@misc{9714,
  author       = {Gómez Sicilia, Àngel and Sikora, Mateusz K and Cieplak, Marek and Carrión Vázquez, Mariano},
  publisher    = {Public Library of Science},
  title        = {{An exploration of the universe of polyglutamine structures - submission to PLOS journals}},
  doi          = {10.1371/journal.pcbi.1004541.s001},
  year         = {2015},
}

@article{1555,
  abstract     = {We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations.},
  author       = {Knipl, Diána and Pilarczyk, Pawel and Röst, Gergely},
  issn         = {1536-0040},
  journal      = {SIAM Journal on Applied Dynamical Systems},
  number       = {2},
  pages        = {980 -- 1017},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Rich bifurcation structure in a two patch vaccination model}},
  doi          = {10.1137/140993934},
  volume       = {14},
  year         = {2015},
}

@article{2034,
  abstract     = {Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers.},
  author       = {Bérard, Béatrice and Chatterjee, Krishnendu and Sznajder, Nathalie},
  journal      = {Information Processing Letters},
  number       = {1},
  pages        = {52 -- 59},
  publisher    = {Elsevier},
  title        = {{Probabilistic opacity for Markov decision processes}},
  doi          = {10.1016/j.ipl.2014.09.001},
  volume       = {115},
  year         = {2015},
}

@article{1542,
  abstract     = {The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. },
  author       = {Paixao, Tiago and Badkobeh, Golnaz and Barton, Nicholas H and Çörüş, Doğan and Dang, Duccuong and Friedrich, Tobias and Lehre, Per and Sudholt, Dirk and Sutton, Andrew and Trubenova, Barbora},
  journal      = {Journal of Theoretical Biology},
  pages        = {28 -- 43},
  publisher    = {Elsevier},
  title        = {{Toward a unifying framework for evolutionary processes}},
  doi          = {10.1016/j.jtbi.2015.07.011},
  volume       = {383},
  year         = {2015},
}

@inproceedings{1656,
  abstract     = {Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.},
  author       = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
  booktitle    = {Proceedings - Symposium on Logic in Computer Science},
  location     = {Kyoto, Japan},
  publisher    = {IEEE},
  title        = {{Nested weighted automata}},
  doi          = {10.1109/LICS.2015.72},
  volume       = {2015-July},
  year         = {2015},
}

@misc{5436,
  abstract     = {Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time.
In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.},
  author       = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
  issn         = {2664-1690},
  pages        = {29},
  publisher    = {IST Austria},
  title        = {{Nested weighted automata}},
  doi          = {10.15479/AT:IST-2015-170-v2-2},
  year         = {2015},
}

@article{1792,
  abstract     = {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.},
  author       = {Pausinger, Florian and Svane, Anne},
  journal      = {Journal of Complexity},
  number       = {6},
  pages        = {773 -- 797},
  publisher    = {Academic Press},
  title        = {{A Koksma-Hlawka inequality for general discrepancy systems}},
  doi          = {10.1016/j.jco.2015.06.002},
  volume       = {31},
  year         = {2015},
}

@phdthesis{1399,
  abstract     = {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.},
  author       = {Pausinger, Florian},
  issn         = {2663-337X},
  pages        = {144},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{On the approximation of intrinsic volumes}},
  year         = {2015},
}

@article{1709,
  abstract     = {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.},
  author       = {Reiter, Johannes and Kanodia, Ayush and Gupta, Raghav and Nowak, Martin and Chatterjee, Krishnendu},
  journal      = {Proceedings of the Royal Society of London Series B Biological Sciences},
  number       = {1812},
  publisher    = {Royal Society},
  title        = {{Biological auctions with multiple rewards}},
  doi          = {10.1098/rspb.2015.1041},
  volume       = {282},
  year         = {2015},
}

@phdthesis{1400,
  abstract     = {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.},
  author       = {Reiter, Johannes},
  issn         = {2663-337X},
  pages        = {183},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The subclonal evolution of cancer}},
  year         = {2015},
}

@article{1666,
  abstract     = {Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.},
  author       = {Tugrul, Murat and Paixao, Tiago and Barton, Nicholas H and Tkacik, Gasper},
  journal      = {PLoS Genetics},
  number       = {11},
  publisher    = {Public Library of Science},
  title        = {{Dynamics of transcription factor binding site evolution}},
  doi          = {10.1371/journal.pgen.1005639},
  volume       = {11},
  year         = {2015},
}

@inproceedings{1633,
  abstract     = {We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.

Our system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.

Separating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix.},
  author       = {Hahn, David and Wojtan, Christopher J},
  location     = {Los Angeles, CA, United States},
  number       = {4},
  publisher    = {ACM},
  title        = {{High-resolution brittle fracture simulation with boundary elements}},
  doi          = {10.1145/2766896},
  volume       = {34},
  year         = {2015},
}

@article{1830,
  abstract     = {To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.},
  author       = {Theis, Fabian and Ugelvig, Line V and Marr, Carsten and Cremer, Sylvia},
  issn         = {1471-2970},
  journal      = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
  number       = {1669},
  publisher    = {Royal Society},
  title        = {{Opposing effects of allogrooming on disease transmission in ant societies}},
  doi          = {10.1098/rstb.2014.0108},
  volume       = {370},
  year         = {2015},
}

@misc{9721,
  abstract     = {To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.},
  author       = {Theis, Fabian and Ugelvig, Line V and Marr, Carsten and Cremer, Sylvia},
  publisher    = {Dryad},
  title        = {{Data from: Opposing effects of allogrooming on disease transmission in ant societies}},
  doi          = {10.5061/dryad.dj2bf},
  year         = {2015},
}

@article{1811,
  abstract     = {Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.},
  author       = {Safari, Laleh and Santos, José and Amaro, Pedro and Jänkälä, Kari and Fratini, Filippo},
  journal      = {Journal of Mathematical Physics},
  number       = {5},
  publisher    = {AIP Publishing},
  title        = {{Analytical evaluation of atomic form factors: Application to Rayleigh scattering}},
  doi          = {10.1063/1.4921227},
  volume       = {56},
  year         = {2015},
}

@article{1677,
  abstract     = {We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale.},
  author       = {Alt, Johannes},
  journal      = {Journal of Mathematical Physics},
  number       = {10},
  publisher    = {AIP Publishing},
  title        = {{The local semicircle law for random matrices with a fourfold symmetry}},
  doi          = {10.1063/1.4932606},
  volume       = {56},
  year         = {2015},
}

@article{1587,
  abstract     = {We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.},
  author       = {Amaro, Pedro and Fratini, Filippo and Safari, Laleh and Antognini, Aldo and Indelicato, Paul and Pohl, Randolf and Santos, José},
  journal      = {Physical Review A},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Quantum interference shifts in laser spectroscopy with elliptical polarization}},
  doi          = {10.1103/PhysRevA.92.062506},
  volume       = {92},
  year         = {2015},
}

@article{1940,
  abstract     = {We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.},
  author       = {Sokolowski, Thomas R and Tkacik, Gasper},
  journal      = {Physical Review E},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Optimizing information flow in small genetic networks. IV. Spatial coupling}},
  doi          = {10.1103/PhysRevE.91.062710},
  volume       = {91},
  year         = {2015},
}

@article{1883,
  abstract     = {We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.
},
  author       = {Keller-Schmidt, Stephanie and Tugrul, Murat and Eguíluz, Víctor and Hernandez Garcia, Emilio and Klemm, Konstantin},
  journal      = {Physical Review E},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Anomalous scaling in an age-dependent branching model}},
  doi          = {10.1103/PhysRevE.91.022803},
  volume       = {91},
  year         = {2015},
}

@inproceedings{1820,
  abstract     = {We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.},
  author       = {Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Raghav and Kanodia, Ayush},
  booktitle    = {Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence },
  location     = {Austin, TX, USA},
  pages        = {3496--3502},
  publisher    = {AAAI Press},
  title        = {{Optimal cost almost-sure reachability in POMDPs}},
  doi          = {10.1609/aaai.v29i1.9683},
  volume       = {5},
  year         = {2015},
}