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Using density functional theory calculations, we investigated the magnetization and magnetic anisotropy of O2, H, and OH adsorbates on diamond surfaces. Our findings reveal that these adsorbates possess significant magnetic moments, with O2 having 2.0 μB and H and OH having 1.0 μB, respectively. Furthermore, they exhibit a non-negligible exchange coupling with the spin of the nitrogen-vacancy (NV) center positioned a few layers beneath the surface. Given the extremely small magnetic anisotropy energies of all of these systems (

Silicon quantum dot qubits show great promise but suffer from charge noise with a 1/fα spectrum, where f is frequency and α≲1. It has recently been proposed that 1/fα noise spectra can emerge from a few thermally activated two-level fluctuators in the presence of sub-bath temperature fluctuations associated with a two-dimensional electron gas (2DEG). We investigate this proposal by performing Monte Carlo simulations of a single Ising spin in a bath with a fluctuating temperature. We find that to obtain noise with a 1/fα spectrum with α≲1 down to low frequencies, the duration of temperature fluctuations must be comparable to the inverse of the lowest frequency at which the noise is measured. This result is consistent with an analytic calculation in which the fluctuator is a two-state system with dynamics governed by time-dependent switching rates. In this case we find that the noise spectrum follows a Lorentzian at frequencies lower than the inverse of the average duration of the lowest switching rate. We then estimate relaxation times of thermal fluctuations by considering thermal diffusion in an electron gas in a confined geometry. We conclude that temperature fluctuations in a 2DEG sub-bath would require unphysically long durations to be consistent with experimental measurements of 1/f-like charge noise in quantum dots at frequencies extending well below 1 Hz.

The thermal, acoustic, and dielectric properties of glasses below 1 K are dictated by the interaction of two-level systems (TLS) with strain and electric fields. In a previous paper, we proposed a modified TLS model to quantitatively account for the universally small phonon scattering in glasses at low temperatures. A key ingredient of this model was a wide distribution of couplings between TLS and phonons, contrary to the standard model which assumes a single averaged value is sufficient. In this paper, we expand on this view and include couplings to strain as well as electric fields. We then compare our theoretical results to measurements obtained using superconducting qubits. We find that the predictions of the modified TLS model are more consistent with experiments than those of the standard model. For the distribution of couplings between TLS and the strain field, there is a better agreement with experiments if we include a random distribution of local strains. Such a distribution of local strains is consistent with those found from molecular dynamics simulations.

Post-translational modification of tubulin provides differential functions to microtubule networks. Here, we address the role of tubulin acetylation on the penetrative capacity of cells undergoing radial intercalation, which is the process by which cells move apically, insert between outer cells, and join an epithelium. There are opposing forces that regulate intercalation, namely, the restrictive forces of the epithelial barrier versus the penetrative forces of the intercalating cell. Positively and negatively modulating tubulin acetylation in intercalating cells alters the developmental timing such that cells with more acetylation penetrate faster. We find that intercalating cells preferentially penetrate higher-order vertices rather than the more prevalent tricellular vertices. Differential timing in the ability of cells to penetrate different vertices reveals that lower-order vertices represent more restrictive sites of insertion. We shift the accessibility of intercalating cells toward more restrictive junctions by increasing tubulin acetylation, and we provide a geometric-based mathematical model that describes our results.

Post-translational modification of tubulin provides differential functions to microtubule networks. Here, we address the role of tubulin acetylation on the penetrative capacity of cells undergoing radial intercalation, which is the process by which cells move apically, insert between outer cells, and join an epithelium. There are opposing forces that regulate intercalation, namely, the restrictive forces of the epithelial barrier versus the penetrative forces of the intercalating cell. Positively and negatively modulating tubulin acetylation in intercalating cells alters the developmental timing such that cells with more acetylation penetrate faster. We find that intercalating cells preferentially penetrate higher-order vertices rather than the more prevalent tricellular vertices. Differential timing in the ability of cells to penetrate different vertices reveals that lower-order vertices represent more restrictive sites of insertion. We shift the accessibility of intercalating cells toward more restrictive junctions by increasing tubulin acetylation, and we provide a geometric-based mathematical model that describes our results.

While tumor infiltration by CD8+ T cells is now widely accepted to predict outcomes, the clinical significance of intratumoral B cells is less clear. We hypothesized that spatial distribution rather than density of B cells within tumors may provide prognostic significance. We developed statistical techniques (fractal dimension differences and a box-counting method 'occupancy') to analyze the spatial distribution of tumor-infiltrating lymphocytes (TILs) in human triple-negative breast cancer (TNBC). Our results indicate that B cells in good outcome tumors (no recurrence within 5 years) are spatially dispersed, while B cells in poor outcome tumors (recurrence within 3 years) are more confined. While most TILs are located within the stroma, increased numbers of spatially dispersed lymphocytes within cancer cell islands are associated with a good prognosis. B cells and T cells often form lymphocyte clusters (LCs) identified via density-based clustering. LCs consist either of T cells only or heterotypic mixtures of B and T cells. Pure B cell LCs were negligible in number. Compared to tertiary lymphoid structures (TLS), LCs have fewer lymphocytes at lower densities. Both types of LCs are more abundant and more spatially dispersed in good outcomes compared to poor outcome tumors. Heterotypic LCs in good outcome tumors are smaller and more numerous compared to poor outcome. Heterotypic LCs are also closer to cancer islands in a good outcome, with LC size decreasing as they get closer to cancer cell islands. These results illuminate the significance of the spatial distribution of B cells and LCs within tumors.

The goal of immunotherapy is to mobilize the immune system to kill cancer cells. Immunotherapy is more effective and, in general, the prognosis is better, when more immune cells infiltrate the tumor. We explore the question of whether the spatial distribution rather than just the density of immune cells in the tumor is important in forecasting whether cancer recurs. After reviewing previous work on this issue, we introduce a novel application of maximum entropy to quantify the spatial distribution of discrete point-like objects. We apply our approach to B and T cells in images of tumor tissue taken from triple negative breast cancer patients. We find that the immune cells are more spatially dispersed in good clinical outcome (no recurrence of cancer within at least 5 years of diagnosis) compared to poor clinical outcome (recurrence within 3 years of diagnosis). Our results highlight the importance of spatial distribution of immune cells within tumors with regard to clinical outcome, and raise new questions on their role in cancer recurrence.

The goal of immunotherapy is to mobilize the immune system to kill cancer cells. Immunotherapy is more effective and, in general, the prognosis is better, when more immune cells infiltrate the tumor. We explore the question of whether the spatial distribution rather than just the density of immune cells in the tumor is important in forecasting whether cancer recurs. After reviewing previous work on this issue, we introduce a novel application of maximum entropy to quantify the spatial distribution of discrete point-like objects. We apply our approach to B and T cells in images of tumor tissue taken from triple negative breast cancer patients. We find that the immune cells are more spatially dispersed in good clinical outcome (no recurrence of cancer within at least 5 years of diagnosis) compared to poor clinical outcome (recurrence within 3 years of diagnosis). Our results highlight the importance of spatial distribution of immune cells within tumors with regard to clinical outcome, and raise new questions on their role in cancer recurrence.

While tumor infiltration by CD8+ T cells is now widely accepted to predict outcomes, the clinical significance of intratumoral B cells is less clear. We hypothesized that spatial distribution rather than density of B cells within tumors may provide prognostic significance. We developed statistical techniques (fractal dimension differences and a box-counting method 'occupancy') to analyze the spatial distribution of tumor-infiltrating lymphocytes (TILs) in human triple-negative breast cancer (TNBC). Our results indicate that B cells in good outcome tumors (no recurrence within 5 years) are spatially dispersed, while B cells in poor outcome tumors (recurrence within 3 years) are more confined. While most TILs are located within the stroma, increased numbers of spatially dispersed lymphocytes within cancer cell islands are associated with a good prognosis. B cells and T cells often form lymphocyte clusters (LCs) identified via density-based clustering. LCs consist either of T cells only or heterotypic mixtures of B and T cells. Pure B cell LCs were negligible in number. Compared to tertiary lymphoid structures (TLS), LCs have fewer lymphocytes at lower densities. Both types of LCs are more abundant and more spatially dispersed in good outcomes compared to poor outcome tumors. Heterotypic LCs in good outcome tumors are smaller and more numerous compared to poor outcome. Heterotypic LCs are also closer to cancer islands in a good outcome, with LC size decreasing as they get closer to cancer cell islands. These results illuminate the significance of the spatial distribution of B cells and LCs within tumors.

Favorable outcomes have been associated with high densities of tumor infiltrating lymphocytes (TILs) such as cytotoxic ([Formula: see text]) T cells. However, the clinical significance of the spatial distribution of TILs is less well understood. We have developed novel statistical techniques to characterize the spatial distribution of TILs at various length scales. These include a box counting method that we call “occupancy” and novel applications of fractal dimensions. We apply these techniques to the spatial distribution of [Formula: see text] T cells in the tumor microenvironment of tissue resected from 35 triple negative breast cancer patients. We find that there is a distinct difference in the spatial distribution of [Formula: see text] T cells between good clinical outcome (no recurrence within at least 5 years of diagnosis) and poor clinical outcome (recurrence within 3 years of diagnosis). The statistical significance of the difference between good and poor outcome in the occupancy, fractal dimension (FD), and FD difference of [Formula: see text] T cells is comparable to that of the [Formula: see text] T cell density. Even when we randomly exclude some of the cells so that the images have the same cell density, we still find that the fractal dimension at short length scales is correlated with cancer recurrence, implying that the actual spatial distribution of [Formula: see text] cells, and not just the [Formula: see text] cell density, is associated with clinical outcome. The occupancy and FD difference indicate that the [Formula: see text] T cells are more spatially dispersed in good outcome and more aggregated in poor outcome. We discuss possible interpretations.

Favorable outcomes have been associated with high densities of tumor infiltrating lymphocytes (TILs) such as cytotoxic ([Formula: see text]) T cells. However, the clinical significance of the spatial distribution of TILs is less well understood. We have developed novel statistical techniques to characterize the spatial distribution of TILs at various length scales. These include a box counting method that we call “occupancy” and novel applications of fractal dimensions. We apply these techniques to the spatial distribution of [Formula: see text] T cells in the tumor microenvironment of tissue resected from 35 triple negative breast cancer patients. We find that there is a distinct difference in the spatial distribution of [Formula: see text] T cells between good clinical outcome (no recurrence within at least 5 years of diagnosis) and poor clinical outcome (recurrence within 3 years of diagnosis). The statistical significance of the difference between good and poor outcome in the occupancy, fractal dimension (FD), and FD difference of [Formula: see text] T cells is comparable to that of the [Formula: see text] T cell density. Even when we randomly exclude some of the cells so that the images have the same cell density, we still find that the fractal dimension at short length scales is correlated with cancer recurrence, implying that the actual spatial distribution of [Formula: see text] cells, and not just the [Formula: see text] cell density, is associated with clinical outcome. The occupancy and FD difference indicate that the [Formula: see text] T cells are more spatially dispersed in good outcome and more aggregated in poor outcome. We discuss possible interpretations.

We present a novel view of the standard model of tunneling two level systems (TLSs) to explain the puzzling universal value of a quantity, C∼3×10^{-4}, that characterizes phonon scattering in glasses below 1 K as reflected in thermal conductivity, ultrasonic attenuation, internal friction, and the change in sound velocity. Physical considerations lead to a broad distribution of phonon-TLS couplings that (1) exponentially renormalize tunneling matrix elements, and (2) reduce the TLS density of states through TLS-TLS interactions. We find good agreement between theory and experiment for a variety of individual glasses.

We present a novel view of the standard model of tunneling two level systems (TLSs) to explain the puzzling universal value of a quantity, C∼3×10^{-4}, that characterizes phonon scattering in glasses below 1 K as reflected in thermal conductivity, ultrasonic attenuation, internal friction, and the change in sound velocity. Physical considerations lead to a broad distribution of phonon-TLS couplings that (1) exponentially renormalize tunneling matrix elements, and (2) reduce the TLS density of states through TLS-TLS interactions. We find good agreement between theory and experiment for a variety of individual glasses.

Superconducting qubits are hampered by flux noise produced by surface spins from a variety of microscopic sources. Recent experiments indicated that hydrogen (H) atoms may be one of those sources. Using density functional theory calculations, we report that H atoms either embedded in, or adsorbed on, an α-Al2O3(0001) surface have sizable spin moments ranging from 0.81 to 0.87μB with energy barriers for spin reorientation as low as ∼10mK. Furthermore, H adatoms on the surface attract gas molecules such as O2, producing new spin sources. We propose coating the surface with graphene to eliminate H-induced surface spins and to protect the surface from other adsorbates.

BackgroundWhy does a tumor start where it does within an organ? Location is traditionally viewed as a random event, yet the statistics of the location of tumors argues against this being a random occurrence. There are numerous examples including that of breast cancer. More than half of invasive breast cancer tumors start in the upper outer quadrant of the breast near the armpit, even though it is estimated that only 35 to 40% of breast tissue is in this quadrant. This suggests that there is an unknown microenvironmental factor that significantly increases the risk of cancer in a spatial manner and that is not solely due to genes or toxins. We hypothesize that tumors are more prone to form in healthy tissue at microvascular 'hot spots' where there is a high local concentration of microvessels providing an increased blood flow that ensures an ample supply of oxygen, nutrients, and receptors for growth factors that promote the generation of new blood vessels.ResultsTo show the plausibility of our hypothesis, we calculated the fractional probability that there is at least one microvascular hot spot in each region of the breast assuming a Poisson distribution of microvessels in two-dimensional cross sections of breast tissue. We modulated the microvessel density in various regions of the breast according to the total hemoglobin concentration measured by near infrared diffuse optical spectroscopy in different regions of the breast. Defining a hot spot to be a circle of radius 200 μm with at least 5 microvessels, and using a previously measured mean microvessel density of 1 microvessel/mm2, we find good agreement of the fractional probability of at least one hot spot in different regions of the breast with the observed invasive tumor occurrence. However, there is no reason to believe that the microvascular distribution obeys a Poisson distribution.ConclusionsThe spatial location of a tumor in an organ is not entirely random, indicating an unknown risk factor. Much work needs to be done to understand why a tumor occurs where it does.

In developing tissues, cell polarization and proliferation are regulated by morphogens and signaling pathways. Cells throughout the Drosophila wing primordium typically show subcellular localization of the unconventional myosin Dachs on the distal side of cells (nearest the center of the disc). Dachs localization depends on the spatial distribution of bonds between the protocadherins Fat (Ft) and Dachsous (Ds), which form heterodimers between adjacent cells; and the Golgi kinase Four-jointed (Fj), which affects the binding affinities of Ft and Ds. The Fj concentration forms a linear gradient while the Ds concentration is roughly uniform throughout most of the wing pouch with a steep transition region that propagates from the center to the edge of the pouch during the third larval instar. Although the Fj gradient is an important cue for polarization, it is unclear how the polarization is affected by cell division and the expanding Ds transition region, both of which can alter the distribution of Ft-Ds heterodimers around the cell periphery. We have developed a computational model to address these questions. In our model, the binding affinity of Ft and Ds depends on phosphorylation by Fj. We assume that the asymmetry of the Ft-Ds bond distribution around the cell periphery defines the polarization, with greater asymmetry promoting cell proliferation. Our model predicts that this asymmetry is greatest in the radially-expanding transition region that leaves polarized cells in its wake. These cells naturally retain their bond distribution asymmetry after division by rapidly replenishing Ft-Ds bonds at new cell-cell interfaces. Thus we predict that the distal localization of Dachs in cells throughout the pouch requires the movement of the Ds transition region and the simple presence, rather than any specific spatial pattern, of Fj.

Long-distance intracellular axonal transport is predominantly microtubule-based, and its impairment is linked to neurodegeneration. Here we review recent theoretical and experimental evidence that suggest that near the axon boundaries (walls), the effective viscosity can become large enough to impede cargo transport in small (but not large) caliber axons. Theoretical work suggests that this opposition to motion increases rapidly as the cargo approaches the wall. However, having parallel microtubules close enough together to enable a cargo to simultaneously engage motors on more than one microtubule dramatically enhances motor activity, and thus decreases the effects due to such opposition. Experimental evidence supports this hypothesis: in small caliber axons, microtubule density is higher, increasing the probability of having parallel microtubules close enough that they can be used simultaneously by motors on a cargo. For transport toward the minus-end of microtubules, e.g., toward the cell body in an axon, a recently discovered force adaptation system can also contribute to overcoming such opposition to motion.

Long-distance intracellular axonal transport is predominantly microtubule-based, and its impairment is linked to neurodegeneration. Here we review recent theoretical and experimental evidence that suggest that near the axon boundaries (walls), the effective viscosity can become large enough to impede cargo transport in small (but not large) caliber axons. Theoretical work suggests that this opposition to motion increases rapidly as the cargo approaches the wall. However, having parallel microtubules close enough together to enable a cargo to simultaneously engage motors on more than one microtubule dramatically enhances motor activity, and thus decreases the effects due to such opposition. Experimental evidence supports this hypothesis: in small caliber axons, microtubule density is higher, increasing the probability of having parallel microtubules close enough that they can be used simultaneously by motors on a cargo. For transport toward the minus-end of microtubules, e.g., toward the cell body in an axon, a recently discovered force adaptation system can also contribute to overcoming such opposition to motion.

In developing tissues, cell polarization and proliferation are regulated by morphogens and signaling pathways. Cells throughout the Drosophila wing primordium typically show subcellular localization of the unconventional myosin Dachs on the distal side of cells (nearest the center of the disc). Dachs localization depends on the spatial distribution of bonds between the protocadherins Fat (Ft) and Dachsous (Ds), which form heterodimers between adjacent cells; and the Golgi kinase Four-jointed (Fj), which affects the binding affinities of Ft and Ds. The Fj concentration forms a linear gradient while the Ds concentration is roughly uniform throughout most of the wing pouch with a steep transition region that propagates from the center to the edge of the pouch during the third larval instar. Although the Fj gradient is an important cue for polarization, it is unclear how the polarization is affected by cell division and the expanding Ds transition region, both of which can alter the distribution of Ft-Ds heterodimers around the cell periphery. We have developed a computational model to address these questions. In our model, the binding affinity of Ft and Ds depends on phosphorylation by Fj. We assume that the asymmetry of the Ft-Ds bond distribution around the cell periphery defines the polarization, with greater asymmetry promoting cell proliferation. Our model predicts that this asymmetry is greatest in the radially-expanding transition region that leaves polarized cells in its wake. These cells naturally retain their bond distribution asymmetry after division by rapidly replenishing Ft-Ds bonds at new cell-cell interfaces. Thus we predict that the distal localization of Dachs in cells throughout the pouch requires the movement of the Ds transition region and the simple presence, rather than any specific spatial pattern, of Fj.

BackgroundWhy does a tumor start where it does within an organ? Location is traditionally viewed as a random event, yet the statistics of the location of tumors argues against this being a random occurrence. There are numerous examples including that of breast cancer. More than half of invasive breast cancer tumors start in the upper outer quadrant of the breast near the armpit, even though it is estimated that only 35 to 40% of breast tissue is in this quadrant. This suggests that there is an unknown microenvironmental factor that significantly increases the risk of cancer in a spatial manner and that is not solely due to genes or toxins. We hypothesize that tumors are more prone to form in healthy tissue at microvascular 'hot spots' where there is a high local concentration of microvessels providing an increased blood flow that ensures an ample supply of oxygen, nutrients, and receptors for growth factors that promote the generation of new blood vessels.ResultsTo show the plausibility of our hypothesis, we calculated the fractional probability that there is at least one microvascular hot spot in each region of the breast assuming a Poisson distribution of microvessels in two-dimensional cross sections of breast tissue. We modulated the microvessel density in various regions of the breast according to the total hemoglobin concentration measured by near infrared diffuse optical spectroscopy in different regions of the breast. Defining a hot spot to be a circle of radius 200 μm with at least 5 microvessels, and using a previously measured mean microvessel density of 1 microvessel/mm2, we find good agreement of the fractional probability of at least one hot spot in different regions of the breast with the observed invasive tumor occurrence. However, there is no reason to believe that the microvascular distribution obeys a Poisson distribution.ConclusionsThe spatial location of a tumor in an organ is not entirely random, indicating an unknown risk factor. Much work needs to be done to understand why a tumor occurs where it does.

Magnetic flux noise is a dominant source of dephasing and energy relaxation in superconducting qubits. The noise power spectral density varies with frequency as 1/fα, with α1, and spans 13 orders of magnitude. Recent work indicates that the noise is from unpaired magnetic defects on the surfaces of the superconducting devices. Here, we demonstrate that adsorbed molecular O2 is the dominant contributor to magnetism in superconducting thin films. We show that this magnetism can be reduced by appropriate surface treatment or improvement in the sample vacuum environment. We observe a suppression of static spin susceptibility by more than an order of magnitude and a suppression of 1/f magnetic flux noise power spectral density of up to a factor of 5. These advances open the door to the realization of superconducting qubits with improved quantum coherence.

This corrects the article DOI: 10.1103/PhysRevLett.115.077002.

This corrects the article DOI: 10.1103/PhysRevLett.115.077002.

A major obstacle to using superconducting quantum interference devices (SQUIDs) as qubits is flux noise. We propose that the heretofore mysterious spins producing flux noise could be O_{2} molecules adsorbed on the surface. Using density functional theory calculations, we find that an O_{2} molecule adsorbed on an α-alumina surface has a magnetic moment of ~1.8 μ_{B}. The spin is oriented perpendicular to the axis of the O-O bond, the barrier to spin rotations is about 10 mK. Monte Carlo simulations of ferromagnetically coupled, anisotropic XY spins on a square lattice find 1/f magnetization noise, consistent with flux noise in Al SQUIDs.

A major obstacle to using superconducting quantum interference devices (SQUIDs) as qubits is flux noise. We propose that the heretofore mysterious spins producing flux noise could be O_{2} molecules adsorbed on the surface. Using density functional theory calculations, we find that an O_{2} molecule adsorbed on an α-alumina surface has a magnetic moment of ~1.8 μ_{B}. The spin is oriented perpendicular to the axis of the O-O bond, the barrier to spin rotations is about 10 mK. Monte Carlo simulations of ferromagnetically coupled, anisotropic XY spins on a square lattice find 1/f magnetization noise, consistent with flux noise in Al SQUIDs.

Long-distance intracellular axonal transport is predominantly microtubule-based, and its impairment is linked to neurodegeneration. In this study, we present theoretical arguments that suggest that near the axon boundaries (walls), the effective viscosity can become large enough to impede cargo transport in small (but not large) caliber axons. Our theoretical analysis suggests that this opposition to motion increases rapidly as the cargo approaches the wall. We find that having parallel microtubules close enough together to enable a cargo to simultaneously engage motors on more than one microtubule dramatically enhances motor activity, and thus minimizes the effects of any opposition to transport. Even if microtubules are randomly placed in axons, we find that the higher density of microtubules found in small-caliber axons increases the probability of having parallel microtubules close enough that they can be used simultaneously by motors on a cargo. The boundary effect is not a factor in transport in large-caliber axons where the microtubule density is lower.

Long-distance intracellular axonal transport is predominantly microtubule-based, and its impairment is linked to neurodegeneration. In this study, we present theoretical arguments that suggest that near the axon boundaries (walls), the effective viscosity can become large enough to impede cargo transport in small (but not large) caliber axons. Our theoretical analysis suggests that this opposition to motion increases rapidly as the cargo approaches the wall. We find that having parallel microtubules close enough together to enable a cargo to simultaneously engage motors on more than one microtubule dramatically enhances motor activity, and thus minimizes the effects of any opposition to transport. Even if microtubules are randomly placed in axons, we find that the higher density of microtubules found in small-caliber axons increases the probability of having parallel microtubules close enough that they can be used simultaneously by motors on a cargo. The boundary effect is not a factor in transport in large-caliber axons where the microtubule density is lower.

Intra-cellular transport via the microtubule motors kinesin and dynein plays animportant role in maintaining cell structure and function. Often, multiple kinesinor dynein motors move the same cargo. Their collective function dependscritically on the single motors’ detachment kinetics under load. Single Kinesin’sand Dynein’s super-force off rates have been measured using anoptical-trap based method. We rapidly increased the force on a moving beadand measured the time to detachment. From such events, detachment time distributionsfor specific super-force values have been measured. In contrast toa possible constant off-rate kinesin has an off-rate increasing with force. Atlow loads, dynein is sensitive to load; detaching easily but at higher load it exhibiteda catch-bond type behavior, with off rate decreasing with load. Thesuper-force experiments also allowed us to determine the probability of backwardstepping for the motors. Kinesin and dynein can back-step under load, butthis was relatively rare in both directions (

Planar cell polarization represents the ability of cells to orient within the plane of a tissue orthogonal to the apical basal axis. The proper polarized function of multiciliated cells requires the coordination of cilia spacing and cilia polarity as well as the timing of cilia beating during metachronal synchrony. The planar cell polarity pathway and hydrodynamic forces have been shown to instruct cilia polarity. In this paper, we show how intracellular effectors interpret polarity to organize cellular morphology in accordance with asymmetric cellular function. We observe that both cellular actin and microtubule networks undergo drastic reorganization, providing differential roles during the polarized organization of cilia. Using computational angular correlation analysis of cilia orientation, we report a graded cellular organization downstream of cell polarity cues. Actin dynamics are required for proper cilia spacing, global coordination of cilia polarity, and coordination of metachronic cilia beating, whereas cytoplasmic microtubule dynamics are required for local coordination of polarity between neighboring cilia.

Planar cell polarization represents the ability of cells to orient within the plane of a tissue orthogonal to the apical basal axis. The proper polarized function of multiciliated cells requires the coordination of cilia spacing and cilia polarity as well as the timing of cilia beating during metachronal synchrony. The planar cell polarity pathway and hydrodynamic forces have been shown to instruct cilia polarity. In this paper, we show how intracellular effectors interpret polarity to organize cellular morphology in accordance with asymmetric cellular function. We observe that both cellular actin and microtubule networks undergo drastic reorganization, providing differential roles during the polarized organization of cilia. Using computational angular correlation analysis of cilia orientation, we report a graded cellular organization downstream of cell polarity cues. Actin dynamics are required for proper cilia spacing, global coordination of cilia polarity, and coordination of metachronic cilia beating, whereas cytoplasmic microtubule dynamics are required for local coordination of polarity between neighboring cilia.

The spatial organization of the cell depends upon intracellular trafficking of cargos hauled along microtubules and actin filaments by the molecular motor proteins kinesin, dynein, and myosin. Although much is known about how single motors function, there is significant evidence that cargos in vivo are carried by multiple motors. While some aspects of multiple motor function have received attention, how the cargo itself - and motor organization on the cargo-affects transport has not been considered. To address this, we have developed a three-dimensional Monte Carlo simulation of motors transporting a spherical cargo, subject to thermal fluctuations that produce both rotational and translational diffusion. We found that these fluctuations could exert a load on the motor(s), significantly decreasing the mean travel distance and velocity of large cargos, especially at large viscosities. In addition, the presence of the cargo could dramatically help the motor to bind productively to the microtubule: the relatively slow translational and rotational diffusion of moderately sized cargos gave the motors ample opportunity to bind to a microtubule before the motor/cargo ensemble diffuses out of range of that microtubule. For rapidly diffusing cargos, the probability of their binding to a microtubule was high if there were nearby microtubules that they could easily reach by translational diffusion. Our simulations found that one reason why motors may be approximately 100 nm long is to improve their 'on' rates when attached to comparably sized cargos. Finally, our results suggested that to efficiently regulate the number of active motors, motors should be clustered together rather than spread randomly over the surface of the cargo. While our simulation uses the specific parameters for kinesin, these effects result from generic properties of the motors, cargos, and filaments, so they should apply to other motors as well.

We show that charge noise $S_Q$ in Josephson qubits can be produced byfluctuating two level systems (TLS) with electric dipole moments in thesubstrate using a flat density of states. At high frequencies the frequency andtemperature dependence of the charge noise depends on the ratio $J/J_c$ of theelectromagnetic flux $J$ to the critical flux $J_c$. It is not widelyappreciated that TLS in small qubits can easily be strongly saturated with$J/J_c\gg 1$. Our results are consistent with experimental conclusions that$S_Q\sim 1/f$ at low frequencies and $S_Q\sim f$ at high frequencies.