broken up into four constituents: αs1, αs2, β, and κ. Each casein constituent affects how kinesin adheres to the glass and ultimately the speed at which microtubules are observed to glide at. Building on the work of Verma et.al., we have found that each constituent individually produces different outcomes in gliding assays. We will present these findings and discuss implications they have for use of gliding assays to study kinesin and use of kinesin-microtubule system in microdevices. 

[1] Chaen, S, N Yamamoto, I Shirakawa, and H Sugi. 2001. Effect of deuterium oxide on actomyosin motility in vitro. _Biochimica et biophysica acta_ 1506, no. 3: 218-23. 
[2] Vivek Verma, William O Hancock, Jeffrey M Catchmark, "The role of casein in supporting the operation of surface bound kinesin," _J. Biol. Eng._ 2008; 2: 14.

Acknowledgements: This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008.
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Program in electro-physical studies - Microcircuit models and diagnostic techniques for environmental failure mode prediction

Microcircuit models and computer program for predicting failure modes under adverse environmental condition

Effect of 2H and 18O water isotopes in kinesin-1 gliding assay

We show for the first time the effects of heavy-hydrogen water (2H2O) and heavy-oxygen water (H218O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We also show that gliding microtubule speed returns to its original speed after being treated with heavy-hydrogen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for using heavy waters in biomolecular devices incorporating molecular motors

Osmotic stress and water isotope effects in kinesin-1 gliding motility assays

The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions. As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1]. In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules. To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin. We're currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes. We will describe our open-source, automated analysis platform for extracting microtubule gliding speeds from image series. We will also show our preliminary analyses of the changes seen in gliding assays when done in heavy water (either heavy-hydrogen or heavy-oxygen) or osmolytes (betaine). We will discuss whether osmotic stress and isotopes, particularly heavy-oxygen water, might be an important tool for probing effects of water on binding interactions between kinesin and microtubules. We will also discuss potential applications of deuterium water for stabilizing microtubules and kinesin for lab or device applications.
[1] Parsegian, V. A., Rand, R. P., & Rau, D. C. (1995). Macromolecules and water: probing with osmotic stress. Methods in Enzymology, 259.

This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008 in collaboration with Dr. Susan Atlas lab (UNM).
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Influence of gas flow rate on liquid distribution in trickle-beds using perforated plates as liquid distributors

Two wire mesh tomography devices and a liquid collector were used to study the influence of the gas flow rate on liquid distribution when fluids distribution on top of the reactor is ensured by a perforated plate. In opposition to most of the studies realized by other authors, conditions in which the gas has a negative impact in liquid distribution were evidenced. Indeed, the obtained results show that the influence of gas flow rate depends on the quality of the initial distribution, as the gas forces the liquid to "respect" the distribution imposed at the top of the reactor. Finally, a comparison between the two measuring techniques shows the limitations of the liquid collector and the improper conclusions to which its use could lead