@inproceedings{8129, abstract = {Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function. Overall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts.}, author = {Costa, Rui Ponte and Assael, Yannis M. and Shillingford, Brendan and Freitas, Nando de and Vogels, Tim P}, booktitle = {Advances in Neural Information Processing Systems}, issn = {10495258}, location = {Long Beach, CA, United States}, pages = {272--283}, publisher = {Neural Information Processing Systems Foundation}, title = {{Cortical microcircuits as gated-recurrent neural networks}}, volume = {30}, year = {2017}, } @article{817, abstract = {Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4. Å resolution structure determined by subtomogram averaging.}, author = {Turoňová, Beata and Schur, Florian and Wan, William and Briggs, John}, journal = {Journal of Structural Biology}, number = {3}, pages = {187--195}, publisher = {Academic Press}, title = {{Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å}}, doi = {10.1016/j.jsb.2017.07.007}, volume = {199}, year = {2017}, } @phdthesis{818, abstract = {Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. }, author = {Mitosch, Karin}, issn = {2663-337X}, pages = {113}, publisher = {Institute of Science and Technology Austria}, title = {{Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics}}, doi = {10.15479/AT:ISTA:th_862}, year = {2017}, } @phdthesis{819, abstract = {Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. }, author = {Pull, Christopher}, issn = {2663-337X}, pages = {122}, publisher = {Institute of Science and Technology Austria}, title = {{Disease defence in garden ants}}, doi = {10.15479/AT:ISTA:th_861}, year = {2017}, } @article{1528, abstract = {We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized.}, author = {Bao, Zhigang and Erdös, László}, issn = {01788051}, journal = {Probability Theory and Related Fields}, number = {3-4}, pages = {673 -- 776}, publisher = {Springer}, title = {{Delocalization for a class of random block band matrices}}, doi = {10.1007/s00440-015-0692-y}, volume = {167}, year = {2017}, } @article{169, abstract = {We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3.}, author = {Browning, Timothy D and Kumaraswamy, Vinay and Steiner, Rapael}, journal = {International Mathematics Research Notices}, publisher = {Oxford University Press}, title = {{Twisted Linnik implies optimal covering exponent for S3}}, doi = {10.1093/imrn/rnx116}, year = {2017}, } @article{172, abstract = {We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg.}, author = {Browning, Timothy D and Schindler, Damaris}, journal = {International Mathematics Research Notices}, publisher = {Oxford University Press}, title = {{Strong approximation and a conjecture of Harpaz and Wittenberg}}, doi = {10.1093/imrn/rnx252}, year = {2017}, } @article{2016, abstract = {The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.}, author = {Martin Del Campo Sanchez, Abraham and Cepeda Humerez, Sarah A and Uhler, Caroline}, issn = {03036898}, journal = {Scandinavian Journal of Statistics}, number = {2}, pages = {285 -- 306}, publisher = {Wiley-Blackwell}, title = {{Exact goodness-of-fit testing for the Ising model}}, doi = {10.1111/sjos.12251}, volume = {44}, year = {2017}, } @phdthesis{202, abstract = {Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.}, author = {Pleska, Maros}, issn = {2663-337X}, pages = {126}, publisher = {Institute of Science and Technology Austria}, title = {{Biology of restriction-modification systems at the single-cell and population level}}, doi = {10.15479/AT:ISTA:th_916}, year = {2017}, } @article{1336, abstract = {Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.}, author = {Paixao, Tiago and Pérez Heredia, Jorge and Sudholt, Dirk and Trubenova, Barbora}, issn = {01784617}, journal = {Algorithmica}, number = {2}, pages = {681 -- 713}, publisher = {Springer}, title = {{Towards a runtime comparison of natural and artificial evolution}}, doi = {10.1007/s00453-016-0212-1}, volume = {78}, year = {2017}, } @article{1337, abstract = {We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes.}, author = {Ajanki, Oskari H and Erdös, László and Krüger, Torben H}, issn = {01788051}, journal = {Probability Theory and Related Fields}, number = {3-4}, pages = {667 -- 727}, publisher = {Springer}, title = {{Universality for general Wigner-type matrices}}, doi = {10.1007/s00440-016-0740-2}, volume = {169}, year = {2017}, } @article{1338, abstract = {We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively.}, author = {Cerny, Pavol and Clarke, Edmund and Henzinger, Thomas A and Radhakrishna, Arjun and Ryzhyk, Leonid and Samanta, Roopsha and Tarrach, Thorsten}, journal = {Formal Methods in System Design}, number = {2-3}, pages = {97 -- 139}, publisher = {Springer}, title = {{From non-preemptive to preemptive scheduling using synchronization synthesis}}, doi = {10.1007/s10703-016-0256-5}, volume = {50}, year = {2017}, } @article{13380, abstract = {Although dissipative self-assembly is ubiquitous in nature, where it gives rise to structures and functions critical to life, examples of artificial systems featuring this mode of self-assembly are rare. Here, we identify the presence of ephemeral assemblies during seeded growth of gold nanoparticles. In this process, hydrazine reduces Au(III) ions, which attach to the existing nanoparticles “seeds”. The attachment is accompanied by a local increase in the concentration of a surfactant, which therefore forms a bilayer on nanoparticle surfaces, inducing their assembly. The resulting aggregates gradually disassemble as the surfactant concentration throughout the solution equilibrates. The lifetimes of the out-of-equilibrium aggregates depend on and can be controlled by the size of the constituent nanoparticles. We demonstrate the utility of our out-of-equilibrium aggregates to form transient reflective coatings on polar surfaces.}, author = {Sawczyk, Michał and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {49}, pages = {17973--17978}, publisher = {American Chemical Society}, title = {{Out-of-equilibrium aggregates and coatings during seeded growth of metallic nanoparticles}}, doi = {10.1021/jacs.7b09111}, volume = {139}, year = {2017}, } @article{13381, abstract = {Self-assembly of inorganic nanoparticles has been used to prepare hundreds of different colloidal crystals, but almost invariably with the restriction that the particles must be densely packed. Here, we show that non–close-packed nanoparticle arrays can be fabricated through the selective removal of one of two components comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle superlattices were prepared at the liquid-air interface, including several arrangements that were previously unknown. Molecular dynamics simulations revealed the particular role of the liquid in templating the formation of superlattices not achievable through self-assembly in bulk solution. Second, upon stabilization, all of these binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous materials having the same chemical composition but differing in their nanoscale architectures.}, author = {Udayabhaskararao, Thumu and Altantzis, Thomas and Houben, Lothar and Coronado-Puchau, Marc and Langer, Judith and Popovitz-Biro, Ronit and Liz-Marzán, Luis M. and Vuković, Lela and Král, Petr and Bals, Sara and Klajn, Rafal}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6362}, pages = {514--518}, publisher = {American Association for the Advancement of Science}, title = {{Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices}}, doi = {10.1126/science.aan6046}, volume = {358}, year = {2017}, } @article{13382, author = {van Esch, Jan H. and Klajn, Rafal and Otto, Sijbren}, issn = {1460-4744}, journal = {Chemical Society Reviews}, keywords = {General Chemistry}, number = {18}, pages = {5474--5475}, publisher = {Royal Society of Chemistry}, title = {{Chemical systems out of equilibrium}}, doi = {10.1039/c7cs90088k}, volume = {46}, year = {2017}, } @article{13383, abstract = {Two novel donor–acceptor Stenhouse adducts (DASAs) featuring the catechol moiety were synthesized and characterized. Both compounds bind strongly to the surfaces of magnetite nanoparticles. An adrenaline-derived DASA renders the particles insoluble in all common solvents, likely because of poor solvation of the zwitterionic isomer generated on the nanoparticle surfaces. Well-soluble nanoparticles were successfully obtained using dopamine-derived DASA equipped with a long alkyl chain. Upon its attachment to nanoparticles, this DASA undergoes an irreversible decoloration reaction owing to the formation of the zwitterionic form. The reaction follows first-order kinetics and proceeds more rapidly on large nanoparticles. Interestingly, decoloration can be suppressed in the presence of free DASA molecules in solution or at high nanoparticle concentrations.}, author = {Ahrens, Johannes and Bian, Tong and Vexler, Tom and Klajn, Rafal}, issn = {2367-0932}, journal = {ChemPhotoChem}, keywords = {Organic Chemistry, Physical and Theoretical Chemistry, Analytical Chemistry}, number = {5}, pages = {230--236}, publisher = {Wiley}, title = {{Irreversible bleaching of donor-acceptor stenhouse adducts on the surfaces of magnetite nanoparticles}}, doi = {10.1002/cptc.201700009}, volume = {1}, year = {2017}, } @article{13384, abstract = {Although methane is a volatile gas, it can be efficiently trapped in ice, which can then be readily set on fire. Beyond the curiosity of this “burning ice,” caged methane is of great importance as one of the world's largest natural gas resources. In these materials, known as clathrates, methane molecules are tightly bound in nanometer-sized, regularly interspaced cages. Other inorganic materials, such as the silica mineral chibaite, can similarly encapsulate methane and higher hydrocarbons. Simple organic compounds have also been found to trap various organic molecules upon crystallization.}, author = {Samanta, Dipak and Klajn, Rafal}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6328}, pages = {912--912}, publisher = {American Association for the Advancement of Science}, title = {{Clathrates grow up}}, doi = {10.1126/science.aam7927}, volume = {355}, year = {2017}, } @article{13476, abstract = {Understanding ionizing fluxes of stellar populations is crucial for various astrophysical problems including the epoch of reionization. Short-lived massive stars are generally considered as the main stellar sources. We examine the potential role of less massive stars that lose their envelope through interaction with a binary companion. Here, we focus on the role of metallicity (Z). For this purpose we used the evolutionary code MESA and created tailored atmosphere models with the radiative transfer code CMFGEN. We show that typical progenitors, with initial masses of 12 M⊙, produce hot and compact stars (~ 4 M⊙, 60–80 kK, ~1 R⊙). These stripped stars copiously produce ionizing photons, emitting 60–85% and 30–60% of their energy as HI and HeI ionizing radiation, for Z = 0.0001–0.02, respectively. Their output is comparable to what massive stars emit during their Wolf-Rayet phase, if we account for their longer lifetimes and the favorable slope of the initial mass function. Their relative importance for reionization may be further favored since they emit their photons with a time delay (~ 20 Myr after birth in our fiducial model). This allows time for the dispersal of the birth clouds, allowing the ionizing photons to escape into the intergalactic medium. At low Z, we find that Roche stripping fails to fully remove the H-rich envelope, because of the reduced opacity in the subsurface layers. This is in sharp contrast with the assumption of complete stripping that is made in rapid population synthesis simulations, which are widely used to simulate the binary progenitors of supernovae and gravitational waves. Finally, we discuss the urgency to increase the observed sample of stripped stars to test these models and we discuss how our predictions can help to design efficient observational campaigns.}, author = {Götberg, Ylva Louise Linsdotter and de Mink, S. E. and Groh, J. H.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity}}, doi = {10.1051/0004-6361/201730472}, volume = {608}, year = {2017}, } @article{13477, abstract = {Most massive stars, the progenitors of core-collapse supernovae, are in close binary systems and may interact with their companion through mass transfer or merging. We undertake a population synthesis study to compute the delay-time distribution of core-collapse supernovae, that is, the supernova rate versus time following a starburst, taking into account binary interactions. We test the systematic robustness of our results by running various simulations to account for the uncertainties in our standard assumptions. We find that a significant fraction, 15+9-8%, of core-collapse supernovae are “late”, that is, they occur 50–200 Myr after birth, when all massive single stars have already exploded. These late events originate predominantly from binary systems with at least one, or, in most cases, with both stars initially being of intermediate mass (4–8 M⊙). The main evolutionary channels that contribute often involve either the merging of the initially more massive primary star with its companion or the engulfment of the remaining core of the primary by the expanding secondary that has accreted mass at an earlier evolutionary stage. Also, the total number of core-collapse supernovae increases by 14+15-14% because of binarity for the same initial stellar mass. The high rate implies that we should have already observed such late core-collapse supernovae, but have not recognized them as such. We argue that φ Persei is a likely progenitor and that eccentric neutron star – white dwarf systems are likely descendants. Late events can help explain the discrepancy in the delay-time distributions derived from supernova remnants in the Magellanic Clouds and extragalactic type Ia events, lowering the contribution of prompt Ia events. We discuss ways to test these predictions and speculate on the implications for supernova feedback in simulations of galaxy evolution.}, author = {Zapartas, E. and de Mink, S. E. and Izzard, R. G. and Yoon, S.-C. and Badenes, C. and Götberg, Ylva Louise Linsdotter and de Koter, A. and Neijssel, C. J. and Renzo, M. and Schootemeijer, A. and Shrotriya, T. S.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {A&A}, publisher = {EDP Sciences}, title = {{Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction}}, doi = {10.1051/0004-6361/201629685}, volume = {601}, year = {2017}, } @article{1351, abstract = {The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.}, author = {Giacobbe, Mirco and Guet, Calin C and Gupta, Ashutosh and Henzinger, Thomas A and Paixao, Tiago and Petrov, Tatjana}, issn = {00015903}, journal = {Acta Informatica}, number = {8}, pages = {765 -- 787}, publisher = {Springer}, title = {{Model checking the evolution of gene regulatory networks}}, doi = {10.1007/s00236-016-0278-x}, volume = {54}, year = {2017}, }