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

Resummation for Nonequilibrium Perturbation Theory and Application to Open Quantum Lattices

Lattice models of fermions, bosons, and spins have long served to elucidate the essential physics of quantum phase transitions in a variety of systems. Generalizing such models to incorporate driving and dissipation has opened new vistas to investigate nonequilibrium phenomena and dissipative phase transitions in interacting many-body systems. We present a framework for the treatment of such open quantum lattices based on a resummation scheme for the Lindblad perturbation series. Employing a convenient diagrammatic representation, we utilize this method to obtain relevant observables for the open Jaynes-Cummings lattice, a model of special interest for open-system quantum simulation. We demonstrate that the resummation framework allows us to reliably predict observables for both finite and infinite Jaynes-Cummings lattices with different lattice geometries. The resummation of the Lindblad perturbation series can thus serve as a valuable tool in validating open quantum simulators, such as circuit-QED lattices, currently being investigated experimentally.Comment: 15 pages, 9 figure

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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Observation of a dissipative phase transition in a one-dimensional circuit QED lattice

Condensed matter physics has been driven forward by significant experimental and theoretical progress in the study and understanding of equilibrium phase transitions based on symmetry and topology. However, nonequilibrium phase transitions have remained a challenge, in part due to their complexity in theoretical descriptions and the additional experimental difficulties in systematically controlling systems out of equilibrium. Here, we study a one-dimensional chain of 72 microwave cavities, each coupled to a superconducting qubit, and coherently drive the system into a nonequilibrium steady state. We find experimental evidence for a dissipative phase transition in the system in which the steady state changes dramatically as the mean photon number is increased. Near the boundary between the two observed phases, the system demonstrates bistability, with characteristic switching times as long as 60 ms -- far longer than any of the intrinsic rates known for the system. This experiment demonstrates the power of circuit QED systems for studying nonequilibrium condensed matter physics and paves the way for future experiments exploring nonequilbrium physics with many-body quantum optics

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

Imaging Photon Lattice States by Scanning Defect Microscopy

Microwave photons inside lattices of coupled resonators and superconducting qubits can exhibit surprising matter-like behavior. Realizing such open-system quantum simulators presents an experimental challenge and requires new tools and measurement techniques. Here, we introduce Scanning Defect Microscopy as one such tool and illustrate its use in mapping the normal-mode structure of microwave photons inside a 49-site Kagome lattice of coplanar waveguide resonators. Scanning is accomplished by moving a probe equipped with a sapphire tip across the lattice. This locally perturbs resonator frequencies and induces shifts of the lattice resonance frequencies which we determine by measuring the transmission spectrum. From the magnitude of mode shifts we can reconstruct photon field amplitudes at each lattice site and thus create spatial images of the photon-lattice normal modes