Publications
103 results found
Staniczenko PPA, Lewis OT, Jones NS, et al., 2010, Structural dynamics and robustness of food webs, Ecology Letters, Vol: 13, Pages: 891-899, ISSN: 1461-0248
Ecology Letters (2010) 13: 891–899 Abstract Food web structure plays an important role when determining robustness to cascading secondary extinctions. However, existing food web models do not take into account likely changes in trophic interactions (‘rewiring’) following species loss. We investigated structural dynamics in 12 empirically documented food webs by simulating primary species loss using three realistic removal criteria, and measured robustness in terms of subsequent secondary extinctions. In our model, novel trophic interactions can be established between predators and food items not previously consumed following the loss of competing predator species. By considering the increase in robustness conferred through rewiring, we identify a new category of species – overlap species – which promote robustness as shown by comparing simulations incorporating structural dynamics to those with static topologies. The fraction of overlap species in a food web is highly correlated with this increase in robustness; whereas species richness and connectance are uncorrelated with increased robustness. Our findings underline the importance of compensatory mechanisms that may buffer ecosystems against environmental change, and highlight the likely role of particular species that are expected to facilitate this buffering.
Xue Q, Jones NS, Leake MC, 2010, A GENERAL APPROACH FOR SEGMENTING ELONGATED AND STUBBY BIOLOGICAL OBJECTS: EXTENDING A CHORD LENGTH TRANSFORM WITH THE RADON TRANSFORM, 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Publisher: IEEE, Pages: 161-164, ISSN: 1945-7928
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Little MA, Jones NS, 2010, Sparse Bayesian step-filtering for high-throughput analysis of molecular machine dynamics, Acoustics Speech and Signal Processing (ICASSP), 2010 IEEE International Conference on, Pages: 4162-4165, ISSN: 1520-6149
Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-like motion of these machines with time series from novel experimental assays has recently become possible. These time series are corrupted by molecular and experimental noise that requires removal, but classical signal processing is of limited use for recovering such step-like dynamics. This paper reports simple, novel Bayesian filters that are robust to step-like dynamics in noise, and introduce an L<sub>1</sub>-regularized, global filter whose sparse solution can be rapidly obtained by standard convex optimization methods. We show these techniques outperforming classical filters on simulated time series in terms of their ability to accurately recover the underlying step dynamics. To show the techniques in action, we extract step-like speed transitions from Rhodobacter sphaeroides flagellar motor time series.
Fenn DJ, Porter MA, McDonald M, et al., 2009, Dynamic communities in multichannel data: An application to the foreign exchange market during the 2007--2008 credit crisis, Chaos, Vol: 19, Pages: 033119-8
Smith DMD, Onnela J, Jones NS, 2009, Master-equation analysis of accelerating networks, PRE, Vol: 79
Staniczenko PPA, Lee CF, Jones NS, 2009, Rapidly detecting disorder in rhythmic biological signals: A spectral entropy measure to identify cardiac arrhythmias, Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol: 79, Pages: 011915-011915
Jones NS, 2008, Using the Memories of Multiscale Machines to Characterize Complex Systems, PRL, Vol: 100
Jones NS, Masanes L, 2008, Key Distillation and the Secret-Bit Fraction, Information Theory, IEEE Transactions on, Vol: 54, Pages: 680-691, ISSN: 0018-9448
We consider distillation of secret bits from partially secret noisy correlations P<sub>ABE</sub>, shared between two honest parties and an eavesdropper. The most studied distillation scenario consists of joint operations on a large number of copies of the distribution (P<sub>ABE</sub>)<sup>N</sup>, assisted with public communication. Here we consider distillation with only one copy of the distribution, and instead of rates, the ¿quality¿ of the distilled secret bits is optimized, where the ¿quality¿ is quantified by the secret-bit fraction of the result. The secret-bit fraction of a binary distribution is the proportion which constitutes a secret bit between Alice and Bob. With local operations and public communication the maximal extractable secret-bit fraction from a distribution P<sub>ABE</sub> is found, and is denoted by ¿[P<sub>ABE</sub>]. This quantity is shown to be nonincreasing under local operations and public communication, and nondecreasing under eavesdropper's local operations: ¿ is a secrecy monotone. It is shown that if ¿ [P<sub>ABE</sub>] > 1/2 then P<sub>ABE</sub> is distillable, thus providing a sufficient condition for distillability. A simple expression for ¿[P<sub>ABE</sub>] is found when the eavesdropper is decoupled, and when the honest parties' information is binary and the local operations are reversible. Intriguingly, for general distributions the (optimal) operation requires local degradation of the data.
Jones NS, Stace TM, 2006, Photon frequency-mode matching using acousto-optic frequency beam splitters, PRA, Vol: 73
Jones NS, Masanes L, 2005, Interconversion of nonlocal correlations, PRA, Vol: 72
Gutin G, Jones N, Rafiey A, et al., 2005, Mediated digraphs and quantum nonlocality, Discrete Applied Mathematics, Vol: 150, Pages: 41-50, ISSN: 0166-218X
A digraph D = ( V , A ) is mediated if for each pair x , y of distinct vertices of D , either xy ∈ A or yx ∈ A or there is a vertex z such that both xz , yz ∈ A . For a digraph D , Δ - ( D ) is the maximum in-degree of a vertex in D . The n th mediation number μ ( n ) is the minimum of Δ - ( D ) over all mediated digraphs on n vertices. Mediated digraphs and μ ( n ) are of interest in the study of quantum nonlocality. We obtain a lower bound f ( n ) for μ ( n ) and determine infinite sequences of values of n for which μ ( n ) = f ( n ) and μ ( n ) > f ( n ) , respectively. We derive upper bounds for μ ( n ) and prove that μ ( n ) = f ( n ) ( 1 + o ( 1 ) ) . We conjecture that there is a constant c such that μ ( n ) ⩽ f ( n ) + c . Methods and results of design theory and number theory are used.
Jones NS, Linden N, Massar S, 2005, Extent of multiparticle quantum nonlocality, Physical Review A, Vol: 71, Pages: 042329-042329, ISSN: 1050-2947
Jones NS, Linden N, 2005, Parts of quantum states, Physical Review A, Vol: 71, Pages: 012324-012324, ISSN: 1050-2947
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