TY - CONF AU - Martius, Georg S AU - Olbrich, Eckehard ID - 12881 SN - 9780262330275 T2 - Proceedings of the 13th European Conference on Artificial Life TI - Quantifying self-organizing behavior of autonomous robots ER - TY - JOUR AB - SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity. AU - Johnson, Kaeli C.M. AU - Xia, Shitou AU - Feng, Xiaoqi AU - Li, Xin ID - 12196 IS - 8 JF - Plant and Cell Physiology KW - Cell Biology KW - Plant Science KW - Physiology KW - General Medicine SN - 0032-0781 TI - The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity VL - 56 ER - TY - JOUR AB - The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution. AU - Zhao, Hui AU - Sen, Soumyo AU - Udayabhaskararao, T. AU - Sawczyk, Michał AU - Kučanda, Kristina AU - Manna, Debasish AU - Kundu, Pintu K. AU - Lee, Ji-Woong AU - Král, Petr AU - Klajn, Rafal ID - 13392 JF - Nature Nanotechnology KW - Electrical and Electronic Engineering KW - Condensed Matter Physics KW - General Materials Science KW - Biomedical Engineering KW - Atomic and Molecular Physics KW - and Optics KW - Bioengineering SN - 1748-3387 TI - Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks VL - 11 ER - TY - JOUR AB - The ability to guide the assembly of nanosized objects reversibly with external stimuli, in particular light, is of fundamental importance, and it contributes to the development of applications as diverse as nanofabrication and controlled drug delivery. However, all the systems described to date are based on nanoparticles (NPs) that are inherently photoresponsive, which makes their preparation cumbersome and can markedly hamper their performance. Here we describe a conceptually new methodology to assemble NPs reversibly using light that does not require the particles to be functionalized with light-responsive ligands. Our strategy is based on the use of a photoswitchable medium that responds to light in such a way that it modulates the interparticle interactions. NP assembly proceeds quantitatively and without apparent fatigue, both in solution and in gels. Exposing the gels to light in a spatially controlled manner allowed us to draw images that spontaneously disappeared after a specific period of time. AU - Kundu, Pintu K. AU - Samanta, Dipak AU - Leizrowice, Ron AU - Margulis, Baruch AU - Zhao, Hui AU - Börner, Martin AU - Udayabhaskararao, T. AU - Manna, Debasish AU - Klajn, Rafal ID - 13394 JF - Nature Chemistry KW - General Chemical Engineering KW - General Chemistry SN - 1755-4330 TI - Light-controlled self-assembly of non-photoresponsive nanoparticles VL - 7 ER - TY - JOUR AB - Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials (“frustrated” nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light. AU - Manna, Debasish AU - Udayabhaskararao, Thumu AU - Zhao, Hui AU - Klajn, Rafal ID - 13393 IS - 42 JF - Angewandte Chemie International Edition KW - General Chemistry KW - Catalysis SN - 1433-7851 TI - Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes VL - 54 ER - TY - JOUR AB - Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate. AU - Lee, Ji-Woong AU - Klajn, Rafal ID - 13395 IS - 11 JF - Chemical Communications KW - Materials Chemistry KW - Metals and Alloys KW - Surfaces KW - Coatings and Films KW - General Chemistry KW - Ceramics and Composites KW - Electronic KW - Optical and Magnetic Materials KW - Catalysis SN - 1359-7345 TI - Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2 VL - 51 ER - TY - JOUR AB - Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs. AU - Moldt, Thomas AU - Brete, Daniel AU - Przyrembel, Daniel AU - Das, Sanjib AU - Goldman, Joel R. AU - Kundu, Pintu K. AU - Gahl, Cornelius AU - Klajn, Rafal AU - Weinelt, Martin ID - 13396 IS - 3 JF - Langmuir KW - Electrochemistry KW - Spectroscopy KW - Surfaces and Interfaces KW - Condensed Matter Physics KW - General Materials Science SN - 0743-7463 TI - Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature VL - 31 ER - TY - JOUR AB - Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light. AU - Singh, Gurvinder AU - Chan, Henry AU - Udayabhaskararao, T. AU - Gelman, Elijah AU - Peddis, Davide AU - Baskin, Artem AU - Leitus, Gregory AU - Král, Petr AU - Klajn, Rafal ID - 13397 JF - Faraday Discussions KW - Physical and Theoretical Chemistry SN - 1359-6640 TI - Magnetic field-induced self-assembly of iron oxide nanocubes VL - 181 ER - TY - JOUR AU - Sun, Yugang AU - Scarabelli, Leonardo AU - Kotov, Nicholas AU - Tebbe, Moritz AU - Lin, Xiao-Min AU - Brullot, Ward AU - Isa, Lucio AU - Schurtenberger, Peter AU - Moehwald, Helmuth AU - Fedin, Igor AU - Velev, Orlin AU - Faivre, Damien AU - Sorensen, Christopher AU - Perzynski, Régine AU - Chanana, Munish AU - Li, Zhihai AU - Bresme, Fernando AU - Král, Petr AU - Firlar, Emre AU - Schiffrin, David AU - Souza Junior, Joao Batista AU - Fery, Andreas AU - Shevchenko, Elena AU - Tarhan, Ozgur AU - Alivisatos, Armand Paul AU - Disch, Sabrina AU - Klajn, Rafal AU - Ghosh, Suvojit ID - 13398 JF - Faraday Discussions KW - Physical and Theoretical Chemistry SN - 1359-6640 TI - Field-assisted self-assembly process: General discussion VL - 181 ER - TY - JOUR AB - The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results. AU - Zhang, Song Bin AU - Baykusheva, Denitsa Rangelova AU - Kraus, Peter M. AU - Wörner, Hans Jakob AU - Rohringer, Nina ID - 14017 IS - 2 JF - Physical Review A KW - Atomic and Molecular Physics KW - and Optics SN - 1050-2947 TI - Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation VL - 91 ER - TY - JOUR AB - All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies. AU - Kraus, P. M. AU - Tolstikhin, O. I. AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A. AU - Schneider, J. AU - Bisgaard, C. Z. AU - Morishita, T. AU - Jensen, F. AU - Madsen, L. B. AU - Wörner, H. J. ID - 14016 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Observation of laser-induced electronic structure in oriented polyatomic molecules VL - 6 ER - TY - JOUR AB - The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes. AU - Kraus, P. M. AU - Mignolet, B. AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A. AU - Horný, L. AU - Penka, E. F. AU - Grassi, G. AU - Tolstikhin, O. I. AU - Schneider, J. AU - Jensen, F. AU - Madsen, L. B. AU - Bandrauk, A. D. AU - Remacle, F. AU - Wörner, H. J. ID - 14013 IS - 6262 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Measurement and laser control of attosecond charge migration in ionized iodoacetylene VL - 350 ER - TY - JOUR AB - We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes. AU - Kraus, P M AU - Mignolet, B AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A AU - Horný, L AU - Penka, E F AU - Tolstikhin, O I AU - Schneider, J AU - Jensen, F AU - Madsen, L B AU - Bandrauk, A D AU - Remacle, F AU - Wörner, H J ID - 14015 IS - 11 JF - Journal of Physics: Conference Series KW - General Physics and Astronomy SN - 1742-6588 TI - Attosecond charge migration and its laser control VL - 635 ER - TY - JOUR AB - We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons. AU - Walt, Samuel G AU - Ram, N Bhargava AU - von Conta, Aaron AU - Baykusheva, Denitsa Rangelova AU - Atala, Marcos AU - Wörner, Hans Jakob ID - 14014 IS - 11 JF - Journal of Physics: Conference Series KW - General Physics and Astronomy SN - 1742-6588 TI - Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography VL - 635 ER - TY - GEN AB - Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance. AU - Wielgoss, Sébastien AU - Bergmiller, Tobias AU - Bischofberger, Anna M. AU - Hall, Alex R. ID - 9719 TI - Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria ER - TY - THES AB - The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views. AU - Sharmanska, Viktoriia ID - 1401 SN - 2663-337X TI - Learning with attributes for object recognition: Parametric and non-parametrics views ER - TY - JOUR AB - The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards. AU - Reiter, Johannes AU - Kanodia, Ayush AU - Gupta, Raghav AU - Nowak, Martin AU - Chatterjee, Krishnendu ID - 1709 IS - 1812 JF - Proceedings of the Royal Society of London Series B Biological Sciences TI - Biological auctions with multiple rewards VL - 282 ER - TY - THES AB - Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease. AU - Reiter, Johannes ID - 1400 SN - 2663-337X TI - The subclonal evolution of cancer ER - TY - JOUR AB - Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology. AU - Pausinger, Florian AU - Svane, Anne ID - 1792 IS - 6 JF - Journal of Complexity TI - A Koksma-Hlawka inequality for general discrepancy systems VL - 31 ER - TY - THES AB - This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold. AU - Pausinger, Florian ID - 1399 SN - 2663-337X TI - On the approximation of intrinsic volumes ER -