AN EXPERIMENTAL AND MODELING STUDY OF ELECTROOSMOTIC BULK AND NEAR-WALL FLOWS IN TWO-DIMENSIONAL MICRO-AND NANOCHANNELS

ABSTRACT Electrokinetically driven flow of electrolyte solutions through micro-and nanochannels is of interest in microelectromechanical systems (MEMS) and nanotechnology applications. In this work, fully developed and steady electroosmotic flow (EOF) of dilute sodium tetraborate and sodium chloride aqueous solutions in a rectangular channel where the channel height h is comparable to its width W is examined. EOF is also studied under conditions of electric double layer (EDL) overlap, or λ/h ~ O(1), where λ is the Debye thickness, for very dilute solutions. The initial experimental data and model results are in very good agreement for dilute sodium tetraborate solutions. The experimental work uses the new nano-particle image velocimetry (nPIV) technique. Evanescent waves from the total internal reflection of light with a wavelength of 488 nm at a refractive index interface is used to illuminate 100 nm neutrally buoyant fluorescent particles in the near-wall region of the flow. The images of these tracer particles over time are processed to obtain the two components of the velocity field parallel to the wall in fully developed EOF of sodium tetraborate at concentrations up to 2 mM in fused quartz rectangular channels with height h up to 10 microns. The spatial resolution of these velocity field data along the dimension normal to the wall is about 100 nm, and the data are obtained within a distance of approximately 100 nm of the wall based upon the 1/e intensity point, or penetration depth. A set of equations modeling EOF in a long channel are solved where h/L << 1, and L is the lengthscale along the flow direction. Unlike most previous models, this work does not use the Debye-Huckel approximation, nor does it assume symmetric boundary conditions. For the case where λ/h << 1, analytical solutions for the velocity, potential and mole fractions are obtained using an asymptotic perturbation approach

Robust circadian clocks from coupled protein modification and transcription-translation cycles

The cyanobacterium Synechococcus elongatus uses both a protein phosphorylation cycle and a transcription-translation cycle to generate circadian rhythms that are highly robust against biochemical noise. We use stochastic simulations to analyze how these cycles interact to generate stable rhythms in growing, dividing cells. We find that a protein phosphorylation cycle by itself is robust when protein turnover is low. For high decay or dilution rates (and co mpensating synthesis rate), however, the phosphorylation-based oscillator loses its integrity. Circadian rhythms thus cannot be generated with a phosphorylation cycle alone when the growth rate, and consequently the rate of protein dilution, is high enough; in practice, a purely post-translational clock ceases to function well when the cell doubling time drops below the 24 hour clock period. At higher growth rates, a transcription-translation cycle becomes essential for generating robust circadian rhythms. Interestingly, while a transcription-translation cycle is necessary to sustain a phosphorylation cycle at high growth rates, a phosphorylation cycle can dramatically enhance the robustness of a transcription-translation cycle at lower protein decay or dilution rates. Our analysis thus predicts that both cycles are required to generate robust circadian rhythms over the full range of growth conditions.Comment: main text: 7 pages including 5 figures, supplementary information: 13 pages including 9 figure

Secondary-Structure Design of Proteins by a Backbone Torsion Energy

We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles phi and psi. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both phi and psi can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the alpha-helix-forming-tendencies by lowering/raising the torsion-energy surface in the alpha-helix region and likewise increase/decrease the beta-sheet-forming tendencies by lowering/raising the surface in the beta-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming-tendencies by performing folding simulations of alpha-helical and beta-hairpin peptides.Comment: 13 pages, (Revtex4), 5 figure

Development of Time- and Energy-Resolved Synchrotron-Radiation-Based Mössbauer Spectroscopy

14th International Conference on Synchrotron Radiation Instrumentation (SRI 2021) 28.03.2022 - 01.04.2022 OnlineSynchrotron-radiation based Mössbauer spectroscopy has become a useful technique capable for investigating various Mössbauer isotopes. For a typical experimental setup, the information associated with the pulse height (that is, energy) in an avalanche photodiode (APD) detector has not been used effectively. By using a system for simultaneous measurement system of time and energy associated with the APD signal, a system for the time- and energy-resolved Mössbauer spectroscopy has been developed. In this system, the pulse height information was converted to the time information through an amplitude-to-time converter applied to one of the divided signals from the APD. The corresponding time information was processed separately from another one of the divided signals. Both signals are recorded by a multi-channel scaler in an event-by-event data acquisition process. The velocity information from the Mössbauer transducer was also recorded as a tag for each signal event. Thus, the Mössbauer spectra with any time- and energy-window can be reconstructed after the data collection process. This system can be used for many purposes in time- and energy-resolved Mössbauer spectroscopy, and shows significant promise for use with other fast detectors and for various types of experiments

Electronic and Magnetic Phase Diagram of a Superconductor, SmFeAsO1-xFx

A crystallographic and magnetic phase diagram of SmFeAsO1-xFx is determined as a function of x in terms of temperature based on electrical transport and magnetization, synchrotron powder x-ray diffraction, 57Fe Mossbauer spectra (MS), and 149Sm nuclear resonant forward scattering (NRFS) measurements. MS revealed that the magnetic moments of Fe were aligned antiferromagnetically at ~144 K (TN(Fe)). The magnetic moment of Fe (MFe) is estimated to be 0.34 myuB/Fe at 4.2 K for undoped SmFeAsO; MFe is quenched in superconducting F-doped SmFeAsO. 149Sm NRFS spectra revealed that the magnetic moments of Sm start to order antiferromagnetically at 5.6 K (undoped) and 4.4 K (TN(Sm)) (x = 0.069). Results clearly indicate that the antiferromagnetic Sm sublattice coexists with the superconducting phase in SmFeAsO1-xFx below TN(Sm), while antiferromagnetic Fe sublattice does not coexist with the superconducting phase.Comment: Accepted in New Journal of Physic

Spin-boson models for quantum decoherence of electronic excitations of biomolecules and quantum dots in a solvent

We give a theoretical treatment of the interaction of electronic excitations (excitons) in biomolecules and quantum dots with the surrounding polar solvent. Significant quantum decoherence occurs due to the interaction of the electric dipole moment of the solute with the fluctuating electric dipole moments of the individual molecules in the solvent. We introduce spin boson models which could be used to describe the effects of decoherence on the quantum dynamics of biomolecules which undergo light-induced conformational change and on biomolecules or quantum dots which are coupled by Forster resonant energy transfer.Comment: More extended version, to appear in Journal of Physics: Condensed Matter. 13 pages, 3 figure

Glycotope structures and intramolecular affinity factors of plant lectins for Tn/T antigens

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