arXiv subjects

Hawoong Jeong

Publications and source records attributed to Hawoong Jeong.

At least 73 records · Page 4Linked to original sources

arXiv2011

Global organization of protein complexome in the yeast Saccharomyces cerevisiae

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. 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. 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.

q-bio.QM↗

arXiv2011

Map equation for link community

Community structure exists in many real-world networks and has been reported being related to several functional properties of the networks. The conventional approach was partitioning nodes into communities, while some recent studies start partitioning links instead of nodes to find overlapping communities of nodes efficiently. We extended the map equation method, which was originally developed for node communities, to find link communities in networks. This method is tested on various kinds of networks and compared with the metadata of the networks, and the results show that our method can identify the overlapping role of nodes effectively. The advantage of this method is that the node community scheme and link community scheme can be compared quantitatively by measuring the unknown information left in the networks besides the community structure. It can be used to decide quantitatively whether or not the link community scheme should be used instead of the node community scheme. Furthermore, this method can be easily extended to the directed and weighted networks since it is based on the random walk.

physics.soc-ph↗

arXiv2010

Finite-size scaling in random $K$-satisfiability problems

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 $2\le K \le 3$.

cond-mat.stat-mech↗

arXiv2010

Market behavior and performance of different strategy evaluation schemes

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 $\le 2$. 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 zig-zag 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.

q-fin.PM↗

arXiv2010

Googling Social Interactions: Web Search Engine Based Social Network Construction

Social network analysis has long been an untiring topic of sociology. However, until the era of information technology, the availability of data, mainly collected by the traditional method of personal survey, was highly limited and prevented large-scale analysis. Recently, the exploding amount of automatically generated data has completely changed the pattern of research. For instance, the enormous amount of data from so-called high-throughput biological experiments has introduced a systematic or network viewpoint to traditional biology. Then, is "high-throughput" sociological data generation possible? Google, which has become one of the most influential symbols of the new Internet paradigm within the last ten years, might provide torrents of data sources for such study in this (now and forthcoming) digital era. We investigate social networks between people by extracting information on the Web and introduce new tools of analysis of such networks in the context of statistical physics of complex systems or socio-physics. As a concrete and illustrative example, the members of the 109th United States Senate are analyzed and it is demonstrated that the methods of construction and analysis are applicable to various other weighted networks.

physics.soc-ph↗

arXiv2009

Critical behavior of the Ising model in annealed scale-free networks

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.

cond-mat.stat-mech↗

arXiv2009

Statistical properties of sampled networks

We study the statistical properties of the sampled scale-free networks, deeply related to the proper identification of various real-world networks. We exploit three methods of sampling and investigate the topological properties such as degree and betweenness centrality distribution, average path length, assortativity, and clustering coefficient of sampled networks compared with those of original networks. It is found that the quantities related to those properties in sampled networks appear to be estimated quite differently for each sampling method. We explain why such a biased estimation of quantities would emerge from the sampling procedure and give appropriate criteria for each sampling method to prevent the quantities from being overestimated or underestimated.

cond-mat.dis-nn↗

arXiv2009

LinkRank: Finding communities in directed networks

To identify communities in directed networks, we propose a generalized form of modularity in directed networks by introducing a new quantity LinkRank, which can be considered as the PageRank of links. This generalization is consistent with the original modularity in undirected networks and the modularity optimization methods developed for undirected networks can be directly applied to directed networks by optimizing our new modularity. Also, a model network, which can be used as a benchmark network in further community studies, is proposed to verify our method. Our method is supposed to find communities effectively in citation- or reference-based directed networks.

physics.soc-ph↗

arXiv2009

Consistent Community Identification in Complex Networks

We have found that known community identification algorithms produce inconsistent communities when the node ordering changes at input. We propose two metrics to quantify the level of consistency across multiple runs of an algorithm: pairwise membership probability and consistency. Based on these two metrics, we address the consistency problem without compromising the modularity. Our solution uses pairwise membership probabilities as link weights and generates consistent communities within six or fewer cycles. It offers a new tool in the study of community structures and their evolutions.

physics.soc-ph↗

arXiv2009

Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells

Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell proliferation and apoptosis, development, immune responses, and pathogenesis. One of the major types of glycans, N-linked glycans, is formed by sequential attachments of monosaccharides to proteins by a limited number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thereby generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigated the large-scale organization of such N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation pathways are extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis. This unique structural property allows the glycan production between modules to be controlled by the upstream region. Although the enzymes act on multiple glycan substrates, indicating cross-talk between modules, the impact of the cross-talk on the module-specific enhancement of glycan synthesis may be confined within a moderate range by transcription-level control. The findings of the present study provide experimentally-testable predictions for glycosylation processes, and may be applicable to therapeutic glycoprotein engineering.

q-bio.MN↗

arXiv2009

Anomalous Scaling Behavior in Polymer Thin Film Growth by Vapor Deposition

As a first step to understand anomalous kinetic roughening with multifractality in recent experiments of the vapor deposition polymerization (VDP) growth, we study a simple toy model of the VDP growth in a (1+1)-dimensional lattice, along with monomer diffusion, polymer nucleation, limited active end bonding, and shadowing effects. Using extensive numerical simulations, we observe that the global roughness exponent is different from the local one. It is argued that such anomalies in VDP growth are attributed to the instability induced by the nonlocal shadowing effects on active ends of polymers. As varying the ratio of diffusion coefficient to the deposition rate by cosine flux, we also discuss the role of diffusion in kinetic roughening of the polymer thin film growth, which is quite different from that of the metal or semiconductor film growth. Finally, we suggest its (2+1)-dimensional version, which can be directly compared with experimental results.

cond-mat.stat-mech↗

arXiv2008

The Price of Anarchy in Transportation Networks: Efficiency and Optimality Control

Uncoordinated individuals in human society pursuing their personally optimal strategies do not always achieve the social optimum, the most beneficial state to the society as a whole. Instead, strategies form Nash equilibria which are often socially suboptimal. Society, therefore, has to pay a price of anarchy for the lack of coordination among its members. Here we assess this price of anarchy by analyzing the travel times in road networks of several major cities. Our simulation shows that uncoordinated drivers possibly waste a considerable amount of their travel time. Counterintuitively,simply blocking certain streets can partially improve the traffic conditions. We analyze various complex networks and discuss the possibility of similar paradoxes in physics.

physics.soc-ph↗

arXiv2008

Korean Family Name Distribution in the Past

We empirically study the genealogical trees of ten families for about five centuries in Korea. Although each family tree contains only the paternal part, the family names of women married to the family have been recorded, which allows us to estimate roughly the family name distributions for the past five hundred years. Revealed is the fact that the unique Korean family name distribution, characterized by a logarithmic form of the cumulative distribution and an exponentially decaying rank-size plot often called the Zipf plot, has remained unchanged for a long time. We discuss the implications of our results within a recently suggested theoretical model and compare them with observations in other countries in which power-law forms are abundantly found.

physics.soc-ph↗

arXiv2007

Emergence of Chaotic Itinerancy in Simple Ecological Systems

Chaotic itinerancy is a universal dynamical concept that describes itinerant motion among many different ordered states through chaotic transition in dynamical systems. Unlike the expectation of the prevalence of chaotic itinerancy in high-dimensional systems, we identify chaotic itinerant behavior from a relatively simple ecological system, which consists only of two coupled consumer-resource pairs. The system exhibits chaotic bursting activity, in which the explosion and the shrinkage of the population alternate indefinitely, while the explosion of one pair co-occurs with the shrinkage of the other pair. We analyze successfully the bursting activity in the framework of chaotic itinerancy, and find that large duration times of bursts tend to cluster in time, allowing the effective burst prognosis. We also investigate the control schemes on the bursting activity, and demonstrate that invoking the competitive rise of the consumer in one pair can even elongate the burst of the other pair rather than shorten it.

nlin.CD↗

arXiv2007

Topological Properties of Stock Networks Based on Random Matrix Theory in Financial Time Series

We investigated the topological properties of stock networks through a comparison of the original stock network with the estimated stock network from the correlation matrix created by the random matrix theory (RMT). We used individual stocks traded on the market indices of Korea, Japan, Canada, the USA, Italy, and the UK. The results are as follows. As the correlation matrix reflects the more eigenvalue property, the estimated stock network from the correlation matrix gradually increases the degree of consistency with the original stock network. Each stock with a different number of links to other stocks in the original stock network shows a different response. In particular, the largest eigenvalue is a significant deterministic factor in terms of the formation of a stock network.

q-fin.ST↗

arXiv2007

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by using redundant or alternative pathways. Thus, only a limited number of genes have been identified to be lethal to the cell. In this regard, the reaction-centric gene deletion study has a limitation in understanding the metabolic robustness. Here, we report the use of flux-sum, which is the summation of all incoming or outgoing fluxes around a particular metabolite under pseudo-steady state conditions, as a good conserved property for elucidating such robustness of E. coli from the metabolite point of view. The functional behavior, as well as the structural and evolutionary properties of metabolites essential to the cell survival, was investigated by means of a constraints-based flux analysis under perturbed conditions. The essential metabolites are capable of maintaining a steady flux-sum even against severe perturbation by actively redistributing the relevant fluxes. Disrupting the flux-sum maintenance was found to suppress cell growth. This approach of analyzing metabolite essentiality provides insight into cellular robustness and concomitant fragility, which can be used for several applications, including the development of new drugs for treating pathogens.

q-bio.MN↗

arXiv2007

Reliability of rank order in sampled networks

In complex scale-free networks, ranking the individual nodes based upon their importance has useful applications, such as the identification of hubs for epidemic control, or bottlenecks for controlling traffic congestion. However, in most real situations, only limited sub-structures of entire networks are available, and therefore the reliability of the order relationships in sampled networks requires investigation. With a set of randomly sampled nodes from the underlying original networks, we rank individual nodes by three centrality measures: degree, betweenness, and closeness. The higher-ranking nodes from the sampled networks provide a relatively better characterisation of their ranks in the original networks than the lower-ranking nodes. A closeness-based order relationship is more reliable than any other quantity, due to the global nature of the closeness measure. In addition, we show that if access to hubs is limited during the sampling process, an increase in the sampling fraction can in fact decrease the sampling accuracy. Finally, an estimation method for assessing sampling accuracy is suggested.

physics.soc-ph↗

arXiv2006

Random field Ising model on networks with inhomogeneous connections

We study a zero-temperature phase transition in the random field Ising model on scale-free networks with the degree exponent $γ$. Using an analytic mean-field theory, we find that the spins are always in the ordered phase for $γ<3$. On the other hand, the spins undergo a phase transition from an ordered phase to a disordered phase as the dispersion of the random fields increases for $γ> 3$. The phase transition may be either continuous or discontinuous depending on the shape of the random field distribution. We derive the condition for the nature of the phase transition. Numerical simulations are performed to confirm the results.

cond-mat.stat-mech↗