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14
Scale Invariance in Biology: Coincidence Or Footprint of a Universal Mechanism?
, 2001
"... In this article, we present a selfcontained review of recent work on complex biological systems which exhibit no characteristic scale. This property can manifest itself with fractals (spatial scale invariance), flicker noise or 1}fnoise where f denotes the frequency of a signal (temporal scale i ..."
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Cited by 23 (1 self)
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In this article, we present a selfcontained review of recent work on complex biological systems which exhibit no characteristic scale. This property can manifest itself with fractals (spatial scale invariance), flicker noise or 1}fnoise where f denotes the frequency of a signal (temporal scale invariance) and power laws (scale invariance in the size and duration of events in the dynamics of the system). A hypothesis recently put forward to explain these scalefree phenomomena is criticality, a notion introduced by physicists while studying phase transitions in materials, where systems spontaneously arrange themselves in an unstable manner similar, for instance, to a row of dominoes. Here, we review in a critical manner work which investigates to what extent this idea can be generalized to biology. More precisely, we start with a brief introduction to the concepts of absence of characteristic scale (powerlaw distributions, fractals and 1}fnoise) and of critical phenomena. We then review typical mathematical models exhibiting such properties : edge of chaos, cellular automata and selforganized critical models. These notions are then brought together to see to what extent they can account for the scale invariance observed in ecology, evolution of species, type III epidemics and some aspects of the central nervous system. This article also discusses how the notion of scale invariance can give important insights into the workings of biological systems.
On the numerical integration of motion for rigid polyatomics: The modified quaternion approach
 Computers in Physics 12
, 1998
"... A revised version of the quaternion approach for numerical integration of the equations of motion for rigid polyatomic molecules is proposed. The modified approach is based on a formulation of the quaternion dynamics with constraints. This allows to resolve the rigidity problem rigorously using cons ..."
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Cited by 7 (1 self)
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A revised version of the quaternion approach for numerical integration of the equations of motion for rigid polyatomic molecules is proposed. The modified approach is based on a formulation of the quaternion dynamics with constraints. This allows to resolve the rigidity problem rigorously using constraint forces. It is shown that the procedure for preservation of molecular rigidity can be realized particularly simply within the Verlet algorithm in velocity form. We demonstrate that the presented method leads to an improved numerical stability with respect to the usual quaternion rescaling scheme and it is roughly as good as the cumbersome atomicconstraint technique. 2 1
Parallel Cluster Labeling on a Network of Workstations
 In Proceedings of the Thirteenth Brazilian Symposium on Computer Networks
, 1995
"... In recent years, encouraged by today's fast workstations and by software systems designed to transform workstation clusters into parallel programming environments, network of workstations have been increasingly used as computational engines. Networked workstations, however, are not ideal replacement ..."
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Cited by 2 (1 self)
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In recent years, encouraged by today's fast workstations and by software systems designed to transform workstation clusters into parallel programming environments, network of workstations have been increasingly used as computational engines. Networked workstations, however, are not ideal replacements for supercomputers, because of the low interconnection capacity provided by current local area networks. In this paper, we present an application using the EcliPSe toolkit, a system for replicationbased parallel processing in heterogeneous environments. Although primarily designed for replicative applications (that generally do not require large amounts of communication), EcliPSe can be used for more general forms of messagepassing parallel processing. We describe the use of the toolkit in the parallelization of a cluster labeling algorithm. The algorithm is designed so that it uses some of EcliPSe's features to reduce communication overhead, making the algorithm suitable for execution o...
A Test Set for Molecular Dynamics Algorithms
, 2002
"... This article describes a collection of model problems for aiding numerical analysts, code developers and others in the design of computational methods for molecular dynamics (MD) simulation. Common types of calculations and desirable features of algorithms are surveyed, and these are used to guide s ..."
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Cited by 2 (0 self)
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This article describes a collection of model problems for aiding numerical analysts, code developers and others in the design of computational methods for molecular dynamics (MD) simulation. Common types of calculations and desirable features of algorithms are surveyed, and these are used to guide selection of representative models. By including essential features of certain classes of molecular systems, but otherwise limiting the physical and quantitative details, it is hoped that the test set can help to facilitate crossdisciplinary algorithm and code development efforts.
AND POWER. IN THE PAST, EDUCATORS WERE CONTENT TO HAVE
"... undergraduates view scientific computation as black boxes (an abstraction of a device in which only its externally visible behavior is considered, not its implementation) and have them wait for graduate school to learn what’s inside. 1 Our increasing reliance on computers makes this less true today, ..."
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undergraduates view scientific computation as black boxes (an abstraction of a device in which only its externally visible behavior is considered, not its implementation) and have them wait for graduate school to learn what’s inside. 1 Our increasing reliance on computers makes this less true today, and much less likely to be true in the future. To adjust to the growing importance of computing in all of science, Oregon State University’s Physics Department now offers a fouryear, researchrich curriculum leading to a bachelor’s degree in computational physics (CP; www.physics. orst.edu/CPUG/). The five computational courses developed for this program act as a bridge connecting physics with the computation, mathematics, and computational science communities.
Firstorder phase transition in a 2D randomfield Ising model with conflicting dynamics
, 901
"... The effects of locally random magnetic fields are considered in a nonequilibrium Ising model defined on a square lattice with nearestneighbors interactions. In order to generate the random magnetic fields, we have considered random variables {h} that change randomly with time according to a double ..."
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The effects of locally random magnetic fields are considered in a nonequilibrium Ising model defined on a square lattice with nearestneighbors interactions. In order to generate the random magnetic fields, we have considered random variables {h} that change randomly with time according to a doublegaussian probability distribution, which consists of two single gaussian distributions, centered at +ho and −ho, with the same width σ. This distribution is very general, and can recover in appropriate limits the bimodal distribution (σ → 0) and the single gaussian one (ho = 0). We performed Monte Carlo simulations in lattices with linear sizes in the range L = 32 − 512. The system exhibits ferromagnetic and paramagnetic steady states. Our results suggest the occurence of firstorder phase transitions between the abovementioned phases at low temperatures and large randomfield intensities ho, for some small values of the width σ. By means of finite size scaling, we estimate the critical exponents in the lowfield region, where we have continuous phase transitions. In addition, we show a sketch of the phase diagram of the model for some values of σ. PACS numbers: 05.10.Ln, 05.50.+q, 64.60.De, 75.10Hk, 75.40.MgFirstorder phase transition in a 2D randomfield Ising model with conflicting dynamics2 1.
unknown title
"... On periodic boundary condition in Monte Carlo simulation of charge transport in disordered organic systems ..."
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On periodic boundary condition in Monte Carlo simulation of charge transport in disordered organic systems