@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},
}

@article{10359,
  abstract     = {Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.},
  author       = {Curk, Tine and Wirnsberger, Peter and Dobnikar, Jure and Frenkel, Daan and Šarić, Anđela},
  issn         = {1530-6992},
  journal      = {Nano Letters},
  keywords     = {mechanical engineering, condensed matter physics},
  number       = {9},
  pages        = {5350--5356},
  publisher    = {American Chemical Society},
  title        = {{Controlling cargo trafficking in multicomponent membranes}},
  doi          = {10.1021/acs.nanolett.8b00786},
  volume       = {18},
  year         = {2018},
}

@article{10360,
  abstract     = {Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.},
  author       = {Cohen, Samuel I. A. and Cukalevski, Risto and Michaels, Thomas C. T. and Šarić, Anđela and Törnquist, Mattias and Vendruscolo, Michele and Dobson, Christopher M. and Buell, Alexander K. and Knowles, Tuomas P. J. and Linse, Sara},
  issn         = {1755-4349},
  journal      = {Nature Chemistry},
  keywords     = {general chemical engineering, general chemistry},
  number       = {5},
  pages        = {523--531},
  publisher    = {Springer Nature},
  title        = {{Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide}},
  doi          = {10.1038/s41557-018-0023-x},
  volume       = {10},
  year         = {2018},
}

@article{10361,
  abstract     = {Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.},
  author       = {Michaels, Thomas C.T. and Šarić, Anđela and Habchi, Johnny and Chia, Sean and Meisl, Georg and Vendruscolo, Michele and Dobson, Christopher M. and Knowles, Tuomas P.J.},
  issn         = {1545-1593},
  journal      = {Annual Review of Physical Chemistry},
  keywords     = {physical and theoretical chemistry},
  number       = {1},
  pages        = {273--298},
  publisher    = {Annual Reviews},
  title        = {{Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation}},
  doi          = {10.1146/annurev-physchem-050317-021322},
  volume       = {69},
  year         = {2018},
}

@article{10362,
  abstract     = {Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.},
  author       = {Fisher, Patrick D. Ellis and Shen, Qi and Akpinar, Bernice and Davis, Luke K. and Chung, Kenny Kwok Hin and Baddeley, David and Šarić, Anđela and Melia, Thomas J. and Hoogenboom, Bart W. and Lin, Chenxiang and Lusk, C. Patrick},
  issn         = {1936-086X},
  journal      = {ACS Nano},
  keywords     = {general physics and astronomy},
  number       = {2},
  pages        = {1508--1518},
  publisher    = {American Chemical Society},
  title        = {{A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement}},
  doi          = {10.1021/acsnano.7b08044},
  volume       = {12},
  year         = {2018},
}

@article{104,
  abstract     = {The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host.},
  author       = {Seitner, Denise and Uhse, Simon and Gallei, Michelle C and Djamei, Armin},
  journal      = {Molecular Plant Pathology},
  number       = {10},
  pages        = {2277 -- 2287},
  publisher    = {Wiley},
  title        = {{The core effector Cce1 is required for early infection of maize by Ustilago maydis}},
  doi          = {10.1111/mpp.12698},
  volume       = {19},
  year         = {2018},
}

@article{106,
  abstract     = {The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below.},
  author       = {Akopyan, Arseniy and Petrunin, Anton},
  journal      = {Mathematical Intelligencer},
  number       = {3},
  pages        = {26 -- 31},
  publisher    = {Springer},
  title        = {{Long geodesics on convex surfaces}},
  doi          = {10.1007/s00283-018-9795-5},
  volume       = {40},
  year         = {2018},
}

@article{10626,
  abstract     = {Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter 
Γ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4.},
  author       = {Polshyn, Hryhoriy and Zhou, H. and Spanton, E. M. and Taniguchi, T. and Watanabe, K. and Young, A. F.},
  issn         = {1079-7114},
  journal      = {Physical Review Letters},
  keywords     = {general physics and astronomy},
  number       = {22},
  publisher    = {American Physical Society},
  title        = {{Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices}},
  doi          = {10.1103/physrevlett.121.226801},
  volume       = {121},
  year         = {2018},
}

@article{10627,
  abstract     = {We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures.},
  author       = {Polshyn, Hryhoriy and Naibert, Tyler R. and Budakian, Raffi},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {18},
  publisher    = {American Physical Society},
  title        = {{Imaging phase slip dynamics in micron-size superconducting rings}},
  doi          = {10.1103/physrevb.97.184501},
  volume       = {97},
  year         = {2018},
}

@article{1064,
  abstract     = {In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets.},
  author       = {Akopyan, Arseniy and Balitskiy, Alexey and Grigorev, Mikhail},
  issn         = {14320444},
  journal      = {Discrete & Computational Geometry},
  number       = {4},
  pages        = {1001--1009},
  publisher    = {Springer},
  title        = {{On the circle covering theorem by A.W. Goodman and R.E. Goodman}},
  doi          = {10.1007/s00454-017-9883-x},
  volume       = {59},
  year         = {2018},
}

@article{107,
  abstract     = {We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.},
  author       = {Dziembowski, Stefan and Pietrzak, Krzysztof Z and Wichs, Daniel},
  journal      = {Journal of the ACM},
  number       = {4},
  publisher    = {ACM},
  title        = {{Non-malleable codes}},
  doi          = {10.1145/3178432},
  volume       = {65},
  year         = {2018},
}

@inproceedings{108,
  abstract     = {Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \'collision graph\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes.},
  author       = {Obremski, Marciej and Skorski, Maciej},
  location     = {Vail, CO, USA},
  publisher    = {IEEE},
  title        = {{Inverted leftover hash lemma}},
  doi          = {10.1109/ISIT.2018.8437654},
  volume       = {2018},
  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},
}