Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors

Nonlinear control techniques by means of a software sensor that are commonly used in chemical engineering could be also applied to genetic regulation processes. We provide here a realistic formulation of this procedure by introducing an additive white Gaussian noise, which is usually found in experimental data. Besides, we include model errors, meaning that we assume we do not know the nonlinear regulation function of the process. In order to illustrate this procedure, we employ the Goodwin dynamics of the concentrations [B.C. Goodwin, Temporal Oscillations in Cells, (Academic Press, New York, 1963)] in the simple form recently applied to single gene systems and some operon cases [H. De Jong, J. Comp. Biol. 9, 67 (2002)], which involves the dynamics of the mRNA, given protein, and metabolite concentrations. Further, we present results for a three gene case in co-regulated sets of transcription units as they occur in prokaryotes. However, instead of considering their full dynamics, we use only the data of the metabolites and a designed software sensor. We also show, more generally, that it is possible to rebuild the complete set of nonmeasured concentrations despite the uncertainties in the regulation function or, even more, in the case of not knowing the mRNA dynamics. In addition, the rebuilding of concentrations is not affected by the perturbation due to the additive white Gaussian noise and also we managed to filter the noisy output of the biological systemComment: 21 pages, 7 figures; also selected in vjbio of August 2005; this version corrects a misorder in the last three references of the published versio

Dynamics of vibrofluidized granular gases in periodic structures

The behavior of a driven granular gas in a container consisting of $M$ connected compartments is studied employing a microscopic kinetic model. After obtaining the governing equations for the occupation numbers and the granular temperatures of each compartment we consider the various dynamical regimes. The system displays interesting analogies with the ordering processes of phase separating mixtures quenched below the their critical point. In particular, we show that below a certain value of the driving intensity the populations of the various compartments become unequal and the system clusterizes. Such a phenomenon is not instantaneous, but is characterized by a time scale, $\tau$, which follows a Vogel-Vulcher exponential behavior. On the other hand, the reverse phenomenon which involves the ``evaporation'' of a cluster due to the driving force is also characterized by a second time scale which diverges at the limit of stability of the cluster.Comment: 11 pages, 17 figure

Rotatable microfluidic device for simultaneous study of bilateral chemosensory neurons in Caenorhabditis elegans

The nematode Caenorhabditis elegans is a leading model system in genetics, development and neurobiology; its transparent body and small size make it particularly suitable for fluorescent imaging of cells and neurons within microfluidic setups. Simultaneously recording activity in bilaterally symmetric cells has proved difficult in C. elegans because the worm enters the chip and is then immobilised when it is lying on one side of the body. We developed a side-view rotatable microfluidic device that allows us to image a pair of bilateral neurons in a single focal plane of an epi-fluorescence microscope. We demonstrated the utility of the device by recording the responses of immobilised worms to controlled stimuli, focusing on the responses of two classes of head sensory neurons to changes in NaCl concentration. The results indicate that responses of ASE left and right and ASH left and right sensory neurons are stochastic. Simultaneous recordings of ASH left and right neurons tend to synchronise, pointing to a role of gap junctional connectivity. The anatomy of the C. elegans nerve ring makes this microfluidic approach ideally suited for the study of spatially extended pairs of neurons or larger neuronal circuits that lie within a limited depth of field

Homogeneous Freezing of Water Using Microfluidics

The homogeneous freezing of water is important in the formation of ice in clouds, but there remains a great deal of variability in the representation of the homogeneous freezing of water in the literature. The development of new instrumentation, such as droplet microfluidic platforms, may help to constrain our understanding of the kinetics of homogeneous freezing via the analysis of monodisperse, size-selected water droplets in temporally and spatially controlled environments. Here, we evaluate droplet freezing data obtained using the Lab-on-a-Chip Nucleation by Immersed Particle Instrument (LOC-NIPI), in which droplets are generated and frozen in continuous flow. This high-throughput method was used to analyse over 16,000 water droplets (86 μm diameter) across three experimental runs, generating data with high precision and reproducibility that has largely been unrepresented in the microfluidic literature. Using this data, a new LOC-NIPI parameterisation of the volume nucleation rate coefficient (JV(T)) was determined in the temperature region of −35.1 to −36.9 °C, covering a greater JV(T) compared to most other microfluidic techniques thanks to the number of droplets analysed. Comparison to recent theory suggests inconsistencies in the theoretical representation, further implying that microfluidics could be used to inform on changes to parameterisations. By applying classical nucleation theory (CNT) to our JV(T) data, we have gone a step further than other microfluidic homogeneous freezing examples by calculating the stacking-disordered ice–supercooled water interfacial energy, estimated to be 22.5 ± 0.7 mJ m−2, again finding inconsistencies when compared to theoretical predictions. Further, we briefly review and compile all available microfluidic homogeneous freezing data in the literature, finding that the LOC-NIPI and other microfluidically generated data compare well with commonly used non-microfluidic datasets, but have generally been obtained with greater ease and with higher numbers of monodisperse droplets

On-chip analysis of atmospheric ice-nucleating particles in continuous flow

Ice-nucleating particles (INPs) are of atmospheric importance because they catalyse the freezing of supercooled cloud droplets, strongly affecting the lifetime and radiative properties of clouds. There is a need to improve our knowledge of the global distribution of INPs, their seasonal cycles and long-term trends, but our capability to make these measurements is limited. Atmospheric INP concentrations are often determined using assays involving arrays of droplets on a cold stage, but such assays are frequently limited by the number of droplets that can be analysed per experiment, often involve manual processing (e.g. pipetting of droplets), and can be susceptible to contamination. Here, we present a microfluidic platform, the LOC-NIPI (Lab-on-a-Chip Nucleation by Immersed Particle Instrument), for the generation of water-in-oil droplets and their freezing in continuous flow as they pass over a cold plate for atmospheric INP analysis. LOC-NIPI allows the user to define the number of droplets analysed by simply running the platform for as long as required. The use of small (∼100 μm diameter) droplets minimises the probability of contamination in any one droplet and therefore allows supercooling all the way down to homogeneous freezing (around −36 °C), while a temperature probe in a proxy channel provides an accurate measure of temperature without the need for temperature modelling. The platform was validated using samples of pollen extract and Snomax®, with hundreds of droplets analysed per temperature step and thousands of droplets being measured per experiment. Homogeneous freezing of purified water was studied using >10 000 droplets with temperature increments of 0.1 °C. The results were reproducible, independent of flow rate in the ranges tested, and the data compared well to conventional instrumentation and literature data. The LOC-NIPI was further benchmarked in a field campaign in the Eastern Mediterranean against other well-characterised instrumentation. The continuous flow nature of the system provides a route, with future development, to the automated monitoring of atmospheric INP at field sites around the globe

On-chip density-based sorting of supercooled droplets and frozen droplets in continuous flow

The freezing of supercooled water to ice and the materials which catalyse this process are of fundamental interest to a wide range of fields. At present, our ability to control, predict or monitor ice formation processes is poor. The isolation and characterisation of frozen droplets from supercooled liquid droplets would provide a means of improving our understanding and control of these processes. Here, we have developed a microfluidic platform for the continuous flow separation of frozen from unfrozen picolitre droplets based on differences in their density, thus allowing the sorting of ice crystals and supercooled water droplets into different outlet channels with 94 ± 2% efficiency. This will, in future, facilitate downstream or off-chip processing of the frozen and unfrozen populations, which could include the analysis and characterisation of ice-active materials or the selection of droplets with a particular ice-nucleating activity

Band Calculations for Ce Compounds with AuCu3_{3}-type Crystal Structure on the basis of Dynamical Mean Field Theory I. CePd3_{3} and CeRh3_{3}

Band calculations for Ce compounds with the AuCu$_{3}$-type crystal structure were carried out on the basis of dynamical mean field theory (DMFT). The auxiliary impurity problem was solved by a method named NCA$f^{2}$vc (noncrossing approximation including the $f^{2}$ state as a vertex correction). The calculations take into account the crystal-field splitting, the spin-orbit interaction, and the correct exchange process of the $f^{1} \rightarrow f^{0},f^{2}$ virtual excitation. These are necessary features in the quantitative band theory for Ce compounds and in the calculation of their excitation spectra. The results of applying the calculation to CePd$_{3}$ and CeRh$_{3}$ are presented as the first in a series of papers. The experimental results of the photoemission spectrum (PES), the inverse PES, the angle-resolved PES, and the magnetic excitation spectra were reasonably reproduced by the first-principles DMFT band calculation. At low temperatures, the Fermi surface (FS) structure of CePd$_{3}$ is similar to that of the band obtained by the local density approximation. It gradually changes into a form that is similar to the FS of LaPd$_{3}$ as the temperature increases, since the $4f$ band shifts to the high-energy side and the lifetime broadening becomes large.}Comment: 12 pasges, 13 figure

Ferromagnetic transition metal implanted ZnO: a diluted magnetic semiconductor?

Recently theoretical works predict that some semiconductors (e.g. ZnO) doped with magnetic ions are diluted magnetic semiconductors (DMS). In DMS magnetic ions substitute cation sites of the host semiconductor and are coupled by free carriers resulting in ferromagnetism. One of the main obstacles in creating DMS materials is the formation of secondary phases because of the solid-solubility limit of magnetic ions in semiconductor host. In our study transition metal ions were implanted into ZnO single crystals with the peak concentrations of 0.5-10 at.%. We established a correlation between structural and magnetic properties. By synchrotron radiation X-ray diffraction (XRD) secondary phases (Fe, Ni, Co and ferrite nanocrystals) were observed and have been identified as the source for ferromagnetism. Due to their different crystallographic orientation with respect to the host crystal these nanocrystals in some cases are very difficult to be detected by a simple Bragg-Brentano scan. This results in the pitfall of using XRD to exclude secondary phase formation in DMS materials. For comparison, the solubility of Co diluted in ZnO films ranges between 10 and 40 at.% using different growth conditions pulsed laser deposition. Such diluted, Co-doped ZnO films show paramagnetic behaviour. However, only the magnetoresistance of Co-doped ZnO films reveals possible s-d exchange interaction as compared to Co-implanted ZnO single crystals.Comment: 27 pages, 8 figure

Small anisotropy of the lower critical field and s±s_\pm-wave two-gap feature in single crystal LiFeAs

The in- and out-of-plane lower critical fields and magnetic penetration depths for LiFeAs were examined. The anisotropy ratio $\gamma_{H_{c1}}(0)$ is smaller than the expected theoretical value, and increased slightly with increasing temperature from 0.6$T_c$ to $T_c$. This small degree of anisotropy was numerically confirmed by considering electron correlation effect. The temperature dependence of the penetration depths followed a power law($\sim$$T^n$) below 0.3$T_c$, with $n$$>$3.5 for both $\lambda_{ab}$ and $\lambda_c$. Based on theoretical studies of iron-based superconductors, these results suggest that the superconductivity of LiFeAs can be represented by an extended $s_\pm$-wave due to weak impurity scattering effect. And the magnitudes of the two gaps were also evaluted by fitting the superfluid density for both the in- and out-of-plane to the two-gap model. The estimated values for the two gaps are consistent with the results of angle resolved photoemission spectroscopy and specific heat experiments.Comment: 10 pages, 5 figure