@article{913, abstract = {Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis.}, author = {Tejos, Ricardo and Rodríguez Furlán, Cecilia and Adamowski, Maciek and Sauer, Michael and Norambuena, Lorena and Friml, Jirí}, issn = {00219533}, journal = {Journal of Cell Science}, number = {2}, publisher = {Company of Biologists}, title = {{PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana}}, doi = {10.1242/jcs.204198}, volume = {131}, year = {2018}, } @article{9134, abstract = {Several studies have shown the existence of a critical latitude where the dissipation of internal tides is strongly enhanced. Internal tides are internal waves generated by barotropic tidal currents impinging rough topography at the seafloor. Their dissipation and concomitant diapycnal mixing are believed to be important for water masses and the large‐scale ocean circulation. The purpose of this study is to clarify the physical processes at the origin of this strong latitudinal dependence of tidal energy dissipation. We find that different mechanisms are involved equatorward and poleward of the critical latitude. Triadic resonant instabilities are responsible for the dissipation of internal tides equatorward of the critical latitude. In particular, a dominant triad involving the primary internal tide and near‐inertial waves is key. At the critical latitude, the peak of energy dissipation is explained by both increased instability growth rates, and smaller scales of secondary waves thus more prone to break and dissipate their energy. Surprisingly, poleward of the critical latitude, the generation of evanescent waves appears to be crucial. Triadic instabilities have been widely studied, but the transfer of energy to evanescent waves has received comparatively little attention. Our work suggests that the nonlinear transfer of energy from the internal tide to evanescent waves (corresponding to the 2f‐pump mechanism described by Young et al., 2008, https://doi.org/10.1017/S0022112008001742) is an efficient mechanism to dissipate internal tide energy near and poleward of the critical latitude. The theoretical results are confirmed in idealized high‐resolution numerical simulations of a barotropic M2 tide impinging sinusoidal topography in a linearly stratified fluid.}, author = {Richet, O. and Chomaz, J.-M. and Muller, Caroline J}, issn = {2169-9275}, journal = {Journal of Geophysical Research: Oceans}, number = {9}, pages = {6136--6155}, publisher = {American Geophysical Union}, title = {{Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude}}, doi = {10.1029/2017jc013591}, volume = {123}, year = {2018}, } @article{9135, abstract = {Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone.}, author = {Muller, Caroline J and Romps, David M.}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {12}, pages = {2930--2935}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Acceleration of tropical cyclogenesis by self-aggregation feedbacks}}, doi = {10.1073/pnas.1719967115}, volume = {115}, year = {2018}, } @article{9136, abstract = {In this study we investigate the scaling of precipitation extremes with temperature in the Mediterranean region by assessing against observations the present day and future regional climate simulations performed in the frame of the HyMeX and MED-CORDEX programs. Over the 1979–2008 period, despite differences in quantitative precipitation simulation across the various models, the change in precipitation extremes with respect to temperature is robust and consistent. The spatial variability of the temperature–precipitation extremes relationship displays a hook shape across the Mediterranean, with negative slope at high temperatures and a slope following Clausius–Clapeyron (CC)-scaling at low temperatures. The temperature at which the slope of the temperature–precipitation extreme relation sharply changes (or temperature break), ranges from about 20 °C in the western Mediterranean to <10 °C in Greece. In addition, this slope is always negative in the arid regions of the Mediterranean. The scaling of the simulated precipitation extremes is insensitive to ocean–atmosphere coupling, while it depends very weakly on the resolution at high temperatures for short precipitation accumulation times. In future climate scenario simulations covering the 2070–2100 period, the temperature break shifts to higher temperatures by a value which is on average the mean regional temperature change due to global warming. The slope of the simulated future temperature–precipitation extremes relationship is close to CC-scaling at temperatures below the temperature break, while at high temperatures, the negative slope is close, but somewhat flatter or steeper, than in the current climate depending on the model. Overall, models predict more intense precipitation extremes in the future. Adjusting the temperature–precipitation extremes relationship in the present climate using the CC law and the temperature shift in the future allows the recovery of the temperature–precipitation extremes relationship in the future climate. This implies negligible regional changes of relative humidity in the future despite the large warming and drying over the Mediterranean. This suggests that the Mediterranean Sea is the primary source of moisture which counteracts the drying and warming impacts on relative humidity in parts of the Mediterranean region.}, author = {Drobinski, Philippe and Silva, Nicolas Da and Panthou, Gérémy and Bastin, Sophie and Muller, Caroline J and Ahrens, Bodo and Borga, Marco and Conte, Dario and Fosser, Giorgia and Giorgi, Filippo and Güttler, Ivan and Kotroni, Vassiliki and Li, Laurent and Morin, Efrat and Önol, Bariş and Quintana-Segui, Pere and Romera, Raquel and Torma, Csaba Zsolt}, issn = {0930-7575}, journal = {Climate Dynamics}, keywords = {Atmospheric Science}, number = {3}, pages = {1237--1257}, publisher = {Springer Nature}, title = {{Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios}}, doi = {10.1007/s00382-016-3083-x}, volume = {51}, year = {2018}, } @article{9229, author = {Danzl, Johann G}, issn = {2500-2295}, journal = {Opera Medica et Physiologica}, number = {S1}, pages = {11}, publisher = {Lobachevsky State University of Nizhny Novgorod}, title = {{Diffraction-unlimited optical imaging for synaptic physiology}}, doi = {10.20388/omp2018.00s1.001}, volume = {4}, year = {2018}, } @article{9471, abstract = {The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.}, author = {Frost, Jennifer M. and Kim, M. Yvonne and Park, Guen Tae and Hsieh, Ping-Hung and Nakamura, Miyuki and Lin, Samuel J. H. and Yoo, Hyunjin and Choi, Jaemyung and Ikeda, Yoko and Kinoshita, Tetsu and Choi, Yeonhee and Zilberman, Daniel and Fischer, Robert L.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {20}, pages = {E4720--E4729}, publisher = {National Academy of Sciences}, title = {{FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis}}, doi = {10.1073/pnas.1713333115}, volume = {115}, year = {2018}, } @article{95, abstract = {Electrostatic charging of insulating fine particles can be responsible for numerous phenomena ranging from lightning in volcanic plumes to dust explosions. However, even basic aspects of how fine particles become charged are still unclear. Studying particle charging is challenging because it usually involves the complexities associated with many-particle collisions. To address these issues, we introduce a method based on acoustic levitation, which makes it possible to initiate sequences of repeated collisions of a single submillimeter particle with a flat plate, and to precisely measure the particle charge in situ after each collision. We show that collisional charge transfer between insulators is dependent on the hydrophobicity of the contacting surfaces. We use glass, which we modify by attaching nonpolar molecules to the particle, the plate, or both. We find that hydrophilic surfaces develop significant positive charges after contacting hydrophobic surfaces. Moreover, we demonstrate that charging between a hydrophilic and a hydrophobic surface is suppressed in an acidic environment and enhanced in a basic one. Application of an electric field during each collision is found to modify the charge transfer, again depending on surface hydrophobicity. We discuss these results within the context of contact charging due to ion transfer, and we show that they lend strong support to OH− ions as the charge carriers.}, author = {Lee, Victor and James, Nicole and Waitukaitis, Scott R and Jaeger, Heinrich}, journal = {Physical Review Materials}, number = {3}, publisher = {American Physical Society}, title = {{Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer}}, doi = {10.1103/PhysRevMaterials.2.035602}, volume = {2}, year = {2018}, } @article{9565, abstract = {Let D(n,p) be the random directed graph on n vertices where each of the n(n-1) possible arcs is present independently with probability p. A celebrated result of Frieze shows that if p≥(logn+ω(1))/n then D(n,p) typically has a directed Hamilton cycle, and this is best possible. In this paper, we obtain a strengthening of this result, showing that under the same condition, the number of directed Hamilton cycles in D(n,p) is typically n!(p(1+o(1)))n. We also prove a hitting-time version of this statement, showing that in the random directed graph process, as soon as every vertex has in-/out-degrees at least 1, there are typically n!(logn/n(1+o(1)))n directed Hamilton cycles.}, author = {Ferber, Asaf and Kwan, Matthew Alan and Sudakov, Benny}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {4}, pages = {592--603}, publisher = {Wiley}, title = {{Counting Hamilton cycles in sparse random directed graphs}}, doi = {10.1002/rsa.20815}, volume = {53}, year = {2018}, } @article{9567, abstract = {Let P be a graph property which is preserved by removal of edges, and consider the random graph process that starts with the empty n-vertex graph and then adds edges one-by-one, each chosen uniformly at random subject to the constraint that P is not violated. These types of random processes have been the subject of extensive research over the last 20 years, having striking applications in extremal combinatorics, and leading to the discovery of important probabilistic tools. In this paper we consider the k-matching-free process, where P is the property of not containing a matching of size k. We are able to analyse the behaviour of this process for a wide range of values of k; in particular we prove that if k=o(n) or if n−2k=o(n−−√/logn) then this process is likely to terminate in a k-matching-free graph with the maximum possible number of edges, as characterised by Erdős and Gallai. We also show that these bounds on k are essentially best possible, and we make a first step towards understanding the behaviour of the process in the intermediate regime.}, author = {Krivelevich, Michael and Kwan, Matthew Alan and Loh, Po‐Shen and Sudakov, Benny}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {4}, pages = {692--716}, publisher = {Wiley}, title = {{The random k‐matching‐free process}}, doi = {10.1002/rsa.20814}, volume = {53}, year = {2018}, } @article{9568, abstract = {An intercalate in a Latin square is a 2×2 Latin subsquare. Let N be the number of intercalates in a uniformly random n×n Latin square. We prove that asymptotically almost surely N≥(1−o(1))n2/4, and that EN≤(1+o(1))n2/2 (therefore asymptotically almost surely N≤fn2 for any f→∞). This significantly improves the previous best lower and upper bounds. We also give an upper tail bound for the number of intercalates in two fixed rows of a random Latin square. In addition, we discuss a problem of Linial and Luria on low-discrepancy Latin squares.}, author = {Kwan, Matthew Alan and Sudakov, Benny}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {2}, pages = {181--196}, publisher = {Wiley}, title = {{Intercalates and discrepancy in random Latin squares}}, doi = {10.1002/rsa.20742}, volume = {52}, year = {2018}, } @article{9587, abstract = {We say a family of sets is intersecting if any two of its sets intersect, and we say it is trivially intersecting if there is an element which appears in every set of the family. In this paper we study the maximum size of a non-trivially intersecting family in a natural “multi-part” setting. Here the ground set is divided into parts, and one considers families of sets whose intersection with each part is of a prescribed size. Our work is motivated by classical results in the single-part setting due to Erdős, Ko and Rado, and Hilton and Milner, and by a theorem of Frankl concerning intersecting families in this multi-part setting. In the case where the part sizes are sufficiently large we determine the maximum size of a non-trivially intersecting multi-part family, disproving a conjecture of Alon and Katona.}, author = {Kwan, Matthew Alan and Sudakov, Benny and Vieira, Pedro}, issn = {0097-3165}, journal = {Journal of Combinatorial Theory Series A}, pages = {44--60}, publisher = {Elsevier}, title = {{Non-trivially intersecting multi-part families}}, doi = {10.1016/j.jcta.2017.12.001}, volume = {156}, year = {2018}, } @article{9659, abstract = {The curvature dependence of interfacial free energy, which is crucial in quantitatively predicting nucleation kinetics and the stability of bubbles and droplets, is quantified by the Tolman length δ. For solid-liquid interfaces, however, δ has never been computed directly due to various theoretical and practical challenges. Here we perform a direct evaluation of the Tolman length from atomistic simulations of a solid-liquid planar interface in out-of-equilibrium conditions, by first computing the surface tension from the amplitude of thermal capillary fluctuations of a localized version of the Gibbs dividing surface and by then calculating how much the surface energy changes when it is defined relative to the equimolar dividing surface. We computed δ for a model potential, and found a good agreement with the values indirectly inferred from nucleation simulations. The agreement not only validates our approach but also suggests that the nucleation free energy of the system can be perfectly described using classical nucleation theory if the Tolman length is taken into account.}, author = {Cheng, Bingqing and Ceriotti, Michele}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, number = {23}, publisher = {AIP Publishing}, title = {{Communication: Computing the Tolman length for solid-liquid interfaces}}, doi = {10.1063/1.5038396}, volume = {148}, year = {2018}, } @article{9665, abstract = {We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic α-iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect. By a sequence of steps in a thought experiment, each involving a thermodynamic integration, we are able to separate out the binding free energy of a proton to a defect into harmonic and anharmonic, and classical and quantum contributions. We find that about 30% of a typical binding free energy of hydrogen to a lattice defect in iron is accounted for by finite temperature effects, and about half of these arise from quantum proton fluctuations. This has huge implications for the comparison between thermal desorption and permeation experiments and standard electronic structure theory. The implications are even greater for the interpretation of muon spin resonance experiments.}, author = {Cheng, Bingqing and Paxton, Anthony T. and Ceriotti, Michele}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {22}, publisher = {American Physical Society}, title = {{Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations}}, doi = {10.1103/physrevlett.120.225901}, volume = {120}, year = {2018}, } @article{9668, abstract = {Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods.}, author = {Cheng, Bingqing and Dellago, Christoph and Ceriotti, Michele}, issn = {1463-9084}, journal = {Physical Chemistry Chemical Physics}, number = {45}, pages = {28732--28740}, publisher = {Royal Society of Chemistry}, title = {{Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics}}, doi = {10.1039/c8cp04561e}, volume = {20}, year = {2018}, } @article{9687, abstract = {The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures.}, author = {Cheng, Bingqing and Ceriotti, Michele}, issn = {2469-9969}, journal = {Physical Review B}, number = {5}, publisher = {American Physical Society}, title = {{Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids}}, doi = {10.1103/physrevb.97.054102}, volume = {97}, year = {2018}, } @phdthesis{10, abstract = {Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.}, author = {Laukoter, Susanne}, issn = {2663-337X}, pages = {1 -- 139}, publisher = {Institute of Science and Technology Austria}, title = {{Role of genomic imprinting in cerebral cortex development}}, doi = {10.15479/AT:ISTA:th1057}, year = {2018}, } @article{1012, abstract = {We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense.}, author = {Erdös, László and Schröder, Dominik J}, issn = {10737928}, journal = {International Mathematics Research Notices}, number = {10}, pages = {3255--3298}, publisher = {Oxford University Press}, title = {{Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues}}, doi = {10.1093/imrn/rnw330}, volume = {2018}, year = {2018}, } @article{10286, abstract = {In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.}, author = {Allini, Elie Noumon and Skórski, Maciej and Petura, Oto and Bernard, Florent and Laban, Marek and Fischer, Viktor}, issn = {2569-2925}, journal = {IACR Transactions on Cryptographic Hardware and Embedded Systems}, number = {3}, pages = {214--242}, publisher = {International Association for Cryptologic Research}, title = {{Evaluation and monitoring of free running oscillators serving as source of randomness}}, doi = {10.13154/tches.v2018.i3.214-242}, volume = {2018}, year = {2018}, } @article{10357, abstract = {The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.}, author = {Dear, Alexander J. and Šarić, Anđela and Michaels, Thomas C. T. and Dobson, Christopher M. and Knowles, Tuomas P. J.}, issn = {1520-5207}, journal = {The Journal of Physical Chemistry B}, keywords = {materials chemistry}, number = {49}, pages = {11721--11730}, publisher = {American Chemical Society}, title = {{Statistical mechanics of globular oligomer formation by protein molecules}}, doi = {10.1021/acs.jpcb.8b07805}, volume = {122}, year = {2018}, } @article{10358, abstract = {Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements.}, author = {Michaels, Thomas C. T. and Liu, Lucie X. and Curk, Samo and Bolhuis, Peter G. and Šarić, Anđela and Knowles, Tuomas P. J.}, issn = {1362-3028}, journal = {Molecular Physics}, keywords = {physical chemistry}, number = {21-22}, pages = {3055--3065}, publisher = {Taylor & Francis}, title = {{Reaction rate theory for supramolecular kinetics: application to protein aggregation}}, doi = {10.1080/00268976.2018.1474280}, volume = {116}, year = {2018}, }