Reproducible Fluctuations Research Articles

3-D shape and velocity measurement of argon gas bubbles rising in liquid sodium by means of ultrafast X-ray CT imaging

We present an evaluation study on the characterization of bubbles rising in liquid sodium by applying two-plane ultrafast X-ray computed tomography (UFXCT). It includes a new method for determining the three-dimensional shape and velocity vector of each individual bubble. In the experimental part, argon gas was injected through a single nozzle located slightly above the bottom of a cylindrical vessel filled with liquid sodium. The gas flow rate was varied between 10 and 635 cm3/min to obtain a chain of individual bubbles. In this parameter range, collisions of bubbles, coalescence or breakup are not expected. Measurements were carried out in a wide spatial range starting near the nozzle up to a height of about 200 mm above it. It was convincingly demonstrated that two-plane UFXCT imaging, in combination with the data processing presented here, allows a reliable characterization of the size, shape and velocity of bubbles with a size of a few millimeters in a sodium column of 54 mm diameter. Moreover, a reproducible fluctuation of shape, position and velocity has been observed in the experiments in the lower part of the column.

An In Vivo CRISPR Screening Platform to Evaluate the Therapeutic Impact of DNA Damage Response Gene Mutations

<h3>Purpose/Objective(s)</h3> Alterations in DNA damage response (DDR) genes are prevalent in human cancers. How these genetic changes modify responses to DNA-directed therapeutics (DDTs) is poorly understood. Here we describe an <i>in vivo</i> CRISPR screening platform to systemically identify DDR gene mutations that confer sensitivity or resistance to different classes of DDTs in a transgenic breast cancer model. <h3>Materials/Methods</h3> Murine breast tumors were induced by mammary intraductal injection of <i>Rosa26^{LSL-Myc;LSL-Cas9};Trp53^flox/flox</i> 6-10 week old female mice with 5 × 10⁵ transduction units of lentivirus expressing Cre recombinase and a library of small guide RNAs targeting 310 DDR genes ("DDR-CRISPR" library). Mammary tumors were analyzed for sgRNA representation by amplicon-based next generation sequencing. A pool of 39 DDR-CRISPR mammary tumor lines was orthotopically injected into a cohort of female <i>NOD/RAG1^−/-</i> mice. When tumors reached 8-10mm in maximal dimension, cohorts of six tumors each were treated with the following DDTs: doxorubicin/hydroxydaunorubicin, Paclitaxel, Capecitabine, Olaparib, AZD6738, 2Gyx4, and 8Gyx1. Tumors were harvested when they reached 15mm in maximal dimension. Statistically significant changes in sgRNA abundance in drug treated tumors versus mock treated controls were identified using two-tailed t-tests. <i>FANCA-</i>knockout clones of MDA-MB-231 cells were generated by dual Cas9-sgRNA targeting. Sensitivity to Olaparib and AZD6738 were assessed by colony forming assay and <i>in vivo</i> by tumor growth analyses in female <i>NOD/RAG1^−/−</i> mice. <h3>Results</h3> Mock-treated mammary tumor pools contained approximately 500 sgRNAs targeting 230 distinct DDR genes. Each type of DDT resulted in distinct yet reproducible fluctuations in sgRNA representation, likely reflecting the variable biological effects of DDR gene mutations on therapeutic sensitivity. Olaparib and AZD6738 treatments resulted in depletion of sgRNAs targeting genes in the canonical homologous recombination (HR) repair pathway (e.g., <i>Brca2, Mre11, Nbn</i>, and <i>Rad54b</i>). However, non-HR genes such as <i>FANCA</i> were also significantly depleted by PARP and ATR inhibitor treatments. Using an isogenic MDA-MB-231 cell line model, we show that <i>FANCA</i> deficiency does not impair HR but results in significant accumulation of single-stranded gaps upon PARP and ATR inhibitor treatment. Single and dual treatment with PARP and/or ATR inhibitors resulted in substantial effects on tumor growth delay and mouse survival. <h3>Conclusion</h3> Our findings illustrate that genetic mixtures of DDR-deficient breast cancers generated through an <i>in vivo</i> CRISPR screen can be used to efficiently quantify the impact of DDR gene mutations on therapeutic sensitivity. Using this platform, we discovered <i>FANCA</i> deficiency as a determinant of sensitivity to PARP and ATR inhibitors due to an accumulation of single-stranded DNA gaps, despite being proficient in HR repair.

Universal Voltage Fluctuations in Disordered Superconductors.

The Aharonov-Casher effect is the analogue of the Aharonov-Bohm effect that applies to neutral particles carrying a magnetic moment. This effect can be manifested by vortices or fluxons flowing in trajectories that encompass an electric charge. These vortices have been predicted to result in a persistent voltage that fluctuates for different sample realizations. Here, we show that disordered superconductors exhibit reproducible voltage fluctuation, which is antisymmetrical with respect to the magnetic field, as a function of various parameters such as the magnetic field amplitude, field orientations, and gate voltage. These results are interpreted as the vortex equivalent of the universal conductance fluctuations typical of mesoscopic disordered metallic systems. We analyze the data in the framework of random matrix theory and show that the fluctuation correlation functions and curvature distributions exhibit behavior that is consistent with Aharonov-Casher physics. The results demonstrate the quantum nature of the vortices in highly disordered superconductors, both above and below T_{c}.

Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae.

Theory and experiments suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors, but the mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.

Spring constant and sensitivity calibration of FluidFM micropipette cantilevers for force spectroscopy measurements

The fluidic force microscope (FluidFM) can be considered as the nanofluidic extension of the atomic force microscope (AFM). This novel instrument facilitates the experimental procedure and data acquisition of force spectroscopy (FS) and is also used for the determination of single-cell adhesion forces (SCFS) and elasticity. FluidFM uses special probes with an integrated nanochannel inside the cantilevers supported by parallel rows of pillars. However, little is known about how the properties of these hollow cantilevers affect the most important parameters which directly scale the obtained spectroscopic data: the inverse optical lever sensitivity (InvOLS) and the spring constant (k). The precise determination of these parameters during calibration is essential in order to gain reliable, comparable and consistent results with SCFS. Demonstrated by our literature survey, the standard error of previously published SCFS results obtained with FluidFM ranges from 11.8% to 50%. The question arises whether this can be accounted for biological diversity or may be the consequence of improper calibration. Thus the aim of our work was to investigate the calibration accuracy of these parameters and their dependence on: (1) the aperture size (2, 4 and 8 µm) of the hollow micropipette type cantilever; (2) the position of the laser spot on the back of the cantilever; (3) the substrate used for calibration (silicon or polystyrene). It was found that both the obtained InvOLS and spring constant values depend significantly on the position of the laser spot. Apart from the theoretically expectable monotonous increase in InvOLS (from the tip to the base of the cantilever, as functions of the laser spot’s position), we discerned a well-defined and reproducible fluctuation, which can be as high as ±30%, regardless of the used aperture size or substrate. The calibration of spring constant also showed an error in the range of −13/+20%, measured at the first 40 µm of the cantilever. Based on our results a calibration strategy is proposed and the optimal laser position which yields the most reliable spring constant values was determined and found to be on the first pair of pillars. Our proposed method helps in reducing the error introduced via improper calibration and thus increases the reliability of subsequent cell adhesion force or elasticity measurements with FluidFM.

Widespread Prion-Based Control of Growth and Differentiation Strategies in &lt;i&gt;Saccharomyces Cerevisiae&lt;/i&gt;

Theory and experiment suggest that organisms can pre-adapt to future stressors based on reproducible environmental fluctuations experienced by their ancestors. Yet the mechanisms driving such pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches can be hidden in plain sight and can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.

Direct single-molecule dynamic detection of chemical reactions.

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Conductance fluctuations in InAs quantum wells possibly driven by Zitterbewegung

The highly successful Dirac equation predicts peculiar phenomena such as Klein tunnelling and Zitterbewegung (ZB) of electrons. From its conception by Erwin Schrödinger, ZB has been considered key in understanding relativistic quantum mechanics. However, observing the ZB of electrons has proved difficult, and instead various emulations of the phenomenon have been proposed producing several successes. Concerning charge transport in semiconductors and graphene, expectations were high but little has been reported. Here, we report a surprisingly large ZB effect on charge transport in a semiconductor nanostructure playing “flat pinball”. The setup is a narrow strip of InAs two-dimensional electron gas with strong Rashba spin–orbit coupling. Six quantum point contacts act as pinball pockets. In transiting between two contacts, ZB appears as a large reproducible conductance fluctuation that depends on the in-plane magnetic field. Numerical simulations successfully reproduced our experimental observations confirming that ZB causes this conductance fluctuation.

New Data on Programmed Risks of Death in Normal Mice and Mutants with Growth Delay.

Study of the lifespans of normal (non mutant) mice and growth delay mutants has shown that mortality rates for both kinds of animals exhibit reproducible fluctuations. In the case of the mutant mice, the positions of peaks on the differential mortality curves (mortality rate plotted against lifespan) coincided in different-sex groups of animals and in same-sex subgroups of animals. Differential mortality curves of the mutant mice also had a peak at 1 month of age that was absent from the differential mortality curves of the normal mice. In the case of normal animals, positions of most peaks were the same in the studied independent subgroups of males, and to a lesser extent- independent subgroups of females, which might be explained by a shift in mortality peak positions due to the reproductive activity of females. Similar positions of mortality rate peaks in the differential mortality curves for animals from independent groups and subgroups indicate the existence of increased risks of death at specific ages. The observed pattern could be due to the programming in the genome of both the periods of increased risk of death and the intermitting intervals of stable development.

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly.

Seasonal community structure and regionally synchronous population dynamics have been observed in natural microbial ecosystems, but have not been well documented in wastewater treatment bioreactors. Few studies of community dynamics in full-scale activated sludge systems facing similar meteorological conditions have been done to compare the importance of deterministic and neutral community assembly mechanisms. We subjected weekly activated sludge samples from six regional full-scale bioreactors at four wastewater treatment plants obtained over 1 year to Illumina sequencing of 16S ribosomal RNA genes, resulting in a library of over 17 million sequences. All samples derived from reactors treating primarily municipal wastewater. Despite variation in operational characteristics and location, communities displayed temporal synchrony at the individual operational taxonomic unit (OTU), broad phylogenetic affiliation and community-wide scale. Bioreactor communities were dominated by 134 abundant and highly regionally synchronized OTU populations that accounted for over 50% of the total reads. Non-core OTUs displayed abundance-dependent population synchrony. Alpha diversity varied by reactor, but showed a highly reproducible and synchronous seasonal fluctuation. Community similarity was dominated by seasonal changes, but individual reactors maintained minor stable differences after 1 year. Finally, the impacts of mass migration driven by direct biomass transfers between reactors was investigated, but had no significant effect on community similarity or diversity in the sink community. Our results show that population dynamics in activated sludge bioreactors are consistent with niche-driven assembly guided by seasonal temperature fluctuations.

Precipitation Effects on the Martensitic Transformation in a Cu-Al-Ni Shape Memory Alloy

This paper describes the effects of precipitation of α-phase on a Cu-Al-Ni shape memory alloy (SMA) with chemical composition bordering on β region. By differential scanning calorimetry, a series of reproducible heat flow fluctuations was determined on heating a hot-rolled martensitic Cu-Al-Ni SMA, which was associated with the precipitation of α-phase. Two heat treatments were given to the SMA so as to “freeze” its states before and after the thermal range for precipitation, respectively. The corresponding microstructures of the two heat-treated states were observed by optical and scanning electron microscopy and were compared with the initial martensitic state. Energy dispersive spectroscopy experiments were carried out to determine the chemical compositions of the different phases formed in heat-treated specimens. The initial as well as the heat-treated specimens with a lamellar shape were further comparatively investigated by dynamic mechanical analysis and two-way shape memory effect (TWSME) tests comprising heating-cooling cycles under a bending load. Temperature scans were applied to the three types of specimens (initial and heat-treated states), so as to bring out the effects of heat treatment. The storage modulus increased, corresponding to the reversion of thermoelastic martensite and disappeared with the formation of precipitates. These features are finally discussed in association with TWSME under bending.

Superelasticity by reversible variants reorientation in a Ni–Mn–Ga microwire with bamboo grains

The link between microstructure and mechanical properties is investigated for a superelastic Ni–Mn–Ga microwire with 226μm diameter, created by solidification via the Taylor method. The wire, which consists of bamboo grains with tetragonal martensite matrix and coarse γ precipitates, exhibits fully reversible superelastic behavior up to 4% tensile strain. Upon multiple tensile load–unload cycles, reproducible stress fluctuations of ∼3MPa are measured on the loading superelastic stress plateau of ∼50MPa. During cycles at various temperatures spanning −70 to 55°C, the plateau stress decreases from 58 to 48MPa near linearly with increasing temperature. Based on in situ synchrotron X-ray diffraction measurements, we conclude that this superelastic behavior is due to reversible martensite variants reorientation (i.e., reversible twinning) with lattice rotation of ∼13°. The reproducible stress plateau fluctuations are assigned to reversible twinning at well-defined locations along the wire. The strain recovery during unloading is attributed to reverse twinning, driven by the internal stress generated on loading between the elastic γ precipitates and the twinning martensite matrix. The temperature dependence of the twining stress on loading is related to the change in tetragonality of the martensite, as measured by X-ray diffraction.

Using light and heat to controllably switch and reset disorder configuration in nanoscale devices

Quantum dots exhibit reproducible conductance fluctuations at low temperatures due to electron quantum interference. These fluctuations are not solely determined by dot geometry; they are also highly sensitive to the underlying disorder potential. Here we exploit this sensitivity to better understand the role that background impurities play in the electronic properties of undoped AlGaAs/GaAs heterostructures, and nanoscale devices based thereon. In particular, we report the remarkable ability to first alter the disorder potential in an undoped AlGaAs/GaAs heterostructure by optical illumination and then reset it back to its initial configuration by room temperature thermal cycling in the dark. We attribute this behavior to a mixture of C background impurities acting as shallow acceptors and deep trapping by Si background donor impurities, i.e., DX centers. This ``alter and reset'' capability is not possible in modulation-doped heterostructures and offers a route to new studies of how background impurities influence transport in nanoscale semiconductor devices.

Weak localization and universal conductance fluctuations in multi-layer graphene

We have performed magneto transport measurements on a multi-layer graphene device fabricated by conventional mechanical exfoliation. Suppression of weak localization (WL) as evidenced by the negative magnetoresistance (NMR) centered at zero field, and reproducible universal conductance fluctuations (UCFs) are observed. Interestingly, it is found that the phase coherence lengths calculated by fitting the observed NMR to conventional WL theory are longer than those determined from fitting the amplitudes of the UCFs to theory in the low temperature regime (T ≤ 8 K). In the high temperature regime (T > 8 K), the phase coherence lengths calculated by fitting the observed NMR to conventional WL theory are shorter than those determined from fitting the amplitudes of the UCFs to theory. Our new results therefore indicate a difference in the electron phase-breaking process between the two models of WL and UCFs in graphene. We speculate that the presence of the capping and bottom graphene layers, which leads the enhancement of disorder in-between, improves the localization condition for WL effect during carrier transportation in the low temperature regime. With increasing temperature, the localization condition for WL in multi-layer graphene becomes much weaker due to strong thermal damping. Therefore, the phase coherence lengths calculated by fitting the observed NMR to conventional WL theory are shorter than those determined from fitting the amplitudes of the UCFs to theory at high temperatures.

Nonlocal resistance and its fluctuations in microstructures of band-inverted HgTe/(Hg,Cd)Te quantum wells

We investigate experimentally transport in gated microsctructures containing a band-inverted HgTe/Hg_{0.3}Cd_{0.7}Te quantum well. Measurements of nonlocal resistances using many contacts prove that in the depletion regime the current is carried by the edge channels, as expected for a two-dimensional topological insulator. However, high and non-quantized values of channel resistances show that the topological protection length (i.e. the distance on which the carriers in helical edge channels propagate without backscattering) is much shorter than the channel length, which is ~100 micrometers. The weak temperature dependence of the resistance and the presence of temperature dependent reproducible quasi-periodic resistance fluctuations can be qualitatively explained by the presence of charge puddles in the well, to which the electrons from the edge channels are tunnel-coupled.

Low temperature transport in p-doped InAs nanowires

We present low temperature electrical measurements of p-type Indium Arsenide nanowires grown via molecular beam epitaxy using Beryllium as a dopant. Growth of p-type wires without stacking faults is demonstrated. Devices in field-effect geometries exhibit ambipolar behavior, and the temperature dependence of electron and hole field effect mobilities are extracted. At low temperatures, we observe reproducible conductance fluctuations as a result of quantum interference, and magnetoconductance data show weak antilocalization.

Statistical properties of fluctuation boiling centers on the wall of a silylated glass cell for n-pentane near the boundary of attainable superheat

High-speed video has been first used to show visually the existence of reproducible fluctuation boiling centers on a solid wall of an experimental cell for liquids superheated to the attainable superheat boundary. The main statistical characteristics of fluctuation centers have been calculated with allowance for censoring. The nonstationarity of a fluctuation process leading to the appearance of a nucleus capable of spontaneous growth has been shown. The change in the density of distribution of probabilities of boiling-up on an ensemble of centers with an increase in their number has been demonstrated. With an increase in the number of centers the probability of observation of large lifetimes of a liquid in the state of superheating decreases rapidly.

Edge state transport through disordered graphene nanoribbons in the quantum Hall regime

The presence of strong disorder in graphene nanoribbons yields low-mobility diffusive transport at high charge densities, whereas a transport gap occurs at low densities. Here, we investigate the longitudinal and transverse magnetoresistance of a narrow ($\ensuremath{\sim}$60 nm) nanoribbon in a six-terminal Hall bar geometry. At $B=$ 11 T, quantum Hall plateaus appear at ${\ensuremath{\sigma}}_{xy}=\ifmmode\pm\else\textpm\fi{}2{e}^{2}/h$, $\ifmmode\pm\else\textpm\fi{}6{e}^{2}/h$, and $\ifmmode\pm\else\textpm\fi{}10{e}^{2}/h$, for which the Landau-level spacing is larger than the Landau-level broadening. Interestingly, the transport gap does not disappear in the quantum Hall regime, when the zero-energy Landau level is present at the charge neutrality point, implying that it cannot originate from a lateral confinement gap. At high charge densities, the longitudinal and Hall resistance exhibit reproducible fluctuations, which are most pronounced at the transition regions between Hall plateaus. Bias-dependent measurements strongly indicate that these fluctuations can be attributed to phase-coherent scattering in the disordered ribbon.

Reproducibility of trace element profiles in a specimen of the deep-water bamboo coral Keratoisis sp.

Bamboo corals (Order Gorgonacea, Family Isididae) are attractive prospects for deep-sea paleoceanographic reconstruction, capturing trace elements in their calcitic skeletons that may serve as environmental proxies with subdecadal resolution over multi-century timescales. We study the reproducibility and fidelity of trace-element profiles (Ba, Mg, Sr, Mn, U, Pb) in a 420-year-old specimen of the bamboo coral Keratoisis sp. from the SE USA. Using laser-ablation ICP-MS to obtain multiple replicate profiles, we use spectral techniques to distinguish noise and irreproducible variations from fully reproducible geochemical fluctuations that are candidates for environmental signals. By quantifying variability between profiles, we assess the fidelity with which the corals potentially record environmental information. Barium is the most reproducible element in the skeleton, with large fluctuations along different growth radii reproducing to within 4%. Both Mg and Sr have very uniform levels within the coral, but display low-amplitude irreproducible variations that might represent an internal biological process. In the case of Mg, which has been proposed as a paleotemperature proxy, this irreproducibility would represent an intrinsic uncertainty of ∼±0.1 to 0.4 °C. Both Mn and Pb contain some irreproducibility superimposed upon broad reproducible profiles that may be environmental signals. Some of the irreproducible Pb fluctuations correlate with cracks and dark bands in the sample suggesting detrital or surface contamination. Uranium displays large amplitude variations which are not reproducible along different radii. This suggests that uranium cannot be used for paleoenvironmental reconstruction, and may show signs of early diagenesis – a possibility that could complicate attempts to date young Keratoisis sp. samples by U-series geochemistry. The highly reproducible Ba signal allows precise alignment of profiles and thus we can show that growth rate along one radius can vary by a factor of two relative to growth along a different radius. There is no evidence that this large variation in relative growth rate affects either the Mg or Sr incorporation. In addition, geochemical anomalies in Ba and Mg indicate that the very central axis of the specimen may represent a different mode of growth. This study suggests that Keratoisis sp. corals are imperfect recorders of geochemical information, but do contain reproducible variations which are good candidates for environmental signals.

Signatures of an anomalous Nernst effect in a mesoscopic two-dimensional electron system

We investigate the Nernst effect in a mesoscopic two-dimensional electron system (2DES) at low magnetic fields, before the onset of Landau level quantization. The overall magnitude of the Nernst signal agrees well with semi-classical predictions. We observe reproducible mesoscopic fluctuations in the signal which diminish significantly with an increase in temperature. We also show that the Nernst effect exhibits an anomalous component which is correlated with an oscillatory Hall effect. This behavior may be able to distinguish between different spin-correlated states in the 2DES.