| 1. |
- Lee, Sang Hoon, 1982-, et al.
(författare)
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Phase-shift inversion in oscillator systems with periodically switching couplings
- 2012
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American Physical Society. - 1539-3755 .- 1550-2376. ; 85:2, s. 027202-
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Tidskriftsartikel (refereegranskat)abstract
- A system's response to external periodic changes can provide crucial information about its dynamical properties. We investigate the synchronization transition, an archetypical example of a dynamic phase transition, in the framework of such a temporal response. The Kuramoto model under periodically switching interactions has the same type of phase transition as the original mean-field model. Furthermore, we see that the signature of the synchronization transition appears in the relative delay of the order parameter with respect to the phase of oscillating interactions as well. Specifically, the phase shift becomes significantly larger as the system gets closer to the phase transition, so that the order parameter at the minimum interaction density can even be larger than that at the maximum interaction density, counterintuitively. We argue that this phase-shift inversion is caused by the diverging relaxation time, in a similar way to the resonance near the critical point in the kinetic Ising model. Our result, based on exhaustive simulations on globally coupled systems as well as scale-free networks, shows that an oscillator system's phase transition can be manifested in the temporal response to the topological dynamics of the underlying connection structure.
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| 2. |
- Baek, Yongjoo, et al.
(författare)
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Market behavior and performance of different strategy evaluation schemes
- 2010
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American Physical Society. - 1063-651X .- 1095-3787. ; 82:026109
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Tidskriftsartikel (refereegranskat)abstract
- Strategy evaluation schemes are a crucial factor in any agent-based market model, as they determine the agents’ strategy preferences and consequently their behavioral pattern. This study investigates how the strategy evaluation schemes adopted by agents affect their performance in conjunction with the market circumstances. We observe the performance of three strategy evaluation schemes, the history-dependent wealth game, the trend-opposing minority game, and the trend-following majority game, in a stock market where the price is exogenously determined. The price is either directly adopted from the real stock market indices or generated with a Markov chain of order ≤2. Each scheme’s success is quantified by average wealth accumulated by the traders equipped with the scheme. The wealth game, as it learns from the history, shows relatively good performance unless the market is highly unpredictable. The majority game is successful in a trendy market dominated by long periods of sustained price increase or decrease. On the other hand, the minority game is suitable for a market with persistent zigzag price patterns. We also discuss the consequence of implementing finite memory in the scoring processes of strategies. Our findings suggest under which market circumstances each evaluation scheme is appropriate for modeling the behavior of real market traders.
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| 3. |
- Bernenko, Dolores, et al.
(författare)
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Exploring 3D community inconsistency in human chromosome contact networks
- 2023
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Ingår i: Journal of physics. Complexity. - : Institute of Physics (IOP). - 2632-072X. ; 4:3
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Researchers developed chromosome capture methods such as Hi-C to better understand DNA's 3D folding in nuclei. The Hi-C method captures contact frequencies between DNA segment pairs across the genome. When analyzing Hi-C data sets, it is common to group these pairs using standard bioinformatics methods (e.g., PCA). Other approaches handle Hi-C data as weighted networks, where connected node represent DNA segments in 3D proximity. In this representation, one can leverage community detection techniques developed in complex network theory to group nodes into mesoscale communities containing similar connection patterns. While there are several successful attempts to analyze Hi-C data in this way, it is common to report and study the most typical community structure. But in reality, there are often several valid candidates. Therefore, depending on algorithm design, different community detection methods focusing on slightly different connectivity features may have differing views on the ideal node groupings. In fact, even the same community detection method may yield different results if using a stochastic algorithm. This ambiguity is fundamental to community detection and shared by most complex networks whenever interactions span all scales in the network. This is known as community inconsistency. This paper explores this inconsistency of 3D communities in Hi-C data for all human chromosomes. We base our analysis on two inconsistency metrics, one local and one global, and quantify the network scales where the community separation is most variable. For example, we find that TADs are less reliable than A/B compartments and that nodes with highly variable node-community memberships are associated with open chromatin. Overall, our study provides a helpful framework for data-driven researchers and increases awareness of some inherent challenges when clustering Hi-C data into 3D communities.
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| 4. |
- Bernenko, Dolores, et al.
(författare)
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Mapping the semi-nested community structure of 3D chromosome contact networks
- 2022
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Mammalian DNA folds into 3D structures that facilitate and regulate genetic processes such as transcription, DNA repair, and epigenetics. Several insights derive from chromosome capture methods, such as Hi-C, which allow researchers to construct contact maps depicting 3D interactions among all DNA segment pairs. These maps show a complex cross-scale organization spanning megabase-pair compartments to short-ranged DNA loops. To better understand the organizing principles, several groups analyzed Hi-C data assuming a Russian-doll-like nested hierarchy where DNA regions of similar sizes merge into larger and larger structures. Apart from being a simple and appealing description, this model explains, e.g., the omnipresent chequerboard pattern seen in Hi-C maps, known as A/B compartments, and foreshadows the co-localization of some functionally similar DNA regions. However, while successful, this model is incompatible with the two competing mechanisms that seem to shape a significant part of the chromosomes’ 3D organization: loop extrusion and phase separation. This paper aims to map out the chromosome’s actual folding hierarchy from empirical data. To this end, we take advantage of Hi-C experiments and treat the measured DNA-DNA interactions as a weighted network. From such a network, we extract 3D communities using the generalized Louvain algorithm. This algorithm has a resolution parameter that allows us to scan seamlessly through the community size spectrum, from A/B compartments to topologically associated domains (TADs). By constructing a hierarchical tree connecting these communities, we find that chromosomes are more complex than a perfect hierarchy. Analyzing how communities nest relative to a simple folding model, we found that chromosomes exhibit a significant portion of nested and non-nested community pairs alongside considerable randomness. In addition, by examining nesting and chromatin types, we discovered that nested parts are often associated with active chromatin. These results highlight that crossscale relationships will be essential components in models aiming to reach a deep understanding of the causal mechanisms of chromosome folding.
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| 5. |
- Holme, Petter, et al.
(författare)
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Atmospheric Reaction Systems as Null-Models to Identify Structural Traces of Evolution in Metabolism
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:5, s. e19759-
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Tidskriftsartikel (refereegranskat)abstract
- The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.
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| 6. |
- Lee, Sang Hoon, 1982-, et al.
(författare)
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Critical behavior of the Ising model in annealed scale-free networks
- 2009
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 80:051127
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Tidskriftsartikel (refereegranskat)abstract
- We study the critical behavior of the Ising model in annealed scale-free (SF) networks of finite system size with forced upper cutoff in degree. By mapping the model onto the weighted fully connected Ising model, we derive analytic results for the finite-size scaling (FSS) near the phase transition, characterized by the cutoff-dependent two-parameter scaling with four distinct scaling regimes, in highly heterogeneous networks. These results are essentially the same as those found for the nonequilibrium contact process in annealed SF networks, except for an additional complication due to the trivial critical point shift in finite systems. The discrepancy of the FSS theories between annealed and quenched SF networks still remains in the equilibrium Ising model, like some other nonequilibrium models. All of our analytic results are confirmed reasonably well by numerical simulations.
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| 7. |
- Lee, Sang Hoon, 1982-, et al.
(författare)
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Effects of substrate network topologies on competition dynamics
- 2006
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 74:026118
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Tidskriftsartikel (refereegranskat)abstract
- We study a competition dynamics, based on the minority game, endowed with various substrate network structures. We observe the effects of the network topologies by investigating the volatility of the system and the structure of follower networks. The topology of substrate structures significantly influences the system efficiency represented by the volatility and such substrate networks are shown to amplify the herding effect and cause inefficiency in most cases. The follower networks emerging from the leadership structure show a power-law incoming degree distribution. This study shows the emergence of scale-free structures of leadership in the minority game and the effects of the interaction among players on the networked version of the game.
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| 8. |
- Lee, Sang Hoon, 1982-, et al.
(författare)
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Exploring maps with greedy navigators
- 2012
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 108:12, s. 8701-
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Tidskriftsartikel (refereegranskat)abstract
- During the last decade of network research focusing on structural and dynamical properties of networks, the role of network users has been more or less underestimated from the bird’s-eye view of global perspective. In this era of global positioning system equipped smartphones, however, a user’s ability to access local geometric information and find efficient pathways on networks plays a crucial role, rather than the globally optimal pathways. We present a simple greedy spatial navigation strategy as a probe to explore spatial networks. These greedy navigators use directional information in every move they take, without being trapped in a dead end based on their memory about previous routes. We suggest that the centralities measures have to be modified to incorporate the navigators’ behavior, and present the intriguing effect of navigators’ greediness where removing some edges may actually enhance the routing efficiency, which is reminiscent of Braess’s paradox. In addition, using samples of road structures in large cities around the world, it is shown that the navigability measure we define reflects unique structural properties, which are not easy to predict from other topological characteristics. In this respect, we believe that our routing scheme significantly moves the routing problem on networks one step closer to reality, incorporating the inevitable incompleteness of navigators’ information.
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| 9. |
- Lee, Sang Hoon, 1982-
(författare)
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Finite-size scaling in random K-satisfiability problems
- 2010
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 82:061109
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Tidskriftsartikel (refereegranskat)abstract
- We provide a comprehensive view of various phase transitions in random K-satisfiability problems solved by stochastic-local-search algorithms. In particular, we focus on the finite-size scaling (FSS) exponent, which is mathematically important and practically useful in analyzing finite systems. Using the FSS theory of nonequilibrium absorbing phase transitions, we show that the density of unsatisfied clauses clearly indicates the transition from the solvable (absorbing) phase to the unsolvable (active) phase as varying the noise parameter and the density of constraints. Based on the solution clustering (percolation-type) argument, we conjecture two possible values of the FSS exponent, which are confirmed reasonably well in numerical simulations for 2≤K≤3.
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| 10. |
- Lee, Sang Hoon, 1982-, et al.
(författare)
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Global organization of protein complexome in the yeast Saccharomyces cerevisiae
- 2011
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Ingår i: BMC Systems Biology. - : BioMed Central. - 1752-0509. ; 5:126, s. 15-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the bipartite network and its projections, where the complexes and proteins are its two distinct components. Compared to conventional protein-protein interaction networks, the networks from the protein complexes show more homogeneous structures than those of the binary protein interactions, implying the formation of complexes that cause a relatively more uniform number of interaction partners. In addition, we suggest a new optimization method to determine the abundance and function of protein complexes, based on the information of their global organization. Estimating abundance and biological functions is of great importance for many researches, by providing a quantitative description of cell behaviors, instead of just a "catalogues" of the lists of protein interactions.Results: With our new optimization method, we present genome-wide assignments of abundance and biological functions for complexes, as well as previously unknown abundance and functions of proteins, which can provide significant information for further investigations in proteomics. It is strongly supported by a number of biologically relevant examples, such as the relationship between the cytoskeleton proteins and signal transduction and the metabolic enzyme Eno2's involvement in the cell division process.Conclusions: We believe that our methods and findings are applicable not only to the specific area of proteomics, but also to much broader areas of systems biology with the concept of optimization principle.
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