@article{7765, abstract = {We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior.}, author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {22}, publisher = {American Physical Society}, title = {{The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior}}, doi = {10.1103/physrevlett.114.225501}, volume = {114}, year = {2015}, } @article{7766, abstract = {We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached.}, author = {Sussman, Daniel M. and Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.}, issn = {1744-683X}, journal = {Soft Matter}, number = {14}, pages = {2745--2751}, publisher = {Royal Society of Chemistry}, title = {{Disordered surface vibrations in jammed sphere packings}}, doi = {10.1039/c4sm02905d}, volume = {11}, year = {2015}, } @article{7767, abstract = {We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength of these interactions leads to migrating swarms, rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble motion, alternating between migration and either rotating or jammed states. Interestingly, although a migrating swarm moves slower than an individual particle, the diffusion constant can be up to three orders of magnitude larger, suggesting that collective motion can be highly advantageous, for example, when searching for food.}, author = {van Drongelen, Ruben and Pal, Anshuman and Goodrich, Carl Peter and Idema, Timon}, issn = {1539-3755}, journal = {Physical Review E}, number = {3}, publisher = {American Physical Society}, title = {{Collective dynamics of soft active particles}}, doi = {10.1103/physreve.91.032706}, volume = {91}, year = {2015}, } @unpublished{7779, abstract = {The fact that a disordered material is not constrained in its properties in the same way as a crystal presents significant and yet largely untapped potential for novel material design. However, unlike their crystalline counterparts, disordered solids are not well understood. One of the primary obstacles is the lack of a theoretical framework for thinking about disorder and its relation to mechanical properties. To this end, we study an idealized system of frictionless athermal soft spheres that, when compressed, undergoes a jamming phase transition with diverging length scales and clean power-law signatures. This critical point is the cornerstone of a much larger "jamming scenario" that has the potential to provide the essential theoretical foundation necessary for a unified understanding of the mechanics of disordered solids. We begin by showing that jammed sphere packings have a valid linear regime despite the presence of "contact nonlinearities." We then investigate the critical nature of the transition, focusing on diverging length scales and finite-size effects. Next, we argue that jamming plays the same role for disordered solids as the perfect crystal plays for crystalline solids. Not only can it be considered an idealized starting point for understanding disordered materials, but it can even influence systems that have a relatively high amount of crystalline order. The behavior of solids can thus be thought of as existing on a spectrum, with the perfect crystal and the jamming transition at opposing ends. Finally, we introduce a new principle wherein the contribution of an individual bond to one global property is independent of its contribution to another. This principle allows the different global responses of a disordered system to be manipulated independently and provides a great deal of flexibility in designing materials with unique, textured and tunable properties.}, author = {Goodrich, Carl Peter}, booktitle = {arXiv}, title = {{Unearthing the anticrystal: Criticality in the linear response of disordered solids}}, doi = {10.48550/arXiv.1510.08820}, year = {2015}, } @inproceedings{778, abstract = {Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead.}, author = {Alistarh, Dan-Adrian and Kopinsky, Justin and Kuznetsov, Petr and Ravi, Srivatsan and Shavit, Nir}, pages = {185 -- 199}, publisher = {Springer}, title = {{Inherent limitations of hybrid transactional memory}}, doi = {10.1007/978-3-662-48653-5_13}, volume = {9363}, year = {2015}, } @inproceedings{779, abstract = {The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU, are either prohibitively expensive or require significant programming expertise, to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated. In this paper, we take a new approach to concurrent memory reclamation: instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads. Initial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.}, author = {Alistarh, Dan-Adrian and Matveev, Alexander and Leiserson, William and Shavit, Nir}, pages = {123 -- 132}, publisher = {ACM}, title = {{ThreadScan: Automatic and scalable memory reclamation}}, doi = {10.1145/2755573.2755600}, volume = {2015-June}, year = {2015}, } @inproceedings{781, abstract = {Population protocols, roughly defined as systems consisting of large numbers of simple identical agents, interacting at random and updating their state following simple rules, are an important research topic at the intersection of distributed computing and biology. One of the fundamental tasks that a population protocol may solve is majority: each node starts in one of two states; the goal is for all nodes to reach a correct consensus on which of the two states was initially the majority. Despite considerable research effort, known protocols for this problem are either exact but slow (taking linear parallel time to converge), or fast but approximate (with non-zero probability of error). In this paper, we show that this trade-off between preciasion and speed is not inherent. We present a new protocol called Average and Conquer (AVC) that solves majority ex-actly in expected parallel convergence time O(log n/(sε) + log n log s), where n is the number of nodes, εn is the initial node advantage of the majority state, and s = Ω(log n log log n) is the number of states the protocol employs. This shows that the majority problem can be solved exactly in time poly-logarithmic in n, provided that the memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case of four memory states per node, and a lower bound of Ω(logn) parallel time for protocols using any number of memory states per node.per node, and a lower bound of (log n) parallel time for protocols using any number of memory states per node.}, author = {Alistarh, Dan-Adrian and Gelashvili, Rati and Vojnović, Milan}, pages = {47 -- 56}, publisher = {ACM}, title = {{Fast and exact majority in population protocols}}, doi = {10.1145/2767386.2767429}, volume = {2015-July}, year = {2015}, } @inproceedings{784, abstract = {We demonstrate an optical switch design that can scale up to a thousand ports with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our design uses a broadcast and select architecture, based on a passive star coupler and fast tunable transceivers. In addition we employ time division multiplexing to achieve very low switching latency. Our demo shows the feasibility of the switch data plane using a small testbed, comprising two transmitters and a receiver, connected through a star coupler.}, author = {Alistarh, Dan-Adrian and Ballani, Hitesh and Costa, Paolo and Funnell, Adam and Benjamin, Joshua and Watts, Philip and Thomsen, Benn}, isbn = {978-1-4503-3542-3}, location = {London, United Kindgdom}, pages = {367 -- 368}, publisher = {ACM}, title = {{A high-radix, low-latency optical switch for data centers}}, doi = {10.1145/2785956.2790035}, year = {2015}, } @article{802, abstract = {Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.}, author = {Engel, Jakob and Schmalhorst, Philipp S and Kruger, Anke and Muller, Christina and Buettner, Falk and Routier, Françoise}, journal = {Glycobiology}, number = {12}, pages = {1423 -- 1430}, publisher = {Oxford University Press}, title = {{Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis}}, doi = {10.1093/glycob/cwv059}, volume = {25}, year = {2015}, } @article{8242, author = {Einhorn, Lukas and Fazekas, Judit and Muhr, Martina and Schoos, Alexandra and Oida, Kumiko and Singer, Josef and Panakova, Lucia and Manzano-Szalai, Krisztina and Jensen-Jarolim, Erika}, issn = {0091-6749}, journal = {Journal of Allergy and Clinical Immunology}, number = {2}, publisher = {Elsevier}, title = {{Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients}}, doi = {10.1016/j.jaci.2014.12.1263}, volume = {135}, year = {2015}, } @article{8456, abstract = {The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.}, author = {Ma, Peixiang and Xue, Yi and Coquelle, Nicolas and Haller, Jens D. and Yuwen, Tairan and Ayala, Isabel and Mikhailovskii, Oleg and Willbold, Dieter and Colletier, Jacques-Philippe and Skrynnikov, Nikolai R. and Schanda, Paul}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Observing the overall rocking motion of a protein in a crystal}}, doi = {10.1038/ncomms9361}, volume = {6}, year = {2015}, } @article{8457, abstract = {We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed.}, author = {Ma, Peixiang and Schanda, Paul}, isbn = {9780470034590}, journal = {eMagRes}, number = {3}, pages = {699--708}, publisher = {Wiley}, title = {{Conformational exchange processes in biological systems: Detection by solid-state NMR}}, doi = {10.1002/9780470034590.emrstm1418}, volume = {4}, year = {2015}, } @article{848, abstract = {The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.}, author = {Usmanova, Dinara and Ferretti, Luca and Povolotskaya, Inna and Vlasov, Peter and Kondrashov, Fyodor}, journal = {Molecular Biology and Evolution}, number = {2}, pages = {542 -- 554}, publisher = {Oxford University Press}, title = {{A model of substitution trajectories in sequence space and long-term protein evolution}}, doi = {10.1093/molbev/msu318}, volume = {32}, year = {2015}, } @article{8495, abstract = {In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.}, author = {Bounemoura, Abed and Kaloshin, Vadim}, issn = {0002-9939}, journal = {Proceedings of the American Mathematical Society}, number = {4}, pages = {1553--1560}, publisher = {American Mathematical Society}, title = {{A note on micro-instability for Hamiltonian systems close to integrable}}, doi = {10.1090/proc/12796}, volume = {144}, year = {2015}, } @article{8498, abstract = {In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\varepsilon H_1(\theta,p,t),\quad \ \theta\in {\mathbb T}^2,\ p\in B^2,\ t\in {\mathbb T}={\mathbb R}/{\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\mathbb T}^2 \times B^2 \times {\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\mathbb T}^2 \times B^2 \times {\mathbb T}$ . Our proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7].}, author = {Kaloshin, Vadim and Zhang, K}, issn = {0951-7715}, journal = {Nonlinearity}, keywords = {Mathematical Physics, General Physics and Astronomy, Applied Mathematics, Statistical and Nonlinear Physics}, number = {8}, pages = {2699--2720}, publisher = {IOP Publishing}, title = {{Arnold diffusion for smooth convex systems of two and a half degrees of freedom}}, doi = {10.1088/0951-7715/28/8/2699}, volume = {28}, year = {2015}, } @article{8499, abstract = {We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time. We establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0