Social networks represent communication channels and therefore also limits on information access in a society. The applet considers agents who try to bypass these information constraints, driving an ever-changing social network. The model emphasizes communication barriers in the system as the driving force behind group formation.

Publications

Expression of genes are regulated by transcription factors (TF) that typically binds to certain operator sites upstream of the promoter for the gene. Procaryotic transcription initiation are mostly regulated through a direct contact between the transcription factor a RNA polymeraze (RNAP) at the promoter. For eucaryotes, the multiplicity of regulatory sites on typical genes and the ubiguetous cooperativity of eucaryotic gene regulation suggest indirect actions of transcription factors. In particular, the fact that upstream regulatory regions of genes often includes tenth of kilo bases of DNA, many operator sites and modulation by multiple transcription factors raises the question on how so many proteins bound on such a wide region of DNA can influence the 20-40nm RNAP-mediator complex on the promoter region.

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The applet simulate 3 basic step that initiates reading the information of DNA. The applet also has options to show burst-like transcription initiations separated by long silence periods due to the recriutment of open complexes or the formation of dead-end complex.

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This applet simulates the regulation of uptake and metabolism of small molecules in cells. The applet allows you to explore the different ways of combining negative and positive feedback to regulate the level and flux of the molecule.

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Social groups with widely different music tastes, political convictions, and religious beliefs emerge and disappear on scales from extreme subcultures to mainstream mass-cultures. Several positive feedback mechanisms drive the diversity of beliefs in social systems. Some of these mechanisms can be analyzed in terms of a hugely simplified model of a dynamic network that incorporates basic feedback between information assembly through communication and formation of social connections.

Publications

0708.0368

The stability and heritability of the modified states of nucleosomes are modeled as a positive feedback, where modified nucleosomes recruit enzymes that modify other nucleosomes. The applet presents an interactive version of this ongoing dynamical process. In particular one may examine the effect of recruitment strength versus external noise, the effect of system size, consequences of various degrees of locality in the recruitment processes, and one can also explore how the stability of heritable states depends on nucleosome replacement at cell division. We encourage the reader to play with the applet and thereby gain intuition on the interplay between assumed processes and final distribution of epigenetic states of the modeled segment of the chromosome.

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This applet presents a model for protein synthesis, where ribosomes move along a mRNA. Initiation rate, termination rate, and the rate of translation for each codon affect the behavior.

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A model which achieves hub-hub separation in scale-free networks while being a small-world. This is done by rewiring according to randomly assigned rankings for each node. The concept of degree-landscapes is illustrated.

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physics/0512075

cond-mat/0308339

This applet presents the known part of the fossil record, as collected by Sepkoski. The applet opens for a illustrative way to examine birth, expansion and collapse of taxonomic orders. The presentation supplements the data analysis of the work referenced below.

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Co-evolution of bacteria, virulent and temperate phages are examined in a network model where where nodes are whole strains of bacteria and phages. Events are speciations and extinctions on the strain lavel, thus coarse graining over population numbers. Basic features of the ecological interactions are incorporated into the model in the form of extinction propabilities that depends on links.

Publications

q-bio.PE/0609031

In our center we make simple models of our surrounding world using the assumption that the complicatedness of the world is an illusion. This applet exemplify this approach by showing that simple rules can give rise to complex behaviour. Also it illustrates that the information horizon of the modelled birds are connected to development of cooperative behaviour, which here takes the form of flok behaviour. The information horizon aspect of the applet is complementary to the applet on interplay between communication and social structure, see M. Rosvall and K. Sneppen, Phys. Rev. E 74, 016108 (2006)

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physics/0512105

cond-mat/0412064

We take that model in "Self-Assembling of Information in Networks" one step further and give the agents a social mobility. The agents can thereby get new acquaintances to meet different interests. The model opens for study of interplay between communication activity/habbits and emergence of social structure.

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physics/0512105

cond-mat/0308399

We show that it is possible to build a reliable perception of the whole through repeated small talks. We simply let agents memorize the acquaintances that provided the newest information about other agents together with the age of this information.

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abs/physics/0603218

The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the functions it directs. This applet illustrates quantitative methods of network comparison based on network architecture and signaling logic.

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q-bio.MN/0511047

A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli. The model deals with the interference between the two promoters pA and pS. The RNAPs are injected onto the DNA through binding and formation of sitting duck complexes at the respective promoters, followed by subsequent formation of elongating complexes.

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Navigation is a challenging problem for everyday life. The problem arises because the amount of available information typically is limited and often insufficient. We here abstract this problem to be navigation between a source and a target on different networks.

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cond-mat/0412051

cond-mat/0407055

cond-mat/0505400

cond-mat/0412064

One way to interpret this merging model of a bipartite network is to consider the nodes as sunspots and the links as the associated magnetic field-lines in the solar atmosphere. Two sunspots of the same polarity merge to a larger sunspot and when two sunspots of different polarity merge the magnetic field-lines annihilate and energy is released.

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cond-mat/0406752

Merging or aggregation is a dynamical process in many systems and it gives rise to fractal size-distributions. For example, companies, the autonomous system of the Internet and the sun activity of magnetic field lines reconnections are networks that undergo processes that resembles the merging process.

Publications

nlin.AO/0403006

cond-mat/0406752

In the unfolded protein response in S. cerevisiae a reservoir of passive mRNA is converted to an active short-lived mRNA that is open for translation. Optimal response is obtained when active mRNA has high decay rate compared to both the conversion rate and the decay rate of passive mRNA. In that case the translation regulation can provide the observed pulse of chaperones that fast restore protein folding conditions in the endoplasmic reticulum.

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In a society the information horizon is set by each individual's social contacts, which in turn is a part of the global network of human communication. One simple goal for individuals is to be central. Thus we model a society where players try to be as close as possible to everybody else by moving their social connections. Local communication gives rise to global organization.

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cond-mat/0308399

Fashions and perception of value is a social phenomenon which is associated to positive feedback and communication in a society. Here we model the how the attention of different products changes as people trade and talks about these products.

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cond-mat/0309549

Speciation and extinction in the evolution, modeled in a coarse grained 1-dimensional ecosystem. Species in the ecosystem do not suffer extinction independently of each other. The overall macroevolutionary pattern supports cooperativity, even on the scale of the global ecosystem.

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This applet deals with a propagating front, which may be water or coffee pushed/dragged through a porous media like paper or one may think about the outer boundary of a bacterial colony. The model is schematic, and in particular assume that movements is always upwards.

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Dyamics of Transcription Initiation. The applet simulate 3 basic step that initiates reading the information of DNA. Also the applet describe different ways this piece of DNA (a gene) can be regulated by another molecule.

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Instabilities and positive feedback are central themes in dynamical systems and sometimes in biology. This applet deals with simplest spatio-temporal instability, where a part of the front gets more ahead when its already ahead.

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