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Journal articleWillis G, Pruessner G, 2017,
Spatio-temporal correlations in the Manna model in one, three and five dimensions
, International Journal of Modern Physics B, Vol: 32, ISSN: 0217-9792Although the paradigm of criticality is centered around spatial correlations and their anomalous scaling, not many studies of self-organized criticality (SOC) focus on spatial correlations. Often, integrated observables, such as avalanche size and duration, are used, not least as to avoid complications due to the unavoidable lack of translational invariance. The present work is a survey of spatio-temporal correlation functions in the Manna Model of SOC, measured numerically in detail in d
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Journal articleFallesen T, Roostalu J, Duellberg C, et al., 2017,
Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement
, Biophysical Journal, Vol: 113, Pages: 2055-2067, ISSN: 0006-3495Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.
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Journal articleClough JR, Evans TS, 2017,
Embedding graphs in Lorentzian spacetime
, PLOS ONE, Vol: 12, ISSN: 1932-6203Geometric approaches to network analysis combine simply defined models with great descriptive power. In this work we provide a method for embedding directed acyclic graphs (DAG) into Minkowski spacetime using Multidimensional scaling (MDS). First we generalise the classical MDS algorithm, defined only for metrics with a Riemannian signature, to manifolds of any metric signature. We then use this general method to develop an algorithm which exploits the causal structure of a DAG to assign space and time coordinates in a Minkowski spacetime to each vertex. As in the causal set approach to quantum gravity, causal connections in the discrete graph correspond to timelike separation in the continuous spacetime. The method is demonstrated by calculating embeddings for simple models of causal sets and random DAGs, as well as real citation networks. We find that the citation networks we test yield significantly more accurate embeddings that random DAGs of the same size. Finally we suggest a number of applications in citation analysis such as paper recommendation, identifying missing citations and fitting citation models to data using this geometric approach.
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Journal articleRochester C, Sartor A, Pruessner G, et al., 2017,
"One dimensional" double layer. The effect of size asymmetry of cations and anions on charge-storage in ultranarrow nanopores-an Ising model theory
, RUSSIAN JOURNAL OF ELECTROCHEMISTRY, Vol: 53, Pages: 1165-1170, ISSN: 1023-1935We develop a statistical mechanical theory of charge storage in quasi-single-file ionophilic nanopores with pure room temperature ionic liquid cations and anions of different size. The theory is mapped to an extension of the Ising model exploited earlier for the case of cations and anions of the same size. We calculate the differential capacitance and the stored energy density per unit surface area of the pore. Both show asymmetry in the dependence on electrode potential with respect to the potential of zero charge, related to the difference in the size of the ions, which will be interesting to investigate experimentally. It also approves the increase of charge storage capacity via obstructed charging, which in these systems emerges for charging nanopores with smaller ions.
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Journal articleGoto H, Viegas E, Jensen HJ, et al., 2017,
Appearance of unstable monopoly state caused by selective and concentrative mergers in business networks
, Scientific Reports, Vol: 7, ISSN: 2045-2322Recently, growth mechanism of firms in complex business networks became new targets of scientific study owing to increasing availability of high quality business firms’ data. Here, we paid attention to comprehensive data of M&A events for 40 years and derived empirical laws by applying methods and concepts of aggregation dynamics of aerosol physics. It is found that the probability of merger between bigger firms is bigger than that between smaller ones, and such tendency is enhancing year by year. We introduced a numerical model simulating the whole ecosystem of firms and showed that the system is already in an unstable monopoly state in which growth of middle sized firms are suppressed.
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Journal articleEvans TS, Rivers RJ, 2017,
Was Thebes necessary? Contingency in spatial modeling
, Frontiers in Digital Humanities, Vol: 4, ISSN: 2297-2668When data are poor, we resort to theory modeling. This is a two-step process. We have first to identify the appropriate type of model for the system under consideration and then to tailor it to the specifics of the case. To understand settlement formation, which is the concern of this article, this involves choosing not only input parameter values such as site separations but also input functions that characterizes the ease of travel between sites. Although the generic behavior of the model is understood, the details are not. Different choices will necessarily lead to different outputs (for identical inputs). We can only proceed if choices that are “close” give outcomes that are similar. Where there are local differences, it suggests that there was no compelling reason for one outcome rather than the other. If these differences are important for the historic record, we may interpret this as sensitivity to contingency. We re-examine the rise of Greek city-states as first formulated by Rihll and Wilson in 1979, initially using the same “retail” gravity model. We suggest that, although cities like Athens owe their position to a combination of geography and proximity to other sites, the rise of Thebes is the most contingent, whose success reflects social forces outside the grasp of simple network modeling.
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Book chapterAchurra Gonzalez PE, Angeloudis P, Zavitsas K, et al., 2017,
Attacker-defender assessment of vulnerability in maritime logistics corridors
, Advances in Shipping Data Analysis and Modeling. Tracking and Mapping Maritime Flows in the Age of Big Data, Editors: Ducruet, Publisher: Routledge -
Journal articleWei N, Pruessner G, 2016,
Comment on “Finite-size scaling of survival probability in branching processes”
, Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, Vol: 94, ISSN: 2470-0045R. Garcia-Millan et al. [Phys. Rev. E 91, 042122 (2015)] reported a universal finite-size scaling form of the survival probability in discrete time branching processes. In this comment, we generalize the argument to a wide range of continuous time branching processes. Owing to the continuity, the resulting differential (rather than difference) equations can be solved in closed form, rendering some approximations by R. Garcia-Millan et al. superfluous, although we work along similar lines. In the case of binary branching, our results are in fact exact. Demonstrating that discrete time and continuous time models have their leading order asymptotics in common, raises the question to what extent corrections are identical.
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Journal articleLee CF, Pruessner G, 2016,
Percolation mechanism drives actin gels to the critically connected state
, Physical Review E, Vol: 93, ISSN: 1539-3755Cell motility and tissue morphogenesis depend crucially on the dynamic remodelling of actomyosinnetworks. An actomyosin network consists of an actin polymer network connected by crosslinkerproteins and motor protein myosins that generate internal stresses on the network. A recent discoveryshows that for a range of experimental parameters, actomyosin networks contract to clusterswith a power-law size distribution [Alvarado J. et al. (2013) Nature Physics 9 591]. Here, weargue that actomyosin networks can exhibit robust critical signature without fine-tuning becausethe dynamics of the system can be mapped onto a modified version of percolation with trapping(PT), which is known to show critical behaviour belonging to the static percolation universalityclass without the need of fine-tuning of a control parameter. We further employ our PT model togenerate experimentally testable predictions.
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Journal articlePruessner G, Lee CF, 2016,
Comment on "Anomalous Discontinuity at the Percolation Critical Point of Active Gels"
, Physical Review Letters, Vol: 116, ISSN: 1079-7114
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