arXiv subjects

K. Kaski

Publications and source records attributed to K. Kaski.

At least 19 recordsLinked to original sources

arXiv2014

Dynamics of polymer ejection from capsid

Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which a viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the escape times scale with polymer length, $τ\sim N^α$. We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) $ρ$ inside the capsid. For very low densities $ρ\le 0.002$ the polymer is only weakly confined by the capsid, and we measure $α= 1.33$, which is close to $α= 1.4$ obtained for polymer translocation. At intermediate densities the scaling exponents $α= 1.25$ and $1.21$ for $ρ= 0.01$ and $0.02$, respectively. These scalings are in accord with a crude derivation for the lower limit $α= 1.2$. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, $ρ\gtrapprox 0.25$. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.

physics.bio-ph↗

arXiv2014

Criteria for minimal model of driven polymer translocation

While the characteristics of the driven translocation for asymptotically long polymers are well understood, this is not the case for finite-sized polymers, which are relevant for real-world experiments and simulation studies. Most notably, the behavior of the exponent $\alpha$, which describes the scaling of the translocation time with polymer length, when the driving force $f_p$ in the pore is changed, is under debate. By Langevin dynamics simulations of regular and modified translocation models using the freely-jointed-chain polymer model we find that a previously reported incomplete model, where the {\it trans} side and fluctuations were excluded, gives rise to characteristics that are in stark contradiction with those of the complete model, for which $\alpha$ increases with $f_p$. Our results suggest that contribution due to fluctuations is important. We construct a minimal model where dynamics is completely excluded to show that close alignment with a full translocation model can be achieved. Our findings set very stringent requirements for a minimal model that is supposed to describe the driven polymer translocation correctly.

physics.bio-ph↗

arXiv2012

Event distributions of polymer translocation

We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of the process. We extract at a high length scale resolution distributions of polymer segments that continuously traverse through a nanoscale pore. The obtained log-normal distributions together with the characteristics of polymer translocation suggest that it is describable as a multiplicative stochastic process. In spite of its clear out-of-equilibrium nature the forced translocation is surprisingly similar to the unforced case. We find forms for the distributions almost unaltered with a common cut-off length. We show that the individual short-segment and short-time movements inside the pore give the scaling relations $τ\sim N^α$ and $τ\sim f^{-β}$ for the polymer translocation.

cond-mat.soft↗

arXiv2010

Small But Slow World: How Network Topology and Burstiness Slow Down Spreading

Communication networks show the small-world property of short paths, but the spreading dynamics in them turns out slow. We follow the time evolution of information propagation through communication networks by using the SI model with empirical data on contact sequences. We introduce null models where the sequences are randomly shuffled in different ways, enabling us to distinguish between the contributions of different impeding effects. The slowing down of spreading is found to be caused mostly by weight-topology correlations and the bursty activity patterns of individuals.

physics.soc-ph↗

arXiv2010

Pore-polymer interaction reveals non-universality in forced polymer translocation

We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced translocation characteristics significantly in the biologically relevant pore force, i.e. driving force, range. Details of the model are shown to change even the obtained scaling relations, which is a strong indication of strongly out-of-equilibrium dynamics in the computational studies which have not yet succeeded in addressing the characteristics of the forced translocation for biopolymers at realistic length scale.

physics.bio-ph↗

arXiv2009

Statistics of collective human behaviors observed in blog entries

Collective human behaviors are analyzed using the time series of word appearances in blogs. As expected, we confirm that the number of fluctuations is approximated by a Poisson distribution for very-low-frequency words. A non-trivial scaling roperty is confirmed for more-frequent words. We propose a simple model that shows that the fluctuations in the number of contributors is playing the central role in this non-Poissonian behavior.

physics.soc-ph↗

arXiv2009

Dynamics of forced biopolymer translocation

We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore potentials in experiments and biological systems. Scaling of translocation time with polymer length varies with pore force and friction. Hydrodynamics affects this scaling and significantly reduces translocation times.

physics.bio-ph↗

arXiv2009

Broad lifetime distributions for ordering dynamics in complex networks

We search for conditions under which a characteristic time scale for ordering dynamics towards either of two absorbing states in a finite complex network of interactions does not exist. With this aim, we study random networks and networks with mesoscale community structure built up from randomly connected cliques. We find that large heterogeneity at the mesoscale level of the network appears to be a sufficient mechanism for the absence of a characteristic time for the dynamics. Such heterogeneity results in dynamical metastable states that survive at any time scale.

physics.soc-ph↗

arXiv2008

Critical evaluation of the computational methods used in the forced polymer translocation

In forced polymer translocation, the average translocation time, $τ$, scales with respect to pore force, $f$, and polymer length, $N$, as $τ\sim f^{-1} N^β$. We demonstrate that an artifact in Metropolis Monte Carlo method resulting in breakage of the force scaling with large $f$ may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent $β\le 1 + ν$ is not universal, but depends on $f$. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and $β$ to arise solely from the initial polymer configuration.

physics.bio-ph↗

arXiv2008

The International Trade Network: weighted network analysis and modelling

Tools of the theory of critical phenomena, namely the scaling analysis and universality, are argued to be applicable to large complex web-like network structures. Using a detailed analysis of the real data of the International Trade Network we argue that the scaled link weight distribution has an approximate log-normal distribution which remains robust over a period of 53 years. Another universal feature is observed in the power-law growth of the trade strength with gross domestic product, the exponent being similar for all countries. Using the 'rich-club' coefficient measure of the weighted networks it has been shown that the size of the rich-club controlling half of the world's trade is actually shrinking. While the gravity law is known to describe well the social interactions in the static networks of population migration, international trade, etc, here for the first time we studied a non-conservative dynamical model based on the gravity law which excellently reproduced many empirical features of the ITN.

q-fin.GN↗

arXiv2008

Limited resolution and multiresolution methods in complex network community detection

Detecting community structure in real-world networks is a challenging problem. Recently, it has been shown that the resolution of methods based on optimizing a modularity measure or a corresponding energy is limited; communities with sizes below some threshold remain unresolved. One possibility to go around this problem is to vary the threshold by using a tuning parameter, and investigate the community structure at variable resolutions. Here, we analyze the resolution limit and multiresolution behavior for two different methods: a q-state Potts method proposed by Reichard and Bornholdt, and a recent multiresolution method by Arenas, Fernandez, and Gomez. These methods are studied analytically, and applied to three test networks using simulated annealing.

physics.soc-ph↗

arXiv2007

Emergence of communities in weighted networks

Topology and weights are closely related in weighted complex networks and this is reflected in their modular structure. We present a simple network model where the weights are generated dynamically and they shape the developing topology. By tuning a model parameter governing the importance of weights, the resulting networks undergo a gradual structural transition from a module free topology to one with communities. The model also reproduces many features of large social networks, including the "weak links" property.

physics.soc-ph↗

arXiv2007

Anomalous lifetime distributions and topological traps in ordering dynamics

We address the role of community structure of an interaction network in ordering dynamics, as well as associated forms of metastability. We consider the voter and AB model dynamics in a network model which mimics social interactions. The AB model includes an intermediate state between the two excluding options of the voter model. For the voter model we find dynamical metastable disordered states with a characteristic mean lifetime. However, for the AB dynamics we find a power law distribution of the lifetime of metastable states, so that the mean lifetime is not representative of the dynamics. These trapped metastable states, which can order at all time scales, originate in the mesoscopic network structure.

physics.soc-ph↗

arXiv2006

Generalizations of the clustering coefficient to weighted complex networks

The recent high level of interest in weighted complex networks gives rise to a need to develop new measures and to generalize existing ones to take the weights of links into account. Here we focus on various generalizations of the clustering coefficient, which is one of the central characteristics in the complex network theory. We present a comparative study of the several suggestions introduced in the literature, and point out their advantages and limitations. The concepts are illustrated by simple examples as well as by empirical data of the world trade and weighted coauthorship networks.

cond-mat.stat-mech↗

arXiv2006

Structure and tie strengths in mobile communication networks

Electronic databases, from phone to emails logs, currently provide detailed records of human communication patterns, offering novel avenues to map and explore the structure of social and communication networks. Here we examine the communication patterns of millions of mobile phone users, allowing us to simultaneously study the local and the global structure of a society-wide communication network. We observe a coupling between interaction strengths and the network's local structure, with the counterintuitive consequence that social networks are robust to the removal of the strong ties, but fall apart following a phase transition if the weak ties are removed. We show that this coupling significantly slows the diffusion process, resulting in dynamic trapping of information in communities, and find that when it comes to information diffusion, weak and strong ties are both simultaneously ineffective.

physics.soc-ph↗

arXiv2006

Spectrum, Intensity and Coherence in Weighted Networks of a Financial Market

We construct a correlation matrix based financial network for a set of New York Stock Exchange (NYSE) traded stocks with stocks corresponding to nodes and the links between them added one after the other, according to the strength of the correlation between the nodes. The eigenvalue spectrum of the correlation matrix reflects the structure of the market, which also shows in the cluster structure of the emergent network. The stronger and more compact a cluster is, the earlier the eigenvalue representing the corresponding business sector occurs in the spectrum. On the other hand, if groups of stocks belonging to a given business sector are considered as a fully connected subgraph of the final network, their intensity and coherence can be monitored as a function of time. This approach indicates to what extent the business sector classifications are visible in market prices, which in turn enables us to gauge the extent of group-behaviour exhibited by stocks belonging to a given business sector.

physics.soc-ph↗

arXiv2006

A Model for Social Networks

Social networks are organized into communities with dense internal connections, giving rise to high values of the clustering coefficient. In addition, these networks have been observed to be assortative, i.e. highly connected vertices tend to connect to other highly connected vertices, and have broad degree distributions. We present a model for an undirected growing network which reproduces these characteristics, with the aim of producing efficiently very large networks to be used as platforms for studying sociodynamic phenomena. The communities arise from a mixture of random attachment and implicit preferential attachment. The structural properties of the model are studied analytically and numerically, using the $k$-clique method for quantifying the communities.

physics.soc-ph↗

arXiv2005

Intensity and coherence of motifs in weighted complex networks

The local structure of unweighted networks can be characterized by the number of times a subgraph appears in the network. The clustering coefficient, reflecting the local configuration of triangles, can be seen as a special case of this approach. In this Letter we generalize this method for weighted networks. We introduce subgraph intensity as the geometric mean of its link weights and coherence as the ratio of the geometric to the corresponding arithmetic mean. Using these measures, motif scores and clustering coefficient can be generalized to weighted networks. To demonstrate these concepts, we apply them to financial and metabolic networks and find that inclusion of weights may considerably modify the conclusions obtained from the study of unweighted characteristics.

cond-mat.stat-mech↗