@article{11976, abstract = {The way organic multistep synthesis is performed is changing due to the adoption of flow chemical techniques, which has enabled the development of improved methods to make complex molecules. The modular nature of the technique provides not only access to target molecules via linear flow approaches but also for the targeting of structural cores with single systems. This perspective article summarizes the state of the art of continuous multistep synthesis and discusses the main challenges and opportunities in this area.}, author = {Pieber, Bartholomäus and Gilmore, Kerry and Seeberger, Peter H.}, issn = {2063-0212}, journal = {Journal of Flow Chemistry}, number = {3-4}, pages = {129--136}, publisher = {AKJournals}, title = {{Integrated flow processing - challenges in continuous multistep synthesis}}, doi = {10.1556/1846.2017.00016}, volume = {7}, year = {2017}, } @article{1199, abstract = {Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.}, author = {Barton, Nicholas H}, journal = {Heredity}, pages = {96 -- 109}, publisher = {Nature Publishing Group}, title = {{How does epistasis influence the response to selection?}}, doi = {10.1038/hdy.2016.109}, volume = {118}, year = {2017}, } @article{1207, abstract = {The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix.}, author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, number = {3}, pages = {947 -- 990}, publisher = {Springer}, title = {{Local law of addition of random matrices on optimal scale}}, doi = {10.1007/s00220-016-2805-6}, volume = {349}, year = {2017}, } @article{1208, abstract = {We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd.}, author = {Zwiernik, Piotr and Uhler, Caroline and Richards, Donald}, issn = {1369-7412}, journal = {Journal of the Royal Statistical Society. Series B: Statistical Methodology}, number = {4}, pages = {1269 -- 1292}, publisher = {Wiley-Blackwell}, title = {{Maximum likelihood estimation for linear Gaussian covariance models}}, doi = {10.1111/rssb.12217}, volume = {79}, year = {2017}, } @article{1211, abstract = {Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.}, author = {Budanur, Nazmi B and Cvitanović, Predrag}, journal = {Journal of Statistical Physics}, number = {3-4}, pages = {636--655}, publisher = {Springer}, title = {{Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system}}, doi = {10.1007/s10955-016-1672-z}, volume = {167}, year = {2017}, } @inbook{1213, abstract = {Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin.}, author = {Baranova, Natalia and Loose, Martin}, booktitle = {Cytokinesis}, editor = {Echard, Arnaud }, issn = {0091-679X}, pages = {355 -- 370}, publisher = {Academic Press}, title = {{Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers}}, doi = {10.1016/bs.mcb.2016.03.036}, volume = {137}, year = {2017}, } @article{265, abstract = {We establish the dimension and irreducibility of the moduli space of rational curves (of fixed degree) on arbitrary smooth hypersurfaces of sufficiently low degree. A spreading out argument reduces the problem to hypersurfaces defined over finite fields of large cardinality, which can then be tackled using a function field version of the Hardy-Littlewood circle method, in which particular care is taken to ensure uniformity in the size of the underlying finite field.}, author = {Browning, Timothy D and Vishe, Pankaj}, issn = {1944-7833}, journal = {Geometric Methods in Algebra and Number Theory}, number = {7}, pages = {1657 -- 1675}, publisher = { Mathematical Sciences Publishers}, title = {{Rational curves on smooth hypersurfaces of low degree}}, doi = {10.2140/ant.2017.11.1657}, volume = {11}, year = {2017}, } @article{266, abstract = {We generalise Birch's seminal work on forms in many variables to handle a system of forms in which the degrees need not all be the same. This allows us to prove the Hasse principle, weak approximation, and the Manin-Peyre conjecture for a smooth and geometrically integral variety X Pm, provided only that its dimension is large enough in terms of its degree.}, author = {Browning, Timothy D and Heath Brown, Roger}, journal = {Journal of the European Mathematical Society}, number = {2}, pages = {357 -- 394}, publisher = {European Mathematical Society Publishing House}, title = {{Forms in many variables and differing degrees}}, doi = {10.4171/JEMS/668}, volume = {19}, year = {2017}, } @article{267, abstract = {Building on recent work of Bhargava, Elkies and Schnidman and of Kriz and Li, we produce infinitely many smooth cubic surfaces defined over the field of rational numbers that contain rational points.}, author = {Browning, Timothy D}, issn = {0025-5793}, journal = {Mathematika}, number = {3}, pages = {818 -- 839}, publisher = {Cambridge University Press}, title = {{Many cubic surfaces contain rational points}}, doi = {10.1112/S0025579317000195}, volume = {63}, year = {2017}, } @article{268, abstract = {We show that any subset of the squares of positive relative upper density contains nontrivial solutions to a translation-invariant linear equation in five or more variables, with explicit quantitative bounds. As a consequence, we establish the partition regularity of any diagonal quadric in five or more variables whose coefficients sum to zero. Unlike previous approaches, which are limited to equations in seven or more variables, we employ transference technology of Green to import bounds from the linear setting.}, author = {Browning, Timothy D and Prendiville, Sean}, issn = {1073-7928}, journal = {International Mathematics Research Notices}, number = {7}, pages = {2219 -- 2248}, publisher = {Oxford University Press}, title = {{A transference approach to a Roth-type theorem in the squares}}, doi = {10.1093/imrn/rnw096}, volume = {2017}, year = {2017}, } @article{269, abstract = {We investigate Fano varieties defined over a number field that contain subvarieties whose number of rational points of bounded height is comparable to the total number on the variety.}, author = {Browning, Timothy D and Loughran, Daniel}, journal = {Mathematische Zeitschrift}, number = {3-4}, pages = {1249 -- 1267}, publisher = {Springer}, title = {{Varieties with too many rational points}}, doi = {10.1007/s00209-016-1746-2}, volume = {285}, year = {2017}, } @article{270, abstract = {Given a symmetric variety Y defined over Q and a non-zero polynomial with integer coefficients, we use techniques from homogeneous dynamics to establish conditions under which the polynomial can be made r-free for a Zariski dense set of integral points on Y . We also establish an asymptotic counting formula for this set. In the special case that Y is a quadric hypersurface, we give explicit bounds on the size of r by combining the argument with a uniform upper bound for the density of integral points on general affine quadrics defined over Q.}, author = {Browning, Timothy D and Gorodnik, Alexander}, issn = {0024-6115}, journal = {Proceedings of the London Mathematical Society}, number = {6}, pages = {1044 -- 1080}, publisher = {Wiley}, title = {{Power-free values of polynomials on symmetric varieties}}, doi = {10.1112/plms.12030}, volume = {114}, year = {2017}, } @article{272, abstract = {Given a number field K/Q and a polynomial P ε Q [t], all of whose roots are Q, let X be the variety defined by the equation NK (x) = P (t). Combining additive combinatiorics with descent we show that the Brauer-Manin obstruction is the only obstruction to the Hesse principle and weak approximation on any smooth and projective model of X.}, author = {Browning, Timothy D and Matthiesen, Lilian}, journal = {Annales Scientifiques de l'Ecole Normale Superieure}, number = {6}, pages = {1383 -- 1446}, publisher = {Societe Mathematique de France}, title = {{Norm forms for arbitrary number fields as products of linear polynomials}}, doi = {10.24033/asens.2348}, volume = {50}, year = {2017}, } @inproceedings{274, abstract = {We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation.}, author = {Kolmogorov, Vladimir}, booktitle = {Proceedings of the 31st Conference On Learning Theory}, pages = {228--249}, publisher = {ML Research Press}, title = {{A faster approximation algorithm for the Gibbs partition function}}, volume = {75}, year = {2017}, } @inproceedings{313, abstract = {Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.}, author = {Camus, Nicolas and Yakaboylu, Enderalp and Fechner, Lutz and Klaiber, Michael and Laux, Martin and Mi, Yonghao and Hatsagortsyan, Karen and Pfeifer, Thomas and Keitel, Cristoph and Moshammer, Robert}, issn = {1742-6588}, location = {Kazan, Russian Federation}, number = {1}, publisher = {American Physical Society}, title = {{Experimental evidence for Wigner's tunneling time}}, doi = {10.1088/1742-6596/999/1/012004}, volume = {999}, 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}, }