@article{22052,
  abstract     = {We consider the focusing cubic nonlinear Schrödinger equation (NLS) in the exterior Ω of a smooth, compact, strictly convex obstacle in three dimensions. We prove that the threshold for global existence and scattering is the same as for the problem posed on Euclidean space. Specifically, we prove that if E(u0)M(u0)<E(Q)M(Q) and ||u0||2||u0||2<\|\nabla Q||2||Q||2, the corresponding solution to the initial value problem with Dirichlet boundary conditions exists globally and scatters to linear evolutions asymptotically in the future and in the past. Here, Q(x) denotes the ground state for the focusing cubic NLS in ℝ3. },
  author       = {Killip, Rowan and Visan, Monica and Zhang, Xiaoyi},
  issn         = {1687-1197},
  journal      = {Applied Mathematics Research eXpress},
  number       = {1},
  pages        = {146--180},
  publisher    = {Oxford University Press},
  title        = {{The focusing cubic NLS on exterior domains in three dimensions}},
  doi          = {10.1093/amrx/abv012},
  volume       = {2016},
  year         = {2016},
}

@article{22073,
  abstract     = {We prove scale-invariant Strichartz inequalities for the Schrödinger equation on rectangular tori (rational or irrational) in all dimensions. We use these estimates to give a simpler treatment of local well-posedness of the energy-critical nonlinear Schrödinger equation in dimensions three and four.},
  author       = {Killip, Rowan and Visan, Monica},
  issn         = {1945-001X},
  journal      = {Mathematical Research Letters},
  number       = {2},
  pages        = {445--472},
  publisher    = {International Press},
  title        = {{Scale-invariant Strichartz estimates on tori and applications}},
  doi          = {10.4310/mrl.2016.v23.n2.a8},
  volume       = {23},
  year         = {2016},
}

@article{1223,
  abstract     = {We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder.},
  author       = {Froese, Richard and Lee, Darrick and Sadel, Christian and Spitzer, Wolfgang and Stolz, Günter},
  journal      = {Journal of Spectral Theory},
  number       = {3},
  pages        = {557 -- 600},
  publisher    = {EMS Press},
  title        = {{Localization for transversally periodic random potentials on binary trees}},
  doi          = {10.4171/JST/132},
  volume       = {6},
  year         = {2016},
}

@article{1170,
  abstract     = {The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.},
  author       = {Lang, Moritz and Stelling, Jörg},
  journal      = {SIAM Journal on Scientific Computing},
  number       = {6},
  pages        = {B988 -- B1008},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Modular parameter identification of biomolecular networks}},
  doi          = {10.1137/15M103306X},
  volume       = {38},
  year         = {2016},
}

@article{1377,
  abstract     = {We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.},
  author       = {Kolmogorov, Vladimir and Pock, Thomas and Rolinek, Michal},
  journal      = {SIAM Journal on Imaging Sciences},
  number       = {2},
  pages        = {605 -- 636},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Total variation on a tree}},
  doi          = {10.1137/15M1010257},
  volume       = {9},
  year         = {2016},
}

@article{1272,
  abstract     = {We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams.},
  author       = {Held, Martin and Huber, Stefan and Palfrader, Peter},
  journal      = {Computer-Aided Design and Applications},
  number       = {5},
  pages        = {712 -- 721},
  publisher    = {Taylor & Francis},
  title        = {{Generalized offsetting of planar structures using skeletons}},
  doi          = {10.1080/16864360.2016.1150718},
  volume       = {13},
  year         = {2016},
}

@article{1254,
  abstract     = {We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.},
  author       = {Golmakani, Ali and Luzzatto, Stefano and Pilarczyk, Pawel},
  journal      = {Experimental Mathematics},
  number       = {2},
  pages        = {116 -- 124},
  publisher    = {Taylor & Francis},
  title        = {{Uniform expansivity outside a critical neighborhood in the quadratic family}},
  doi          = {10.1080/10586458.2015.1048011},
  volume       = {25},
  year         = {2016},
}

@article{1188,
  abstract     = {We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. 
In the asymptotic regime of slow
diffusion, that coincides with the relevant experimental range, the resulting
non-linear Fokker–Planck equation is solved for the steady state in the WKB
approximation that maps it into the ground state of a quantum particle in an
Airy potential plus a centrifugal term. We retrieve scaling laws for growth rate
fluctuations and time response with respect to the distance from the maximum
growth rate suggesting that suboptimal populations can have a faster response
to perturbations.},
  author       = {De Martino, Daniele and Masoero, Davide},
  journal      = {Journal of Statistical Mechanics: Theory and Experiment},
  number       = {12},
  publisher    = {IOP Publishing},
  title        = {{Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth}},
  doi          = {10.1088/1742-5468/aa4e8f},
  volume       = {2016},
  year         = {2016},
}

@article{1441,
  abstract     = {Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.},
  author       = {Gschaider-Reichhart, Eva and Inglés Prieto, Álvaro and Tichy, Alexandra-Madelaine and Mckenzie, Catherine and Janovjak, Harald L},
  journal      = {Angewandte Chemie International Edition},
  number       = {21},
  pages        = {6339 -- 6342},
  publisher    = {Wiley},
  title        = {{A phytochrome sensory domain permits receptor activation by red light}},
  doi          = {10.1002/anie.201601736},
  volume       = {55},
  year         = {2016},
}

@article{1339,
  abstract     = {We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive
actuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By
measuring the resonance frequencies of the system, we show that the comb-drive actuator and the
silicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate
(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)
placed close to the silicon beam. In contrast, the effective spring constant of the system is insensitive
to either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator
can be used to switch between different coupling rates with a frequency of at least 10 kHz.
},
  author       = {Verbiest, Gerard and Xu, Duo and Goldsche, Matthias and Khodkov, Timofiy and Barzanjeh, Shabir and Von Den Driesch, Nils and Buca, Dan and Stampfer, Christoph},
  journal      = {Applied Physics Letter},
  publisher    = {American Institute of Physics},
  title        = {{Tunable mechanical coupling between driven microelectromechanical resonators}},
  doi          = {10.1063/1.4964122},
  volume       = {109},
  year         = {2016},
}

@article{22171,
  abstract     = {We show that over the binary field [Formula: see text], the Bar-Natan perturbation of Khovanov homology splits as the direct sum of its two reduced theories, which we also prove are isomorphic. This extends Shumakovitch’s analogous result for ordinary Khovanov homology, without the perturbation. },
  author       = {Wigderson, Yuval},
  issn         = {1793-6527},
  journal      = {Journal of Knot Theory and Its Ramifications},
  keywords     = {Khovanov homology, categorification, Bar-Natan theory, link homology},
  number       = {04},
  publisher    = {World Scientific Publishing},
  title        = {{The Bar-Natan theory splits}},
  doi          = {10.1142/s0218216516500140},
  volume       = {25},
  year         = {2016},
}

@article{22202,
  abstract     = {We use modular symmetric designs to study the existence of Hadamard matrices modulo certain primes. We solve the 7-modular and 11-modular versions of the Hadamard conjecture for all but a finite number of cases. In doing so, we state a conjectural sufficient condition for the existence of a p-modular Hadamard matrix for all but finitely many cases. When 2 is a primitive root of a prime p, we conditionally solve this conjecture and therefore the p-modular version of the Hadamard conjecture for all but finitely many cases when p ≡ 3(mod 4), and prove a weaker result for p ≡ 1 (mod 4). Finally, we look at constraints on the existence of m-modular Hadamard matrices when the size of the matrix is small compared to m.},
  author       = {Kuperberg, Vivian Zieve},
  issn         = {1520-6610},
  journal      = {Journal of Combinatorial Designs},
  keywords     = {modular hadamard matrices, modular symmetric designs},
  number       = {9},
  pages        = {393--405},
  publisher    = {Wiley},
  title        = {{Hadamard matrices modulo p and small modular Hadamard matrices}},
  doi          = {10.1002/jcd.21522},
  volume       = {24},
  year         = {2016},
}

@article{1100,
  abstract     = {During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.},
  author       = {Sako, Keisuke and Pradhan, Saurabh and Barone, Vanessa and Inglés Prieto, Álvaro and Mueller, Patrick and Ruprecht, Verena and Capek, Daniel and Galande, Sanjeev and Janovjak, Harald L and Heisenberg, Carl-Philipp J},
  journal      = {Cell Reports},
  number       = {3},
  pages        = {866 -- 877},
  publisher    = {Cell Press},
  title        = {{Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation}},
  doi          = {10.1016/j.celrep.2016.06.036},
  volume       = {16},
  year         = {2016},
}

@article{1321,
  abstract     = {Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.},
  author       = {Leithner, Alexander F and Eichner, Alexander and Müller, Jan and Reversat, Anne and Brown, Markus and Schwarz, Jan and Merrin, Jack and De Gorter, David and Schur, Florian and Bayerl, Jonathan and De Vries, Ingrid and Wieser, Stefan and Hauschild, Robert and Lai, Frank and Moser, Markus and Kerjaschki, Dontscho and Rottner, Klemens and Small, Victor and Stradal, Theresia and Sixt, Michael K},
  journal      = {Nature Cell Biology},
  pages        = {1253 -- 1259},
  publisher    = {Nature Publishing Group},
  title        = {{Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes}},
  doi          = {10.1038/ncb3426},
  volume       = {18},
  year         = {2016},
}

@article{1183,
  abstract     = {Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.},
  author       = {Tarlungeanu, Dora-Clara and Deliu, Elena and Dotter, Christoph and Kara, Majdi and Janiesch, Philipp and Scalise, Mariafrancesca and Galluccio, Michele and Tesulov, Mateja and Morelli, Emanuela and Sönmez, Fatma and Bilgüvar, Kaya and Ohgaki, Ryuichi and Kanai, Yoshikatsu and Johansen, Anide and Esharif, Seham and Ben Omran, Tawfeg and Topcu, Meral and Schlessinger, Avner and Indiveri, Cesare and Duncan, Kent and Caglayan, Ahmet and Günel, Murat and Gleeson, Joseph and Novarino, Gaia},
  journal      = {Cell},
  number       = {6},
  pages        = {1481 -- 1494},
  publisher    = {Cell Press},
  title        = {{Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder}},
  doi          = {10.1016/j.cell.2016.11.013},
  volume       = {167},
  year         = {2016},
}

@inproceedings{1437,
  abstract     = {We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.},
  author       = {Chatterjee, Krishnendu and Goharshady, Amir and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
  location     = {St. Petersburg, FL, USA},
  pages        = {733 -- 747},
  publisher    = {ACM},
  title        = {{Algorithms for algebraic path properties in concurrent systems of constant treewidth components}},
  doi          = {10.1145/2837614.2837624},
  volume       = {20-22},
  year         = {2016},
}

@inproceedings{1386,
  abstract     = {We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.},
  author       = {Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir},
  location     = {Toronto, Canada},
  pages        = {3 -- 22},
  publisher    = {Springer},
  title        = {{Termination analysis of probabilistic programs through Positivstellensatz's}},
  doi          = {10.1007/978-3-319-41528-4_1},
  volume       = {9779},
  year         = {2016},
}