Random network behaviour of protein structures

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus imperative that, apart from the protein backbone, other tunable degrees of freedom be accountable. Here, we focus on side-chain interactions, which non-covalently link amino acids in folded proteins to form a network structure. At a coarse-grained level, we show that the network conforms remarkably well to realizations of random graphs and displays associated percolation behavior. Thus, within the rigid framework of the protein backbone that restricts the structure space, the side-chain interactions exhibit an element of randomness, which account for the functional flexibility and diversity shown by proteins. However, at a finer level, the network exhibits deviations from these random graphs which, as we demonstrate for a few specific examples, reflect the intrinsic uniqueness in the structure and stability, and perhaps specificity in the functioning of biological proteins.

An asymptotically optimal push-pull method for multicasting over a random network

We consider multicast flow problems where either all of the nodes or only a subset of the nodes may be in session. Traffic from each node in the session has to be sent to every other node in the session. If the session does not consist of all the nodes, the remaining nodes act as relays. The nodes are connected by undirected edges whose capacities are independent and identically distributed random variables. We study the asymptotics of the capacity region (with network coding) in the limit of a large number of nodes, and show that the normalized sum rate converges to a constant almost surely. We then provide a decentralized push-pull algorithm that asymptotically achieves this normalized sum rate.

Ising model on a random network with annealed or quenched disorder

We study the equilibrium properties of an Ising model on a disordered random network where the disorder can be quenched or annealed. The network consists of fourfold coordinated sites connected via variable length one-dimensional chains. Our emphasis is on nonuniversal properties and we consider the transition temperature and other equilibrium thermodynamic properties, including those associated with one-dimensional fluctuations arising from the chains. We use analytic methods in the annealed case, and a Monte Carlo simulation for the quenched disorder. Our objective is to study the difference between quenched and annealed results with a broad random distribution of interaction parameters. The former represents a situation where the time scale associated with the randomness is very long and the corresponding degrees of freedom can be viewed as frozen, while the annealed case models the situation where this is not so. We find that the transition temperature and the entropy associated with one-dimensional fluctuations are always higher for quenched disorder than in the annealed case. These differences increase with the strength of the disorder up to a saturating value. We discuss our results in connection to physical systems where a broad distribution of interaction strengths is present.

Synchronised firing patterns in a random network of adaptive exponential integrate-and-fire

Acknowledgements This study was possible by partial financial support from the following Brazilian government agencies: CNPq, CAPES, and FAPESP (2011/19296-1 and 2015/07311-7). We also wish thank Newton Fund and COFAP.

Analysis of a stochastic SIR epidemic on a random network incorporating household structure

This paper is concerned with a stochastic SIR (susceptible-infective-removed) model for the spread of an epidemic amongst a population of individuals, with a random network of social contacts, that is also partitioned into households. The behaviour of the model as the population size tends to infinity in an appropriate fashion is investigated. A threshold parameter which determines whether or not an epidemic with few initial infectives can become established and lead to a major outbreak is obtained, as are the probability that a major outbreak occurs and the expected proportion of the population that are ultimately infected by such an outbreak, together with methods for calculating these quantities. Monte Carlo simulations demonstrate that these asymptotic quantities accurately reflect the behaviour of finite populations, even for only moderately sized finite populations. The model is compared and contrasted with related models previously studied in the literature. The effects of the amount of clustering present in the overall population structure and the infectious period distribution on the outcomes of the model are also explored.

Threshold behaviour and final outcome of an epidemic on a random network with household structure

This paper considers a stochastic SIR (susceptible-infective-removed) epidemic model in which individuals may make infectious contacts in two ways, both within 'households' (which for ease of exposition are assumed to have equal size) and along the edges of a random graph describing additional social contacts. Heuristically-motivated branching process approximations are described, which lead to a threshold parameter for the model and methods for calculating the probability of a major outbreak, given few initial infectives, and the expected proportion of the population who are ultimately infected by such a major outbreak. These approximate results are shown to be exact as the number of households tends to infinity by proving associated limit theorems. Moreover, simulation studies indicate that these asymptotic results provide good approximations for modestly-sized finite populations. The extension to unequal sized households is discussed briefly.

UPGRADING AN INTERMITTENT & BRANCHED WATER NETWORK TO A CONTINUOUS & LOOPED NETWORK: A CASE STUDY IN COASTAL PERU

This case study sought to determine how the potable water network of Cerro Prieto, Peru could be improved. The network as it exists now is branched and operated intermittently, exposing residents to water contamination risks and inconvenience. Using EPANET, it was found that the as-built network can support continuous water service, all points could stay over 10 psi, and the current water consumption rate could be maintained. To keep all points over 20 psi, the height of elevated water tank must be increased 6 feet, and the pump switched on whenever the tank drains. It was also found that almost the entire community would benefit from several possible closed loops in the network, but the high cost gives downstream loops higher priority. Due to the scarcity of water in the region, the first action must be assessing the well capacity, and a water conservation plan that may include water meters.

Étude en dynamique moléculaire par approximation des liaisons fortes de l'influence des défauts ponctuels dans la relaxation du silicium amorphe

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Transforming the psychological contract through a continuous innovation methodology

This paper introduces the Corporate Culture Change Cycle: a continuous innovation methodology for transforming the psychological contract in an organisational context. The eight step process is based on the action learning model. The purpose of this methodology is to benchmark the psychological contract against eight changing values of the employment relationship as a basis for facilitating a process of aligning the changing needs of employer and employee. Both the Corporate Culture Change Cycle and the New Employment Relationship Model have been validated in several organisational settings and subsequently refined. This continuous innovation methodology addresses gaps in the psychological contract, change management and continuous innovation research literatures. The approach therefore should be of interest to researchers in these fields of study and from a practical perspective for managers wishing to transform their workplace cultures.

Mechanical properties of bioinspired bicontinuous nanocomposites

Inspired by the wonderful properties of some biological composites in nature, we performed molecular dynamics simulations to investigate the mechanical behavior of bicontinuous nanocomposites. Three representative types of bicontinuous composites, which have regular network, random network, and nacre inspired microstructures respectively, were studied and the results were compared with those of a honeycomb nanocomposite with only one continuous phase. It was found that the mechanical strength of nanocomposites in a given direction strongly depends on the connectivity of microstructure in that direction. Directional isotropy in mechanical strength and easy manufacturability favor the random network nanocomposites as a potentially great bioinspired composite with balanced performances. In addition, the tensile strength of random network nanocomposites is less sensitive to the interfacial failure, owing to its super high interface-to-volume ratio and random distribution of internal interfaces. The results provide a useful guideline for design and optimization of advanced nanocomposites with superior mechanical properties.

A coordination-based approach to elasticity of floppy and stiff random networks

We study the role of connectivity on the linear and nonlinear elastic behavior of amorphous systems using a two-dimensional random network of harmonic springs as a model system. A natural characterization of these systems arises in terms of the network coordination relative to that of an isostatic network $\delta z$; a floppy network has $\delta z<0$, while a stiff network has $\delta z>0$. Under the influence of an externally applied load we observe that the response of both floppy and rigid network are controlled by the same critical point, corresponding to the onset of rigidity. We use numerical simulations to compute the exponents which characterize the shear modulus, the amplitude of non-affine displacements, and the network stiffening as a function of $\delta z$, derive these theoretically and make predictions for the mechanical response of glasses and fibrous networks.

Characterizations of some continuous distributions using partial moments

Inthis paper,we define partial moments for a univariate continuous random variable. A recurrence relationship for the Pearson curve using the partial moments is established. The interrelationship between the partial moments and other reliability measures such as failure rate, mean residual life function are proved. We also prove some characterization theorems using the partial moments in the context of length biased models and equilibrium distributions

Undersampled Critical Branching Processes on Small-World and Random Networks Fail to Reproduce the Statistics of Spike Avalanches

The power-law size distributions obtained experimentally for neuronal avalanches are an important evidence of criticality in the brain. This evidence is supported by the fact that a critical branching process exhibits the same exponent t~3=2. Models at criticality have been employed to mimic avalanche propagation and explain the statistics observed experimentally. However, a crucial aspect of neuronal recordings has been almost completely neglected in the models: undersampling. While in a typical multielectrode array hundreds of neurons are recorded, in the same area of neuronal tissue tens of thousands of neurons can be found. Here we investigate the consequences of undersampling in models with three different topologies (two-dimensional, small-world and random network) and three different dynamical regimes (subcritical, critical and supercritical). We found that undersampling modifies avalanche size distributions, extinguishing the power laws observed in critical systems. Distributions from subcritical systems are also modified, but the shape of the undersampled distributions is more similar to that of a fully sampled system. Undersampled supercritical systems can recover the general characteristics of the fully sampled version, provided that enough neurons are measured. Undersampling in two-dimensional and small-world networks leads to similar effects, while the random network is insensitive to sampling density due to the lack of a well-defined neighborhood. We conjecture that neuronal avalanches recorded from local field potentials avoid undersampling effects due to the nature of this signal, but the same does not hold for spike avalanches. We conclude that undersampled branching-process-like models in these topologies fail to reproduce the statistics of spike avalanches.

Undersampled Critical Branching Processes on Small-World and Random Networks Fail to Reproduce the Statistics of Spike Avalanches

The power-law size distributions obtained experimentally for neuronal avalanches are an important evidence of criticality in the brain. This evidence is supported by the fact that a critical branching process exhibits the same exponent t~3=2. Models at criticality have been employed to mimic avalanche propagation and explain the statistics observed experimentally. However, a crucial aspect of neuronal recordings has been almost completely neglected in the models: undersampling. While in a typical multielectrode array hundreds of neurons are recorded, in the same area of neuronal tissue tens of thousands of neurons can be found. Here we investigate the consequences of undersampling in models with three different topologies (two-dimensional, small-world and random network) and three different dynamical regimes (subcritical, critical and supercritical). We found that undersampling modifies avalanche size distributions, extinguishing the power laws observed in critical systems. Distributions from subcritical systems are also modified, but the shape of the undersampled distributions is more similar to that of a fully sampled system. Undersampled supercritical systems can recover the general characteristics of the fully sampled version, provided that enough neurons are measured. Undersampling in two-dimensional and small-world networks leads to similar effects, while the random network is insensitive to sampling density due to the lack of a well-defined neighborhood. We conjecture that neuronal avalanches recorded from local field potentials avoid undersampling effects due to the nature of this signal, but the same does not hold for spike avalanches. We conclude that undersampled branching-process-like models in these topologies fail to reproduce the statistics of spike avalanches.

Undersampled Critical Branching Processes on Small-World and Random Networks Fail to Reproduce the Statistics of Spike Avalanches

The power-law size distributions obtained experimentally for neuronal avalanches are an important evidence of criticality in the brain. This evidence is supported by the fact that a critical branching process exhibits the same exponent t~3=2. Models at criticality have been employed to mimic avalanche propagation and explain the statistics observed experimentally. However, a crucial aspect of neuronal recordings has been almost completely neglected in the models: undersampling. While in a typical multielectrode array hundreds of neurons are recorded, in the same area of neuronal tissue tens of thousands of neurons can be found. Here we investigate the consequences of undersampling in models with three different topologies (two-dimensional, small-world and random network) and three different dynamical regimes (subcritical, critical and supercritical). We found that undersampling modifies avalanche size distributions, extinguishing the power laws observed in critical systems. Distributions from subcritical systems are also modified, but the shape of the undersampled distributions is more similar to that of a fully sampled system. Undersampled supercritical systems can recover the general characteristics of the fully sampled version, provided that enough neurons are measured. Undersampling in two-dimensional and small-world networks leads to similar effects, while the random network is insensitive to sampling density due to the lack of a well-defined neighborhood. We conjecture that neuronal avalanches recorded from local field potentials avoid undersampling effects due to the nature of this signal, but the same does not hold for spike avalanches. We conclude that undersampled branching-process-like models in these topologies fail to reproduce the statistics of spike avalanches.