Publications
71 results found
Schaub MT, Lehmann J, Yaliraki SN, et al., 2014, Structure of complex networks: Quantifying edge-to-edge relations by failure-induced flow redistribution, Network Science, Vol: 2, Pages: 66-89
The analysis of complex networks has so far revolved mainly around the role of nodes and communities of nodes. However, the dynamics of interconnected systems is often focalized on edge processes, and a dual edge-centric perspective can often prove more natural. Here we present graph-theoretical measures to quantify edge-to-edge relations inspired by the notion of flow redistribution induced by edge failures. Our measures, which are related to the pseudo-inverse of the Laplacian of the network, are global and reveal the dynamical interplay between the edges of a network, including potentially non-local interactions. Our framework also allows us to define the embeddedness of an edge, a measure of how strongly an edge features in the weighted cuts of the network. We showcase the general applicability of our edge-centric framework through analyses of the Iberian power grid, traffic flow in road networks, and the C. elegans neuronal network.
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- Citations: 35
Amor B, Yaliraki SN, Woscholski R, et al., 2014, Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection, MOLECULAR BIOSYSTEMS, Vol: 10, Pages: 2247-2258, ISSN: 1742-206X
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- Citations: 21
Delvenne J-C, Schaub MT, Yaliraki S, et al., 2013, The stability of a graph partition: A dynamics-based framework for community detection, Dynamics On and Of Complex Networks, Volume 2, Editors: Mukherjee, Choudhury, Peruani, Ganguly, Mitra, Publisher: Springer, Pages: 221-242, ISBN: 978-1-4614-6728-1
Recent years have seen a surge of interest in the analysis of complexnetworks, facilitated by the availability of relational data and theincreasingly powerful computational resources that can be employed for theiranalysis. Naturally, the study of real-world systems leads to highly complexnetworks and a current challenge is to extract intelligible, simplifieddescriptions from the network in terms of relevant subgraphs, which can provideinsight into the structure and function of the overall system. Sparked by seminal work by Newman and Girvan, an interesting line of researchhas been devoted to investigating modular community structure in networks,revitalising the classic problem of graph partitioning. However, modular or community structure in networks has notoriously evadedrigorous definition. The most accepted notion of community is perhaps that of agroup of elements which exhibit a stronger level of interaction withinthemselves than with the elements outside the community. This concept hasresulted in a plethora of computational methods and heuristics for communitydetection. Nevertheless a firm theoretical understanding of most of thesemethods, in terms of how they operate and what they are supposed to detect, isstill lacking to date. Here, we will develop a dynamical perspective towards community detectionenabling us to define a measure named the stability of a graph partition. Itwill be shown that a number of previously ad-hoc defined heuristics forcommunity detection can be seen as particular cases of our method providing uswith a dynamic reinterpretation of those measures. Our dynamics-based approachthus serves as a unifying framework to gain a deeper understanding of differentaspects and problems associated with community detection and allows us topropose new dynamically-inspired criteria for community structure.
Byrne SL, Yaliraki SN, Barahona M, et al., 2013, Stability analysis of protein kinases, 9th European-Biophysical-Societies-Association Congress, Publisher: SPRINGER, Pages: S174-S174, ISSN: 0175-7571
Georgiou PS, Barahona M, Yaliraki SN, et al., 2013, Ideal Memristors as Reciprocal Elements, Proceedings of the 20th IEEE International Conference on Electronics, Circuits, and Systems (ICECS), Pages: 301-304
Schaub MT, Delvenne J-C, Yaliraki SN, et al., 2012, Markov Dynamics as a Zooming Lens for Multiscale Community Detection: Non Clique-Like Communities and the Field-of-View Limit, PLOS ONE, Vol: 7, ISSN: 1932-6203
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- Citations: 91
Georgiou PS, Yaliraki SN, Drakakis EM, et al., 2012, Quantitative Measure of Hysteresis for Memristors through Explicit Dynamics, Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, Vol: 468, Pages: 2210-2229, ISSN: 1471-2946
Delmotte A, Tate EW, Yaliraki SN, et al., 2011, Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin-myosin light chain interaction, PHYSICAL BIOLOGY, Vol: 8, ISSN: 1478-3975
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models. We apply the method to four distinct conformations of myosin tail interacting protein, a protein from the molecular motor of the malaria parasite, and study properties that have been experimentally addressed such as the closing mechanism, the presence of conserved clusters, and the identification through computational mutational analysis of key residues for binding.
Krishnamoorthy N, Yacoub MH, Yaliraki SN, 2011, A computational modeling approach for enhancing self-assembly and biofunctionalisation of collagen biomimetic peptides, BIOMATERIALS, Vol: 32, Pages: 7275-7285, ISSN: 0142-9612
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- Citations: 26
Georgiou PS, Barahona M, Yaliraki SN, et al., 2011, Device Properties of Bernoulli Memristors, Proceedings of the IEEE, Vol: 100, Pages: 1-13, ISSN: 0018-9219
Georgiou PS, Barahona M, Yaliraki SN, et al., 2011, Device Properties of Bernoulli Memristors, Proceedings of the IEEE
Delvenne J-C, Yaliraki SN, Barahona M, 2010, Stability of graph communities across time scales, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: {12755-12760}-{12755-12760}, ISSN: 0027-8424
The complexity of biological, social, and engineering networks makes it desirable to find natural partitions into clusters ( or communities) that can provide insight into the structure of the overall system and even act as simplified functional descriptions. Although methods for community detection abound, there is a lack of consensus on how to quantify and rank the quality of partitions. We introduce here the stability of a partition, a measure of its quality as a community structure based on the clustered autocovariance of a dynamic Markov process taking place on the network. Because the stability has an intrinsic dependence on time scales of the graph, it allows us to compare and rank partitions at each time and also to establish the time spans over which partitions are optimal. Hence the Markov time acts effectively as an intrinsic resolution parameter that establishes a hierarchy of increasingly coarser communities. Our dynamical definition provides a unifying framework for several standard partitioning measures: modularity and normalized cut size can be interpreted as one-step time measures, whereas Fiedler’s spectral clustering emerges at long times. We apply our method to characterize the relevance of partitions over time for constructive and real networks, including hierarchical graphs and social networks, and use it to obtain reduced descriptions for atomic-level protein structures over different time scales.
Grima R, Yaliraki SN, Barahona M, 2010, Crowding-Induced Anisotropic Transport Modulates Reaction Kinetics in Nanoscale Porous Media, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 114, Pages: {5380-5385}-{5380-5385}, ISSN: 1520-6106
We quantify the emergence of persistent anisotropy in the diffusion of spherical tracer particles through a nanoscale porous medium composed of a uniform distribution of purely symmetric crowding particles. We focus on the interior of a biological cell as an example of such a medium and find that diffusion is highly directional for distances comparable to the size of some organelles. We use a geometrical procedure that avoids the standard orientational averaging to quantify the anisotropy of diffusive paths and show that the point source distributions are predominantly of prolate ellipsoidal shape as a result of local volume exclusion. This geometrical symmetry breaking strongly skews the distribution of kinetic rates of diffusion-limited reactions toward small values, leading to the result that, for short to intermediate times, almost 80% of the rates measured in an ensemble of heterogeneous media are smaller than the expected rate in an ideal homogeneous medium of similar excluded volume fraction. This crowding-induced modulation may have implications for our understanding and measurement of diffusion-controlled intracellular reaction kinetics and for experimental nanotechnology applications, such as nanoparticle-based bioimaging and drug delivery, where diffusion plays an important role.
Drakakis E, Yaliraki S, Barahona M, 2009, Memristors and Bernoulli Dynamics, Berkeley, IEEE CNNA, Publisher: IEEE, Pages: 1-6
Yaliraki SN, 2008, PHYS 220-Rigidity and graph clustering across time-scales: Coarsegraining biomolecular assemblies from the bottom-up, 235th American-Chemical-Society National Meeting, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Yaliraki SN, Barahona M, 2007, Chemistry across scales: from molecules to cells, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 365, Pages: {2921-2934}-{2921-2934}, ISSN: 1364-503X
Many important biological functions are strongly dependent on specific chemical interactions. Modelling how the physicochemical molecular details emerge at much larger scales is an active area of research, currently pursued with a variety of methods. We describe a series of theoretical and computational approaches that aim to derive bottom-up descriptions that capture the specificity that ensues from atomistic detail by extracting relevant features at the different scales. The multiscale models integrate the descriptions at different length and time scales by exploiting the idea of mechanical responses. The methodologies bring together concepts and tools developed in seemingly unrelated areas of mathematics such as algebraic geometry, model reduction, structural graph theory and non-convex optimization. We showcase the applicability of the framework with examples from protein engineering and enzyme catalysis, protein assembly, and with the description of lipid bilayers at different scales. Many challenges remain as it is clear that no single methodology will answer all questions in such multidimensional complex problems.
Grima R, Yaliraki SN, 2007, Brownian motion of an asymmetrical particle in a potential field, JOURNAL OF CHEMICAL PHYSICS, Vol: 127, ISSN: 0021-9606
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- Citations: 24
Costa JR, Yaliraki SN, 2006, Role of rigidity on the activity of proteinase inhibitors and their peptide mimics, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 110, Pages: 18981-18988, ISSN: 1520-6106
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- Citations: 13
Yaliraki SN, Longo G, Gale E, et al., 2006, Stability and phase separation in mixed self-assembled monolayers, JOURNAL OF CHEMICAL PHYSICS, Vol: 125, ISSN: 0021-9606
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- Citations: 10
Burke MG, Yaliraki SN, 2006, Exploring model energy and geometry surfaces using sum of squares decompositions, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Vol: 2, Pages: 575-587, ISSN: 1549-9618
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- Citations: 1
Hemberg M, Yaliraki SN, Barahona M, 2006, Stochastic kinetics of viral capsid assembly based on detailed protein structures, BIOPHYSICAL JOURNAL, Vol: 90, Pages: {3029-3042}-{3029-3042}, ISSN: 0006-3495
We present a generic computational framework for the simulation of viral capsid assembly which is quantitative and specific. Starting from PDB files containing atomic coordinates, the algorithm builds a coarse-grained description of protein oligomers based on graph rigidity. These reduced protein descriptions are used in an extended Gillespie algorithm to investigate the stochastic kinetics of the assembly process. The association rates are obtained from a diffusive Smoluchowski equation for rapid coagulation, modified to account for water shielding and protein structure. The dissociation rates are derived by interpreting the splitting of oligomers as a process of graph partitioning akin to the escape from a multidimensional well. This modular framework is quantitative yet computationally tractable, with a small number of physically motivated parameters. The methodology is illustrated using two different viruses which are shown to follow quantitatively different assembly pathways. We also show how in this model the quasi-stationary kinetics of assembly can be described as a Markovian cascading process, in which only a few intermediates and a small proportion of pathways are present. The observed pathways and intermediates can be related a posteriori to structural and energetic properties of the capsid oligomers.
Paramonov L, Yaliraki SN, 2005, The directional contact distance of two ellipsoids: Coarse-grained potentials for anisotropic interactions, JOURNAL OF CHEMICAL PHYSICS, Vol: 123, ISSN: 0021-9606
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- Citations: 58
Cubero D, Yaliraki SN, 2005, Formal derivation of dissipative particle dynamics from first principles, PHYSICAL REVIEW E, Vol: 72, ISSN: 1539-3755
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- Citations: 14
Cubero D, Yaliraki SN, 2005, Inhomogeneous multiscale dynamics in harmonic lattices, JOURNAL OF CHEMICAL PHYSICS, Vol: 122, ISSN: 0021-9606
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- Citations: 20
Burke MG, Woscholski R, Yaliraki SN, 2003, Differential hydrophobicity drives self-assembly in Huntington's disease, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 100, Pages: 13928-13933, ISSN: 0027-8424
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- Citations: 34
Yaliraki SN, 2003, Modeling molecular electronic devices: Challenges for electronic structure theory., 225th National Meeting of the American-Chemical-Society, Publisher: AMER CHEMICAL SOC, Pages: U519-U519, ISSN: 0065-7727
Tucknott R, Yaliraki SN, 2002, Aggregation properties of carbon nanotubes at interfaces, CHEMICAL PHYSICS, Vol: 281, Pages: 455-463, ISSN: 0301-0104
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- Citations: 27
Hänggi P, Ratner M, Yaliraki S, 2002, Processes in molecular wires -: Preface, CHEMICAL PHYSICS, Vol: 281, Pages: 111-111, ISSN: 0301-0104
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- Citations: 114
Diehl MR, Yaliraki SN, Beckman RA, et al., 2002, Self-assembled, deterministic carbon nanotube wiring networks, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, Vol: 41, Pages: {353+}-{353+}, ISSN: 1433-7851
Yaliraki SN, Ratner MA, 2002, Interplay of topology and chemical stability on the electronic transport of molecular junctions, New York, Molecular electronics 2000 conference, Kailua Kona, Hawaii, 10 - 14 December 2000, Publisher: New York Academy of Sciences, Pages: 153-162
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