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Eihab Bashier Mohammed

Supervisor:

Dr. Gareth Witten. (University of Cape Town)

An essay submitted in partial fulﬁllment of the requirements for AIMS Postgraduate Diploma in Mathematical Sciences.

May, 2004

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2

Acknowledgement

I am very grateful to Dr. Gareth, who has been helpful to me; Prof. Wesley Kotze, who gave me a part of his valuable time; Dr. Mike Pickles, who stood behind me until I completed this work; and to all AIMS staﬀ.

Dedication

To my parents, my family and all my colleagues; I dedicate this work.

Abstract In this short essay, we aim to explain how do the researchers use the concepts from graph theory to study the networks of complex systems, where the structure of these networks and the dynamics of it’s nodes are the factors which determine the behaviour of the system at all. We explained that, a structure of some network, can be characterized by three important measures, and play the main role in determininning the topological properties of that network. Another important task, is how coupling of the nodes of the network –which themselves are complex systems– can aﬀect the global behaviour of the network, like achieving synchronisation. The researchers aim to know how do the topology of the network and the dynamics of its nodes together, aﬀect the long-term behaviour of the network. Hence, mathematical models were written to describe the dynamics of these networks. These models can not be solved analytically, hence the computational methods are used to ﬁnd numerical solutions for these models. The problem with the computaions in large complex networks, and in particular the biological networks is that, their behaviour is unpredictable. We took as example the genetic regulatory networks as an application to the dynamical complex networks, and discussed brieﬂy some of the methods to model them, and some of the results obtained by these methods.

. . . . . . . . . . 31 2 . . . . . . . . . . . . . .2 What is a Complex Network? . . . . . 1 4 4 6 8 1. . .2 Synchronisation in Regular Networks . . . . . . . . . . . . .1 What is a Network? . . . . . . . . . . . . .3 Synchronisation in Small-World Networks . . . 14 2. . . . . 24 3 Dynamics and Synchrony 26 3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3 Regular Networks . 10 2 Structures of Complex Networks 12 2. . .6 Similarities and Contrasts . . . . .1 Deﬁnitions and Preliminaries . . . 28 3. . . . . . . . . . . . . 31 3. . . . . . . . . . . . . . . .Contents Abstract 1 Introduction 1. . . . . . 12 2. . . . . . . . . . . . . . . . . . 30 3. . . . . .1 Deﬁnitions and Basic Concepts . .5 Scale-Free Networks . . . . .3 Dynamics on Complex Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1. . . . . . . . . . . .1 Stability Analysis . . . . . . . . . . .4 Small-World Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1. . . . 26 3. . .2 Random Networks . . . . . . . . . . . . . . . . 18 2. . . . .4. . . . . . . . . . . . . . . . . . . . .4 Synchronisation in Networks of Complex Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 Synchronisation in Scale-Free Networks . . . . . . . . . 21 2. . . . . . . . . . . . . . 16 2. . . . . . . . . . . . .

. . . . . . . . . .4. . . . . 35 Modelling Genetic Regulatory Networks . . . .1 4. . . .2. . 39 Diﬀerential Equations Models . . . . .3. . . . . . . .3 Boolean Network Model . . . . . . . . . . . . . . . .1 4. . . .2 Background: Regulatory Networks . . . . . . . . . . . . . . . . .2. . . . . . . . . . . . . .2 4. . . . . . . . . . .2. . . . . . . 44 46 48 5 Discussions Bibliography 3 . 41 The Artiﬁcial Genomic Model . . . 39 4. . . . 32 35 4 Application: Genetic Regulatory Networks 4. . .2 Robustness and Fragility of Synchronisation: . . . . . . . . . . . . .

. and the edges represent the predominaly directed chemical reactions in which these substrates can participate. v2 . then k must satisfy the inequality 1 < log(N) < k < N . The Internet is an undirected network (Albert and Barab´si[1]). and hence. Networks observed in reality are called real-world networks. and the edges are the hyper-links. They include: • World Wide Web (WWW): the nodes are web pages. WWW is a directed network (Albert and Barab´si[1]).Chapter 1 Introduction 1. V = {v1 . and a ﬁnite set of edges (links) E. . G20) are the nodes. 4 . . We will assume always that the graph is connected. E). vN }. and E the set of edges. if k denotes the number of edges. a • Internet: The nodes are routers and the edges are the physical connections between them. a • Cellular networks: the substrates (ATP. A graph is often denoted as a pair G(V. directed or undirected and weighted or unweighted. is a subset of the Cartisean product V × V . ADP. where V is the set of vertices. The graph can be connected or disconnected.1 What is a Network? A network can be represented as a graph consisting of a ﬁnite set of vertices (nodes) V . .

Ecological networks are directed networks [3]. . and the edges represent the predator-pray relationships among them. i. . The adjacency matrix R(G) is deﬁned to be: R(G) = [rij ] where. • Protein folding: diﬀerent states of single protein are represented by nodes. . v ) ∈ E i j rij = 0 otherwise For an undirected graph G. whose aggregate activity is nonlinear.• Ecological networks or food webs: the nodes are species. Hence the lower or upper triangular matrix of R(G) is suﬃcient for a complete description of the graph. • Power networks: the nodes are generators. 1 (v . This is undirected network. and the diagonal elements of R(G) are zeros. A complex system is any system which featuring a large number of interacting components. 5 . if connected by either synapse or gap-junction[33]. j ∈ {1. and the edges are high-voltage transmission lines[33]. • Movie actor collaboration network: The nodes are the actors and two nodes are connected if two actors have acted in a movie together. . This is undirected network[33]. N}). the adjacency matrix R(G) is symmetric (rij = rji. 2. transformers and substations. and typically exhibits hierarchical selforganisation under selective pressures[19]. Conformations are linked if they can be obtained from each other by an elementary move. and two neurons are joined together. • Neural networks: The nodes are the neurons. The network topology means the conﬁguration of the connections between its nodes. The number of edges connected to some node is called it’s degree.

much recent research work on complex networks has focused on the structural topology of these networks. for a given two persons A and B. The complexity of a network. aﬀects it’s function. Networks grow and evolve by local events. comes from two diﬀerent sources: 1. are mainly determined by the way the nodes are connected. and whose edges represent the interactions between them. and many complex systems can be described in terms of networks of interacting units. and gave it to some individuals. such as the addition of new nodes and links.1. whose nodes may be the elements of a complex system. For their network. However. i. the interaction patterns among the individuals of the underlying system or process can be embedded onto a regular and perhaps universal structure such as a Euclidean lattice. described a network with complex topology o e by random graph. the connections between the nodes occur in random. In the 1960’s. the Erd¨s-R´nyi networks o e are homogeneous in nature. and the degree P (k) that gives the probability for some given node to be linked to k other nodes is a Poissonian. For over a century. The basic properties of very large networks. Why network anatomy is so important to characterise?[25]. or rewiring of links from one node to another. modelling of physical as well as non-physical systems and processes has been performed under an implicit assumption that.2 What is a Complex Network? A complex network is a network with complex topology. the dynamics of its complex nodes (complexity due to the dynamics). He determined the personal information about the target persons.[30] The two mathematicians Erd¨s and R´nyi. 2. were they linked to each other by a short chains of acquaintances.e. they assumed that. like the spread of information and disease in social networks. the topology of the network (complexity due to the topology). the social psychologist Stanley Milgram wanted to know. the topology of a networks. Therefore. Each starter individual had to choose a single acquaintance to send the letter 6 .

Diﬀerent types o e of networks are observed: from exponential to scale-free (SF). have the property that. a characteristic feature of random graphs. Some complex networks display the so-called small-world (SW) eﬀect: they are highly clustered. the origins of homeostatic stability and the sensibility to perturbations in biological networks. The consequences of the small-world and scale-free patterns can be of great importance in recognise evolutionary paths. mapped the connections of the Web. Then he conducted what is known six degrees of seperation. 7 . They named their network. by rewiring the edges of a regular graph with probability p. They described the transition from the regular lattice. such that. with some of his colleagues at the a o a university of Notre Dame. but the average length between any two randomly chosen nodes in the graph is short. indicating diﬀerent basic types of organisation[13]. As many complex real-life networks are neither completely regular nor completely random. From the completed chains. the connectivity distribution of a network peaks at an average value and decays exponentially[31]. Watts and Strogatz (1998) introduced the concept of small-world networks[33]. A small number of the nodes have a high connectivity with the other nodes. and the surprising result for them was that. the interaction networks displayed by most complex systems are heterogeneous. In 1998. These distributions are thus very diﬀerent from the Poissonian shape expected from a simple (Erd¨s-R´nyi) random graph. the physicist Albert-L´zl´ Barab´si[3]. The small-world networks as the random networks. it formulated as Any one of us is only about six acquaintances away from anyone else[2]. until the letter arrived its target.to. to the random graph. while most of the nodes have a small number of connections. the scale-free network. he found that the median number from the source to the target was six. the target can receive the letter in the shortest way. and the subsequent recipients had to follow the same procedure. and a small number are linked to many other nodes. the structure of the Web does not obey the the Erd¨s-R´nyi random o e model of connectivity. Recent studies have revealed that. Most nodes are connected to a few ones.

the removal of a fraction p of it’s nodes.[23] What can happen to the topology of a network when a randomly fraction p of it’s nodes and their connections are removed? In the scale-free networks.The topology of a network can be characterised by three important properties. Because vaccination of individuals prevents them from catching the disease. is that. The unifying feature of the complex networks . that are the characteristic path length. where x(t) = (x1 (t). when p exceeds a critical value pc called the threshold. Newman explained the importance of the network resilience in epidemiology. the clustering coeﬃcient and the degree distribution. x2 (t). Dynamical systems can often be modelled by diﬀerential equations dx dt = v(x).3 Dynamics on Complex Systems Complex networks are sets of many interacting components whose elaborate collective behaviour cannot be directly predicted and characterised in terms of the behaviour of their individual components. and in addition to that. t is time.[6] Networks vary in their level of resilience against the removal of nodes. Bellow the threshold the network remains connected. their global structure and dynamic evolution are the result of locally interacting agents distributed in the network[5]. the network resilience to the removal of it’s nodes. . . xn (t)) is a vector of state variables. and v(x) = 8 . 1. it may also destroy paths between other individuals by which the disease may spread. When the interactions between single components are suitably modelled.[23] In [23]. will break it down into a smaller disconnected parts. . . An important property that is related to the degree distribution. components can describe many diﬀerent real-world units such as 2 providers. where the removal of vertices in a contact network might correspond for example to vaccination of individuals against a disease. but the lengths between the paths between the nodes will increase.

pages and links are created and lost every minute. guided by the velocity ﬁeld dx dt = v(x) like a speck carried along in a steady. it acts as an attractor for states in its vicinity. so we call x∗ a ﬁxed point. It represents a selfsustained oscillation of the physical system. . . Then the velocity must be zero there. On the WorldWide Web. . . x2 . . vn (x)) is a vector of functions that encode the dynamics. These diﬀerential equations are oftenly nonlinear. . v2 (x). Synapses in the nervous system can be strong or weak. directions and signs.[25] Networks have a number of possible complications: 1. . A third possibility is that x(t) might settle onto a strange attractor. Suppose x(t) eventually comes to rest at some point x∗ . . x∗ is called a stable ﬁxed point. a set of states on which it wanders forever. If all disturbances away from x∗ damp out. xn . viscous ﬂuid. never stopping or repeating. then x∗ is corresponds to an equilibrium state of the physical system being modelled.(v1 (x). If we are modelling a physical system. x(t) ﬂows through state space. but one can gain qualitative insight by imagining an abstract n-dimensional state space with axes x1 . Such nonlinear equations are typically impossible to solve analytically. 2. As the system evolves. Such a loop is called a limit cycle. x(t) ﬂows towards a closed loop and eventually circulates around it forever. 3. 9 . Connection diversity: the links between nodes could have diﬀerent weights.Such erratic. Another long-term possibility is that. Long-term prediction is impossible in a real chaotic system because of this exponential ampliﬁcation of small uncertainties or measurement errors. inhibitory or excitatory. Structural complexity: the wiring diagram could be an intricate tangle. aperiodic motion is considered chaotic if two nearby states ﬂow away from each other exponentially fast. Network evolution: the wiring diagram could change over time.

6. For example. aﬀects its topology. • A synchronous complex systems: contain disparate members which evolve dynamically in time with changing interconnect and usually diﬀerent evolution algorithms for each member.4 Synchronisation in Networks of Complex Systems A particularly interesting form of dynamical behaviour occurs in networks of coupled systems or oscillators when all the subsystems behave in the same fashion. In a gene network or a Josephson junction array. Networks synchronisation has many applications in various ﬁelds. and coupled synchronised lasers and electronic circuit systems. such as the synchronous information exchange in the Internet and the WWW. they all do the same thing at the same time.4. Each complex systems can be described as one of three important types: • Synchronous complex systems: synchronous systems consist of more or less identical members which evolve synchronously with identical time evolution algorithms. Node diversity: there could be many diﬀerent kinds of nodes. network evolution. 5. The biochemical network that controls cell division in mammals consists of a bewildering variety of substrates and enzymes. Many real-world problems have closed relationship with network synchronization. such as the spread of epidemic or computer virus. Such behaviour of a network simulates a continuous system that has a uniform movement. that is. and the synchronous transfer of digital or analog signals in the communication networks. the state of each node can vary in time in complicated ways. 1. models neurons that synchronise. 10 . Dynamical complexity: the nodes could be nonlinear dynamical systems. Meta-levels: the various levels can inﬂuence each other.

• If each node has a stable limit cycle. He proposed to answer this question.• Loosely complex systems are intermediate case between asynchronous and synchronous complex systems. synchronised chaos requires that the coupling be neither too week nor too strong. They are synchronise every now and then. For the fully connected networks the completely synchronise state become likely. and the oscillators are identical and coupled by smooth interactions akin to diﬀusion. • If each node has a chaotic attractor. then the network tends to lock in static pattern. or form patterns depending on the symmetry of the underlying network. then he asked the question what can be said about the collective behaviour if many such systems are coupled together?. typically at the end of an iteration or time step in a solution. then it can synchronise. then these oscillators will oftenly synchronise. Otherwise spatial instabilities are triggered. Strogatz assumed that[25]. To predict the behaviour of a network of coupled dynamical systems. for the network of dynamical systems. But in a wide range of network topologies. each node would exhibit if it were isolated. that: • If each node in the dynamical system has stable ﬁxed point and no other attractors. 11 .

then the distance between two nodes is simply the minimal number of edges.1 Deﬁnitions and Preliminaries As mentioned before. the three key measures of a network are the characteristic path length. If all edges are unweighted and undirected. that must be traversed to get from one node to the other. Mathematically. or more precisely. 12 . The distance between the two nodes vi and vj is denoted by Dij . The characteristic path length L is simply deﬁned as the average distance between any two nodes.Chapter 2 Structures of Complex Networks 2. the clustering coeﬃcient and the degree distribution. the average length of the shortest path connecting each pair of nodes. the characteristic path length denoted by L is deﬁned to be: N L= i=1 Di N where Di is the distance between any pair of vertices. L generally measures the global properties of a graph and is independent of local structure.

x) = 1. In some networks. the more important of it. The larger the degree of a node. who pointed out that most networks are highly clustered. then there would be ki (ki −1) edges among them.e 1 N N C= Ci i=1 The clustering coeﬃcient C is a measure of how clustered. If all the nodes are connected. the most important characteristic of a single node.The diameter of the graph G denoted by Diam(G) is deﬁned to be: Diam(G) = maxi. ki denotes the average degree of the 13 . denoted by Ci as Ci = 2Ei ki (ki − 1) (k) where Ei is the number of all edges that actually exist among all ﬁrst neighbour of selected the node. or locally structured. If ki denotes the degree of the node i then. denoted by Γv is deﬁned to be the set: Γ(k) = {x : D(v. And generally. is its degree distribution[30]. v = x} v The second characteristic feature of real-world networks has been highlighted by Watts and Strogatz[33]. a graph is. The clustering coeﬃcient overall the network is the average of all individual Ci ’s. the k th nearest neighbour of a vertex v. v = x} The set Γv is termed as the nearest neighbour of the vertex v. One can deﬁne a clustering coeﬃcient for a single node vi .j Dij The neighbourhood Γv of a vertex v is deﬁned to be the set: Γv = {x : D(v. i. x) ≤ k.

and connect each pair of the nodes with probability p. The graphs obtained at diﬀerent stages of this process correspond to larger and larger connection probabilities p. the total number of edges is a random variable with expectation value E(n) = p N (N −1) .[12] 2 14 . the probability of obtaining it by this graph construction process is binomial: P (G) = pn (1 − p) N(N−1) −n 2 N(N−1) 2 diﬀerent graphs with N nodes and The construction of a graph is often called the evolution process. 2.node in the network. Erd¨s and E. which gives the probability that. connected with n edges. R´yni. which are chosen randomly from possible edges[5]. then the network is said to be completely random. then in regular networks. eventually obtaining a fully connected graph p → 1 ⇒ n = N (N −1) . They deﬁned random o e graphs as N nodes. Starting with a set of N isolated vertices. The spread of node degrees over a network is characterised by a distribution function P(k). a randomly selected node has exactly k nearest neighbours. the graph develops by the successive addition of random edges. and if p = 1. while in random networks 0 < p ≤ 1.If G is a graph with N nodes 2 and n edges.2 Random Networks N (N −1) 2 Random networks were ﬁrst studied by P. In total there are precisely Cn n edges. Consequently. p = 0. An alternative deﬁnition is the binomial model[24]: we start with N nodes. Generally the networks are divided into two general types: regular networks and random networks. If p is the probability that vi and vj are connected randomly.

and p (0 ≤ p ≤ 1)is the edge probability. Random networks are poorly clustered but have short path lengths. • Algorithm: – Start with N isolated nodes. has a clustering coeﬃcient C ∼ k N ln(N ) . but introduces more links that connect one part of the network to another. the random graph with p = 1. – connect each pair of nodes with the same probability p.Erd¨s-R´nyi Model(ER): o e • Input: (N. 11 00 11 00 11 00 11 00 11 00 1 0 1 0 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 0 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 0 11 00 11 00 11 00 1 0 1 0 1 0 1 0 11 00 11 00 11 00 11 00 11 00 Figure 2. small-world. and a path length L ∼ where k is the number of edges per vertex. Watts and Strogatz [18] showed that.1: Random Network. P (k) = e−<k> λk k! 15 . the random graph. ln(k) << 1. The degree distribution of a random network is Poissonian. is poorly clustered. This is because the randomness makes it less likely that nearby nodes will have lots of connections. p) where N is the number of vertices. Hence. where L grows only logarithmically with N.

as well as for some simpliﬁed models of physical systems such as the Sherrington-Kirkpatrick spin-glass model[22]. Watts and Strogatz [33] showed that.5 p(x) 2 1. and hexagonal lattices. i. Examples of regular networks are a regular grids where all nodes have exactly four links. In regular networks the nearby nodes have large numbers of interconnections.2: Poisson distribution. there is a high density of connections between nearby nodes. 4 Poisson distribution 3.5 1 0. but are highly clustered. to go from one distant node to another one must pass through many intermediate nodes. but distant nodes have few. where each node has exactly the same number of links to its neighbouring nodes.with a peak at P (< k >).3 Regular Networks A regular network is deﬁned as a graph. the regular graph. has a clustering coeﬃcients 16 . It is used in physics as the basis for mean-ﬁeld theory.e. with mean λ = 2 2..e. where each node is connected to three other nodes.5 3 2. i. A famous example of a highly clustered regular graph is the fully-connected graph (ﬁgure 2..3) in which every vertex is connected directly to all others.5 0 0 1 2 3 4 x 5 6 7 8 9 Figure 2. Regular networks have long path lengths.

large world where the length L grows linearly For fully-connected graphs. it’s maximum value. The degree distribution for the regular lattices. and a path length L ∼ 4 with N.11 00 11 00 11 00 11 00 11 00 1 0 1 0 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 11 0 00 11 00 11 00 11 00 11 00 11 00 1 0 1 0 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 0 1 0 1 0 1 0 11 00 11 00 Figure 2.4: fully connected graph.3: example of a regular network 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 0 11 00 11 00 1 0 1 0 1 0 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 0 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 0 1 0 1 0 1 0 1 0 Figure 2. C ∼ 3 . the clustering coeﬃcient C is equal to 1. where k is the number of edges per vertex. N 2k >> 1. is obviously the uniform distribution. 17 . Then the regular lattice is a highly clustered.

They showed that the power grid for the western U. This decision was made at random. or to change it to connect the starting node to a diﬀerent ending one. the graphs retained their properties of being highly clustered. and the Internet Movie Database all have the characteristics -high clustering coeﬃcient but short path length. They started with regular networks and rewired the nodes.S. Their computer experiments indicated that introducing a relatively small number of random connections.5: Small-World Network. the ”clustering coeﬃcient” is over 95% of what it would be for a regular graph. for the ER random graphs.4 Small-World Networks Watts and Strogatz [33] studied what happens between the two extremes. but the average path lengths dropped dramatically. p = 0 and p = 1. Thus. That is. for p = .01. with probability p for each edge. for small values of p. They called these new graphs small-world networks. the resulting network is completely random. The interesting part in their result is that small-world networks seem to be good models for a wide variety of physical situations. the neural network of a nematode worm. For example. That is. 1 0 1 0 1 0 1 0 1 0 1 0 1 0 11 00 11 00 1 0 1 0 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 11 00 11 00 11 00 11 00 11 00 11 00 11 00 11 00 Figure 2.. the original regular network is unchanged.of small18 . dramatically changed the character of the graph. they decided whether to leave each edge connecting a pair of nodes in place. chosen at random.2. but the ”characteristic path length” is less than 20% of what it would be for a regular graph. if p = 0. but if p = 1.

each connected to the k th nearest neighbours. k is the distance in which each vertex can be connected to it’s neighbours by undirected edges. and such networks are called scale-free. • Algorithm: – Start with a ring lattice. Real-world networks are likely to be small-world networks.world networks. Intuitively. k. one can see why small-world networks might provide a good model for a number of situations. – Replace original edges by random ones by probability p. but then one person might move from his city to another city. despite of that. This degree distribution has a power law tail P (k) = k −ν . For example. the functional form of P (k) still deviates from the Poisson distribution expected for a random 19 . p) where N is the number of vertices. with N nodes. there often seem to be surprisingly short connections between unrelated people. is called the scaling exponent. ν is important in deﬁning the topology of a given network. introducing a random edge. Watts-Strogatz Model: • Input: (N. The empirical results for most large networks show distribution that signiﬁcantly deviates from Poisson distribution. whereas ν (2 ≤ ν ≤ 3). but. Some real-world networks display an exponential tail. and p (0 < p ≤ 1) is the probability of rewiring each edge. The results of Watts and Strogatz then provide an explanation for the empirically observed phenomenon that. people tend to form tight clusters of friends and colleagues (a regular network).

N represents the total number of nodes. In the Caveman graph each set of nodes is in a small interconnected ”cave” or cluster. 20 . Within each cluster. The degree distribution for the small-world network.graph[24]. This type of graph has a large clustering coeﬃcient and a short path length. each node knows every other node. Look at the following graph: e−λ λq q! Figure 2. the clustering coeﬃcient is within a small fraction of the maximum possible clustering coeﬃcient of a connected sparse graph. while it is still being sparse. Thus. The graph consists of N k+1 k×N . and some nodes in each cluster are connected to few nodes of other clusters. and very close to 1. 2 clusters.[28] If k represent the average number of connections a node has. in the original Strogatz-WattsNewman model [2]. There is a more interesting phenomena which occurs if the graph is sparse (if the number of links in a graph is small compared to the total number of possible links). Thus. As before. the total number of connections in the graph is The caveman graph is sparse in the sense that k is much smaller than N.6: Caveman graph with 33 nodes and 105 edges It is called the Caveman graph. with k = 1 is given by: Dq = (1 − p)Pq (p) + pPq−1 (p) where Pq (λ) = is the Poisson distribution.

m (m ≤ n0 ) is the no. Instead of the nodes of these networks having a homogeneous distribution. Albert-Barabasi Model: • Input: (n0 . are characterised by an uneven distribution of connectedness.The characteristic path length of a connected caveman graph is of the order of Hence. and t is the no. • Small diameter: The diameters in small-world graphs increase logarithmically with the number of nodes. Properties of Small-World Networks:[12] • Sparseness: In a small-world network. • Clustering: The small-world graph has a much higher clustering coeﬃcient than in a random graph. of added edges. • Algorithm: 21 . N . m. of repetitions. the small-world graph is sparse. • Threshold of the giant cluster appearance. t) where n0 is the initial number of vertices. L grows steadily. as N gets large and the graph remains sparse.5 Scale-Free Networks Scale-free networks. 2 2. Compared with a complete fully-connected graph with the same number of nodes. N . D ∼ log(N). the graph with N nodes has edges closer to O(N) than O(N 2 ). every time one new vertex is added to the graph. |E| > • Scale-free power-law degree distribution. It is small-world graph. some few nodes act as very connected hubs. k The caveman graph thus represents one type of extreme graph – large clustering coeﬃcient and large characteristic path length.

Scale-free networks include many very connected nodes. most would have a number of connections hovering around a small. Put simply. The ratio of very connected nodes to the number of nodes in the rest of the network remains constant as the network changes in size. average value. the red nodes (hubs) are highly connected with the other nodes in the network.Figure 2. 22 Pki . random connectivity distributions (the kinds of models used to study networks like the Internet before Barab´si and his team made their observation). Each existing node has a diﬀerent probability p(ki ). hubs of connectivity that shape the way the network operates. – Start with n0 nodes. Also. that. Scale-free networks have been used to explain behaviours as diverse as those of power grids. p(ki ) = receive the connection from v. cancerous cells and the dispersal of sexually transmitted diseases. predicted a that there would be no well-connected nodes. the relative number of very connected nodes decreases[18]. m edges will be linked to the existing nodes from v. as a randomly distributed network grows. stock market. the nodes of a scale-free network aren’t randomly or evenly connected. In contrast. they would be statistically insigniﬁcant. or that there would be so few.7: Scale-Free Network. j kj to . – Every time we add one new node v. Although not all nodes in that kind of network would be connected to the same degree.

the connectivity of such networks is highly robust against random failures. We have two limit cases for the Barabasi-Albert model[21]: • No preferential attachment: – Start with n0 nodes. – Π(ki ) = • No growth: 23 1 n0 +t−1 ⇒ P (k) = k e −m e m . networks with power law P(k). most vertices have the same low degree.e. The Internet chugs right along despite frequent router failures. with m(≤ n0 ) edges. but vulnerable to attacks.There are two diﬀerent kinds of scale-free networks. The Internet will even lose it’s integrity with 4% of it’s most important routers being destroyed. at each time step add a new node. are considered: • scale-free networks with no local clustering produced by the Barabasi-Albert model and • scale-free networks with high clustering properties as in the model by Klemm and Eguiluz(2002). but a small number of vertices have a much higher degree. the scale-free networks are heterogeneous in nature. On the other hand: the average performance of the Internet would be cut in half.e. i. This is known as the Achilles heel of the Internet. The heterogeneity feature makes a scale-free network error tolerant. i. and their properties are compared to the properties of random graphs (exponential graphs). that is. if 1% of the most highly connected routers were incapacitated. A power-law distribution shows that. most nodes have few connections. and only a small number of nodes have many connections. but it is also extremely fragile to attacks. As we stated before.

all nodes are connected.5 2 2. after T ≈ N 2 time steps. 4 • Small-world: C(p) >> C(1).6 0.3 0. • Random networks: L(1) ∼ • Scale-free networks: L ∼ 2. (highly clustered for small values of p.5 5 Figure 2. lnN .2 0. 2. The shape of the degree distribution changes from an initial power-law to a Gaussian one.1 0 1 1.8 0.8: The power-law distribution – Start with N nodes.1 Power-law distribution 0. (short paths).4 0. lnlnN . and connected with probability Π(ki ) = Pki j kj – P (k) is not stationary.5 0. the clustering drops with increasing p). a node is selected randomly. at each time step.6 Similarities and Contrasts 1. Average path length: • Regular networks: L(0) ≈ N 2k >> 1. and no edges. (short paths). 24 lnN . Clustering coeﬃcient: • Regular networks: C(0) ≈ 3 . • Small-world networks: L(p) is closed to L(1).9 0.5 4 4.5 3 x 3. (long paths). (highly clustered). lnk (short paths).7 0.

75 . N (poorly clustered). 3. Degree distribution: • Regular networks: Uniform distribution. C decreases with the network size. 25 . (highly clustered.• Random: C(1) ∼ k . • Scale-free: C ∼ N −0. of a random graph). 5 times larger than that. k! e−λ λq . 2 < ν ≤ 3. • Small-world networks: Dq = (1 − p)Pq (p) + pPq−1 (p) with Pq (λ) = • Random networks: Poisson distribution P (k) = e−<k> λk . q! • Scale-free networks: Power-low distribution P (k) ∼ Ck −ν .

in which 26 . This dynamical network is described by: N xi = f (xi ) + ˙ j=1 j=i A(t)cij (xj − xi ). . with each node being an n-dimensional dynamical system.1 Deﬁnitions and Basic Concepts Next. . C(t) = (cij )n×n . 2.Chapter 3 Dynamics and Synchrony 3. . i = 1. j ≤ N at time t. N (3. xi2 . representing the coupling strength and topological structure at time t. xin ) ∈ Rn is a state vector representing the state variables of the node i. A(t) = (aij (t)) ∈ RN ×N . especially in regard to coupling strengths in the network? The general complex dynamical model. is the coupling link matrix between node i and node j (i = j). . we will answer the following two important questions: • When can the complex network achieve the synchronous behaviour? • When is such synchronous behaviour stable. . . is the coupling conﬁguration matrix. for all 1 ≤ i. . consists of N identical linearly and diﬀusively coupled nodes. .1) where xi = (xi1 .

i = 1. . . and aij satisﬁes the condition that: if there is a connection between the node i and the node j (j = i). . and the diagonal elements aii are deﬁned by: aii = − j=1 j=i aij = −ki . .5) .3) As a special case. In the Wang-Chen model.aij is deﬁned as follows: if there is a connection between node i and node j. . otherwise aij = 0. then aij = aji = 1 otherwise aij = aji = 0. xin = fn (xi ) ˙ 27 (3. . r2 .2) Now the equation 3. . . the coupling link matrix C(t) can be a constant 0 − 1 matrix in the form Γ = diag{r1 . . . 2. N (3. where c is a constant. . . i = 1.1 can be written as: N xi = f (xi ) + ˙ j=1 A(t)cij xj . . the state equations of the entire network is deﬁned by: N xi1 = f1 (xi ) + c ˙ j=1 aij xj1 xi2 = f2 (xi ) ˙ . Now the model (3. . then aij = 0. 2. . N (3. . .3) reduces to: N xi = f (xi ) + c ˙ j=1 j=i aij Γxj . i = 1. and we obtain a Wang-Chen model[8]. . N (3.4) c is called the coupling strength of the network. rn } and the coupling conﬁguration matrix A(t) = c(aij )N ×N for all time t. 2.

λ1 is less than − T . . = xN (t) = s(t). .4) is said to achieve asymptotically synchronisation. and T > 0 is a positive constant such that. if λ1 is the largest nonzero eigenvalue of the coupling matrix A of the network. The coupled network (3. t→∞ (3. if: λ1 ≤ − T c (3. .6) where s(t) can be an equilibrium point.where the functions fi satisfy fi (0) = 0. the network will synchronise if the eigenvalue λ1 is negative enough.7) where c > 0 is the network coupling strength. Our assumptions about the coupling matrix A imply that.i. c (3. the synchronisation state of network (3. with multiplicity one. and even a chaotic orbit.8) 3. and all the other eigenvalues of A are strictly negative.e. one eigenvalue of A is zero. zn = fn (z) ˙ The stability of the synchronisation of the network can be characterised by the nonzero eigenvalues of the coupling matrix A. if: x1 (t) = x2 (t) = . .2 Synchronisation in Regular Networks Two coupling conﬁgurations were studied in [17]: • the easiest-to-implement nearest neighbour coupling: consists of cells arranged in a 28 . a periodic orbit.4) is asymptotically stable[17]. zero is exponentially stable point of the n-dimensional system: z1 = f1 (z) − T z1 ˙ z2 = f2 (z) ˙ .

if the number of cells is large enough. while the nearest neighbour coupled network can not achieve such synchronisation under the same condition. .7 means that.10) . with a suﬃciently large number of cells and with an arbitrary coupling strength.. . 1 . .. is it possible to achieve synchronisation of the network. . We have the following question: for a nearest-neighbour coupled network. The corresponding coupling matrix is: −2 1 −2 1 1 (3. 1 1 1 −N + 1 .ring and coupled to the nearest neighbours. 1 1 1 . . In the case of nearest-neighbour coupling. the globally coupled network will eventually synchronise. .11) . (3. N − 1} 29 (3. The corresponding coupling matrix is: −N + 1 1 1 . . the entire network will synchronise provided that λ1 is negative enough. . . by a small modiﬁcation of the nearest-neighbour coupling conﬁguration? The condition 3.. . . k = 0. . 1. −N + 1 for any given coupling strength. . . the eigenvalues of the coupling matrix A are {−4sin2 kπ N . .. 1 1 −N + 1 1 ..9) 1 1 1 −2 • the most diﬃcult-to-implement global coupling: any two diﬀerent cells are connected directly. . .

λpN decreases to −N as p increases from 0 to 1. Wang and Chen found that: 1. Now the coupling matrix A is a function in p and N.3 Synchronisation in Small-World Networks Wang and Chen [17]. Let λpN to be the largest nonzero eigenvalue for the coupling matrix A. c there exists a critical value p so that. For any given value of N. the coupling matrix A has zero as a single eigenvalue. 30 . if λpN ≤ − T c the corresponding network with small-world connections will synchronise. where 0 < p < 1. λpN decreases to −∞ as N increases to +∞. aij is set to be equal to aji = 1 with probability p. and so are it’s eigenvalues. if p ≤ p ≤ 1. then. and then. then the diagonal elements aii must be re-computed. considered a one dimensional lattice of N vertices arranged in a ring with connections between only nearest neighbours. Each connection must be rewired with some probability p. If aij = 0. 2. For any given N > T . for any given coupling strength c > 0: 1. and all the other eigenvalues are −N.Therefore the nearest neighbour coupled network will asymptotically synchronise if 4sin2 kπ N ≥ T c In the case of global coupled conﬁguration. hence restructuring the coupling matrix A. ˜ ˜ then the small-world will synchronise. 1). For any given value of p ∈ (0. and therefore the network will asymptotically synchronise if n≥ T c 3.

1 Synchronisation in Scale-Free Networks Stability Analysis Wang and Chen[16] assumed that. then the synchronised states (3. there exists a critical value N so that. is that. . while a few nodes are big with very high degrees (rich get richer phenomena). i) 1 = j=1 aji = 2ki (3. :) 1 = a(:. 3. Then the coupling conﬁguration matrix A = (aij ) ∈ RN ×N is symmetric. 3. irreducible matrix. . then the small-world connected network will synchronise. ≥ λN be the eigenvalues of A. 1). the network is connected in the sense that.2) implies: N a(i. Equation (3.12) The power law connectivity distribution makes a scale-free network extremely nonhomogeneous: the majority of nodes are small nodes with very small degrees. of the function f . N (3. That implies. If s(t) is an equilibrium point. the real parts of the eigenvalues of the matrix Df (s(t)) + cλk Γ are all negative.˜ ˜ 2.4 3. are exponentially stable. :) and the ith column a(:. evaluated at s(t). if N ≥ N. then a necessary and suﬃcient condition for the synchronisation stability.4. The ith row a(i.13) where Df (s(t)) is the Jacobian matrix. and a few row-column pairs have a large 1 − norm. 31 . there are no isolate clusters. Let 0 = λ1 > λ2 ≥ λ3 ≥ . . For any given p ∈ (0. most row-column pairs of the coupling matrix have a small 1 − norm. .6) are exponentially stable. i) of matrix A will be called ith the row-column pair of A. If the N −1 of n-dimensional linear time-varying systems w = (Df (s(t)) + cλk Γ)w. . ˙ k = 2. .

944.14) N →∞ ˆ ¯ which means that. 3.981. 7. satisfying: ˆ ¯ lim λ(m. the synchronizability of network (3. That is due to the selforganisation process of scale-free networks with a large size. N) the coupling matrix of the scale-free dynamical network (3. ¯ ¯ If λ(m.985 respectively. N). then for a ﬁxed value of m. is said to be strong. They argued that.4. In their construction of scale-free network.9 ¯ and −0.Given the dynamics of an isolate node and the inner linking structure Γ. λ(m. considered the robustness against either the randomly or speciﬁcal removal of a small fraction f . then the synchronisation stability of the network will also remain unchanged after the removal of some of it’s nodes. ¯ which has N nodes and m(N − m) connections. Wang and Chen[16].2 Robustness and Fragility of Synchronisation: To check the robustness of synchronisation in a scale-free dynamical network. ¯ and denoted by A(m. 32 . 5. and 11. N) decreases to a negative constant λ(m) as N increases to in¯ ﬁnity. which will change the coupling matrix. λ(m.973.4) with respect to a speciﬁc coupling conﬁguration A. And they concluded that. (0 < f << 1) of nodes in the network. if the network can synchronise with small coupling strength c.4). −0. if the second largest eigenvalue of the coupling matrix remains unchanged. Wang and Chen [16 ]set n0 = m = m. N) is a decreasing and ¯ ¯ ¯ bounded function of N. adding of new nodes in a scale-free network cannot decrease the synchronizability of the network. for m = 3. despite constantly adding of new nodes. N) = λ(m) < 0 ¯ (3. which makes the synchronizability remain almost unchanged. λ(m) ≈ −0. N) is the average value of the ¯ second eigenvalue of A(m. 9. −0. −0. ˆ ¯ Wang and Chen [16] found that.

So the second largest eigenvalue of the coupling matrix A remains 33 (3. the error tolerance of the syncronizability in scale-free networks may be due to their extremely inhomogeneous connectivity distributions. even when as many as 5% of randomly chosen nodes are removed. Hence.15) . described by N = 3000. and λ2 ˜ ˜ and λ2 be the average values of the second largest eigenvalues of A and A respectively.Furthermore. . . i. i2 . and m0 = m = 3. .˜ Let A ∈ RN ×N and A =∈ RN −[f N ]×N −[f N ] be the coupling matrices of the original with N nodes and and the new network after removal [f N] nodes respectively. then against each node ik both of the ith row and column must be removed from the original coupling k ˜ matrix A. the matrix A remains to be an irreducible and symmetric matrix. a matrix B can be obtained. showed that. ˜ λ2 = λ2 which implies that.e. aij = bij ˜ N aii = − ˜ j=1 j=i aij Robustness of Syncronizability Against Failure: Wang and Chen [16]. e. The removal of small nodes does not alter the path structure of the remaining nodes and thus does not destroy the connec˜ tivity of the network. then [f N] nodes will be selected with much higher probability if N >> 1 and f << 1. it was found that. the second largest eigenvalue of the coupling matrix remains almost unchanged. i. They mentioned that. and at the end. i[f N ] are the nodes removed from the network. in the simulation. . The matrix A can be obtained by recomputing the diagonal elements of the matrix B. That is because of most of nodes are small nodes with very low degrees. If the nodes i1 . the syncronizability of the network is almost unaﬀected. a small node with a low degree corresponds to a row-column pair with a small 1-norm.

to simulate the inﬂuence of an attack on the syncronizability of the network. and then continue to remove the node with the next highest degree. when only 1% of the most connected nodes was removed. Fragility of Synchronisation Against Attack: Wang and Chen [16]. 34 . The vulnerability of connectivity and synchronizability to attack in scale-free networks. f ∼ 1. implying that. ˜ λ → 0. and the removal of a small percentage of them. is rooted in their heterogeneity distributions. dominates the network dynamics. one may ﬁrst remove the node with the highest degree. That is. implies that. mentioned that. the magnitude of the second largest eigenvalue of the coupling matrix decreases rapidly –almost decreases to half of its original value in magnitude. They found that. is formed by removing a small percentage of row-column pairs of A. At a low critical threshold. the minor matrix B of A. a small number of big nodes with high degrees. the whole network was broken into isolate clusters.6%. then so nodes are removed in decreasing order of degrees.almost unchanged with the removal of such raw-column pairs with a small 1-norm. with big 1 − norm.

the phosphate and it’s base and is called a nucleotide. and linked together through molecules called bases. . the bases are paired such that. instead of 2’-deoxyribose. The two strands are twisted together into a double helix. 35 1. cytosine (C) and guanene (G). The basic unit of the DNA consists of the sugar.1 Background: Regulatory Networks Each strand has a backbone formed of sugar molecules called 2’-deoxyribose attached to a phosphate residue. • the base thymice (T) is replaced by the base Uracil (U). The diﬀerences between them are that: • the sugar is ribose in RNA. In the DNA. These two pairs are called pairs of complementary basis[10][16]. A is always paired to T and C is always paired to G.Chapter 4 Application: Genetic Regulatory Networks 4. RNA: RNA molecules are similar to the DNA molecules. which also binds to the adenene. 2. There are four bases for the DNA. adenene (A). thymine (T). DNA: The simplest structure of a DNA molecule has two chains called strands.

while the codons TGA. The Central Dogma of Molecular Biology: In Eucaryotic cells. For example. The sequence of amino acids for a given protein is encoded by using triplets of nucleotides called codons to specify each amino acid contained in the protein. structural proteins which are the main building blocks of tissues. 5. while proteins are made in the cytoplasm. and • the DNA performs only one function that of encoding information. A messenger molecule is used to carry the information from the nucleus to the ribosomes in the cytoplasm. and certain contiguous stretches of a chromosome encode information for building proteins. Proteins are divided into two main groups. The beginning of a gene is recognised due to a promoter (DNA region serves 36 . In the ribosome the amino acids are assembled one-by-one according to information encoded in the messenger RNA (mRNA).• the RNA is single stranded. Proteins: a protein is a long chain of molecules called amino acids. and enzymes. AUG encodes methionine but also it encodes the beginning of a gene. Such a stretch of DNA that contains information for building a protein or RNA molecule is called a gene. 3. Genes: each protein or RNA found in an organism is encoded in the DNA. The long chains of amine acids then folding the appropriate proteins. such as mRNA and tRNA[10]. the codon CCG encodes the amino acid glycine. in the cell. while there are diﬀerent types of RNA performing diﬀerent functions. There are twenty diﬀerent amino acids can be observed in the nature. the DNA is found in the nucleus. Each cell of an organism has a few very long DNA molecules called chromosomes. which catylize chemical reactions. Proteins are produced in a structure of the cell called a ribosome. TAA and TAG encode a stop signal. 4.

The codon AUG signals the start of a gene.as an indication of a gene). are amino acids and transfer RNA (tRNA) molecules. In the cytoplasm. which was originally copied from the DNA in the nucleolus. and the two amino acids are chemically joined together. into the cytoplasm. The next tRNA brings its amino acid. The process continue until a whole chain of amino acids (protein) is made according to the code on the mRNA. This process is called the transcription. it is copied to the mRNA. attaches to the other end of the tRNA. which represent only one amino acid. The mRNA travels out of the nucleus. Figure 4. The tRNA which has three bases called anti-codons to ﬁt the ﬁrst three on the mRNA brings it’s amino acid to the ribosome. The corresponding amino acid. while a third tRNA arrives with it’s amino acid.1: Source of this ﬁgure [29] 37 . Having recognised the beginning of the gene by the mRNA polymerase. Each tRNA molecules has three bases at one end. The mRNA moves along by three bases and the ﬁrst tRNA is released. where it joins up with it. This process is called the translation[16].

6. Generally this molecular address is itself a set of DNA sequences that are located near the target gene. known as repressors. the proteome. • Negatively-acting transcription factors.These regulatory sequences are also known as cis-acting factors. deﬁned the set of proteins and their interactions by physical contact. known as activators. Regulation of Gene: The DNA molecules found in chromosomes are millions to hundreds of millions of base pairs in length. it is ﬁrst necessary to ﬁnd the speciﬁc sequence that contains it. This process uses two components. To access a speciﬁc piece of information stored within a DNA molecule. Genetic Regulatory Networks: Indirectly we saw the three components of the cellular network. Whether a transcription factor acts as a repressor or an activator may depend on the context in which it ﬁnds itself. These proteins are known as transcription factors because they regulate transcription. integrated by all metabolites and the pathways which link each other. because they are products of other genes. 7. These sub-networks of the cellular network are very intertwined since for in38 . while cis-acting factors are an essential part of the gene being regulated. suppress transcription. and the metabolic network. the genome in which genes can aﬀect each others level of expression. This address both identiﬁes the informational sequence and contains instructions for determining when and where the information should be used or expressed. First information stored in DNA must have a molecular address. Proteins are used to recognise these regulatory sequences. They are sometimes called trans-acting factors. and the other polypeptides with which it interacts. stimulate transcription. Transcription factors fall into two broad groups: • Positively-acting transcription factors.

. Some metabolic pathways regulated by proteins themselves. A gene may directly or indirectly contribute to regulating itself. 4. where the gene expression pattern needs to be stable but also adaptable. The systems dynamic can be described by[8]: t+1 t t t gi = fi (gj1 . He aimed to ﬁnd properties which would apply to the system in it’s entirety.stance. Genes regulate each other’s activity by coding for transcription factors. so a gene may indirectly inﬂuenced by many genes upstream.1) 39 . . a complex feedback web of genes turning each other on and oﬀ. may be the very ones to catalyse the formation of nucleotides. is the only way to deal with their complexity. Regulatory networks may be irreducible. .2 Modelling Genetic Regulatory Networks Mathematical models of GRN have been developed to allow predictions of the models to be tested. in turn aﬀecting the process of translation[8]. genes can only aﬀect other genes through special proteins. those genes regulate other genes in turn. Kauﬀman adopted the complementary perspective of studying Boolean Networks wired in random. at particular sites. . A cell type depends on the particular subset of active genes. and the computer modelling of them. The result is a genetic regulatory network (GRN). updating their on-oﬀ state in parallel. which may enhance or repress the expression of other genes by binding. according to the combinatorial logic of their inputs.1 Boolean Network Model In Kauﬀman model genes are connected by directed links(transcription factors). 4. gjK ) (4. A given gene may directly regulate just a small set of other genes. gj2.2.

Too much ﬂexibility might allow a perturbation to ﬂip the dynamics too readily into a diﬀerent basin of attraction. to a diﬀerent cell type. or changing. . a state will be reached that has already been visited before. A cell type may be a set of closely related gene expression patterns. and at each time step it jumps to a diﬀerent point. or shifting around within the basin of attraction. S = (g1 . is given by the composite state of all the genes. and p actually tunes the susceptibiliy of the function to changes in the input value. K and p are the only two interesting parameters in this model.1) from the values of their inputs. oﬀ. gN ) S represents a point in the space of all possible states. closing the trajectory into either a loop of a single state. that parallel synchronously updated with the evolution of the time using equation (4. following a trajectory given by the network conﬁguration. Cells constantly need to adapt their gene expression pattern in response to a variety of hormone and growth/diﬀerentiation factors from nearby cells. chaotic dynamics. The model has been criticized for being too simple. Dynamics that settles to a pattern where a large proportion of the genes are permanently on or oﬀ (frozen) may be too inﬂexible for adaptive behaviour. The diﬀerent subsets of the starting states that end in the same loop are called basins of attraction. that is. g2 . on the attractors.The K inputs of each node are chosen at random. The parameter K deﬁnes the average connectivity between nodes. . if this state maps onto itself. In a cell type’s gene expression pattern over a span of time. and 0 with probability 1 − p. among the N units of the system and the functions are chosen such that. the cell will be unstable. a particular gene may. . allwoing an essential measure of ﬂexibility in behaviour. the output have 1 with probability p. 40 . . starting at the chosen initial state. be either on. If a large proprtion of the genes are changing. The global state S of the system. As time goes on.

the regulatory interactions are modelled by the kinetic equations: xi = fi (x). 4. x2 . In this case the basin of attraction ﬁeld remains unchanged. • Positive feedback systems.2 Diﬀerential Equations Models This method models reaction kinetics of the production. resulting in an altered basin of atracion ﬁeld. gene encodes the protein inhibits its own expression. represented by continuous variable xi (t) ∈ R+ .2) The rate of change of variable xi is a function of other concentration variables x = [x1 . Alternatively. and other molecules at the time t. protein production is a continuous process. . in order to make discoveries. or it may be ﬂipped to another basin. the network itself may undergo a mutation. a diﬀerent cell type. Then if x1 denotes the concentration of the mRNA. . .The basins of attraction in random Boolean networks are idealized models for the stability of cell types against mutations. mRNA. and x2 denotes the concentration of the protein. This model provides a mechanism for both the stability and adaptability of gene expression[34]. Now we can describe two types of feedback systems(they are not the only types of systems): • Negative feedback systems. which would temporarily adapt the pattern.2. Then. ˙ 1≤i≤n (4. . the model for the negative feedback systems is 41 . Negative Feedback Systems: In this system. the dynamics may jump to a diﬀerent subtree in the same basin. This method assumes that. 1. The cellular concentrations of proteins. diﬀusion/transport and binding of proteins to genes. and also for their response to perturbation. xn ]′ .

Positive Feedback Systems: In this system.given by the two equations: x1 = −γ1 x1 + κ1 f (x2 ) ˙ x2 = −κ2 x1 + γ2 (x2 ) ˙ where κ1 . γ2 > 0 are the degenerProtein Gene (4. and γ1 . the gene encodes the protein activating its own expression. The values of x1 and x2 are ˙ given by: x1 = 0 : ˙ x2 = 0 : ˙ κ1 f (x2 ) γ1 γ2 x1 = x2 κ2 x1 = θn . κ2 > 0 are the production rate constants. This system has a single steady state at x = 0. after perturbation system will return to steady state (homeostasis). 42 . θ n +xn where θ > 0 is This steady state is stable.2: Negative feedback system ation rate constants.3) − __ mRNA Protein Figure 4. The function f (x) is given by: f (x) = the threshold value. that is. 2.

2 1.4 0. θ n +xn (4.6 Figure 4. γ2 > 0 are the degeneration rate constants.8 x1 0.4: Positive feedback system centration of the protein. and x2 denotes the conProtein Gene − + mRNA Protein Figure 4. and the model for the positive feedback systems is given by the two equations: x1 = −γ1 x1 + κ1 f (x2 ) ˙ x2 = −κ2 x1 + γ2 (x2 ) ˙ where κ1 . x1 denotes the concentration of the mRNA. κ2 > 0 are the production rate constants.4 1.1. and γ1 .8 x2 1 1. the function f (x) this time is given by: f (x) = 43 xn .6 0.4) . But.6 0.2 0.3: The steady states are represented by the intersections between the two curves n γ 1 x1 = κ1 f (x) = θnθ n and the straight line x1 = κ2 x2 γ +x 2 As before.4 0.2 0 0 0.2 1 0.

3 The Artiﬁcial Genomic Model Using artiﬁcial genomes to model genetic networks is a new method ﬁrst used by Torsten Reil[26].8 x2 1 1.2. A TATA box type promoter is deﬁned which in Reil’s model is 0101.2 1 0. The 6 digits preceding this sequence are considered to be a gene.5: The steady states are represented by the intersections between the two curves n γ 1 x1 = κ1 f (x) = θnx n and the straight line x1 = κ2 x2 γ +x 2 There are also other deterministic models as the time delay feedback system model.4 1. gene length.4 0.4 0.6 0.8 x1 0. Reil used this model and found that. The pattern produced is then matched to the rest of the genome. the genome size. and the degree of inhibition.2 1. 1. Four parameters can be modiﬁed in Reil’s implementation. If a pattern matches a position in the genome the next 0101 sequence following from that pattern is found and is then switched on or oﬀ depending on the pattern’s sequence. it produced cycles. When a gene is being transcribed the digits all increase by one so a gene sequence like this 012130 becomes 123241. The method uses a randomly generated string of digits to represent the genome.6 0. base. Whether a pattern represents a repressor or derepressor depends on the patterns sequence.6 Figure 4. 4.2 0 0 0.where θ > 0 is the threshold value. which were like that of cell 44 . that are.2 0.

cycles. such as the model by Hallinan and Wiles[11]. the ﬁrst was the manner in which inhibitory links are implemented. producing cycles which mimic cellular cycles. Manually switching on or oﬀ speciﬁc genes. This system also shows a level of robustness as transient disturbances in the expression proﬁle usually don not alter the expression pattern. 2004. like diﬀerentiation. and high synchrony. More patterns are produced. 45 . Hallinan and Wiles obtained as results. Once the pattern is produced every gene. but knocking out speciﬁc genes. and more genes are turned on and oﬀ. is their update scheme (They used synchrony parameter). does aﬀect the expression proﬁle. and the second. which has this as a promoter is switched on. were constructed to determine the dynamics in the regulatory networks. with some modiﬁcations in it. Many models based on Reil’s model. This system was able to show both stability and multi-periodicity. Their model was diﬀerent from Reil’s model in two major ways. when the programme was started with just one gene switched on. could also cause movement of the cell into a diﬀerent attractor cycle. transient graphs with low synchrony.

if p exceeded a threshold value pc . the characteristic path length.Chapter 5 Discussions The complexity of a network can occur from either it’s structure or the dynamics of it’s complex nodes. To reveal results about the synchronisation in small-world networks. asynchronous or a transient synchronisation behaviour. if the second-largest eigenvalue of the coupled-conﬁguration matrix is small enough. small-world. Random removing of a fraction of nodes with their connections from some network with a probability p. but fragile to removing the highly connected nodes. Wang and Chen 46 . can be always characterised by the three characteristic properties. The dynamics of the nodes in networks. The system can achieve the synchronisation. And the regular lattices can achieve the synchronisation faster than the random networks. may end by synchronous. may cause in breaking down that network into disconnected smaller networks. or probably both of them. and most of large-scale scientiﬁc and engineering computations are synchronous or loosely synchronous. the clustering coeﬃcient and the node degree distribution. The complex networks with diﬀerent topologies (regular. The scale-free networks are more robust than random networks against random node failures. So. networks vary in their resilience to the removal of some of their nodes. completely random or scale-free structures).

and the given information. the synchronizability of a scale-free network is robust to the random removal of nodes. These methods. which explains why many real large networks exhibit atendancy towards synchronisation. Wang and Chen [31] also showed that. the Bayesian methods and the artiﬁcial genome models. included the boolean networks. All the above methods used to model the genetic regulatory networks depend on the computer in understanding the genetic regulatory processes. It is not the case in the real life. the values of the variables are updated synchronously. for any given coupling strength and a suﬃciently large number of cells. the scale-free dynamical network is much easier to achieve synchronisation than the locally regularly coupled dynamical network. and the root of this synchronisation is the scale-free nature of the network. the small-world coupled continuous system can achieve the synchronisation. In the boolean networks model. many researches adopted the technique of the asynchronous updade for the variables of the given models. Generally. For the genetic regulatory networks. many methods of modelling were created to describe the dynamics of these network. 47 . and so in the diﬀerential equations models. the results obtained for the behaviour of the GRN’s. On the otherhand.[32] started with a nearest-neighbour coupled dynamical network. but fragile to the removal of nodes with high connections. They showed that. and revealed the exsistance of pseudo-periodic loose attractors[11]. for small values of p. then used the StrogatzWatt algorithm to construct a small-world network. the genes are activated asynchronously. They found that. depending on the connectivity and degree of inhibition of the network. the diﬀerential equations. ranging from stability to limit cycles to chaotic behaviour. The synchronisation is chaotic. where the choice of approach depend on the aim of the analysis.

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