Amos Maritan

Bio: Amos Maritan is an academic researcher from University of Padua. The author has contributed to research in topics: Phase transition & Population. The author has an hindex of 67, co-authored 493 publications receiving 18976 citations. Previous affiliations of Amos Maritan include Purdue University & University of Bari.

A universal model for mobility and migration patterns

Abstract: A parameter-free model predicts patterns of commuting, phone calls and trade using only population density at all intermediate points. Since the 1940s, planners needing to predict population movement, transport-network usage and even epidemics have turned to a model based on the 'gravity law'. This assumes that the number of individuals travelling between two locations is proportional to the population at the source and destination, and decays with distance. This approach has its limitations, because it looks at the flow between two specific points only. Here, Albert-Laszlo Barabasi and colleagues present an alternative model that takes into account population density at all intermediate points. Their parameter-free radiation model predicts a range of phenomena — from commuting and migrations to phone calls — much more accurately than the gravity model. Needing only data on population densities, which are easy to measure, the system can be used to predict commuting and transport patterns even in areas where data are not collected systematically. Introduced in its contemporary form in 1946 (ref. 1), but with roots that go back to the eighteenth century2, the gravity law1,3,4 is the prevailing framework with which to predict population movement3,5,6, cargo shipping volume7 and inter-city phone calls8,9, as well as bilateral trade flows between nations10. Despite its widespread use, it relies on adjustable parameters that vary from region to region and suffers from known analytic inconsistencies. Here we introduce a stochastic process capturing local mobility decisions that helps us analytically derive commuting and mobility fluxes that require as input only information on the population distribution. The resulting radiation model predicts mobility patterns in good agreement with mobility and transport patterns observed in a wide range of phenomena, from long-term migration patterns to communication volume between different regions. Given its parameter-free nature, the model can be applied in areas where we lack previous mobility measurements, significantly improving the predictive accuracy of most of the phenomena affected by mobility and transport processes11,12,13,14,15,16,17,18,19,20,21,22,23.

Size and form in efficient transportation networks

Abstract: Many biological processes, from cellular metabolism to population dynamics, are characterized by allometric scaling (power-law) relationships between size and rate1,2,3,4,5,6,7,8,9,10 An outstanding question is whether typical allometric scaling relationships—the power-law dependence of a biological rate on body mass—can be understood by considering the general features of branching networks serving a particular volume Distributed networks in nature stem from the need for effective connectivity11, and occur both in biological systems such as cardiovascular and respiratory networks1,2,3,4,5,6,7,8 and plant vascular and root systems1,9,10, and in inanimate systems such as the drainage network of river basins12 Here we derive a general relationship between size and flow rates in arbitrary networks with local connectivity Our theory accounts in a general way for the quarter-power allometric scaling of living organisms1,2,3,4,5,6,7,8,9,10, recently derived8 under specific assumptions for particular network geometries It also predicts scaling relations applicable to all efficient transportation networks, which we verify from observational data on the river drainage basins Allometric scaling is therefore shown to originate from the general features of networks irrespective of dynamical or geometric assumptions

Neutral theory and relative species abundance in ecology.

Abstract: The theory of island biogeography asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell generalized this neutral theory to explore the expected steady-state distribution of relative species abundance (RSA) in the local community under restricted immigration. Here we present a theoretical framework for the unified neutral theory of biodiversity and an analytical solution for the distribution of the RSA both in the metacommunity (Fisher's log series) and in the local community, where there are fewer rare species. Rare species are more extinction-prone, and once they go locally extinct, they take longer to re-immigrate than do common species. Contrary to recent assertions, we show that the analytical solution provides a better fit, with fewer free parameters, to the RSA distribution of tree species on Barro Colorado Island, Panama, than the lognormal distribution.

Global protein function prediction from protein-protein interaction networks

Abstract: Determining protein function is one of the most challenging problems of the post-genomic era. The availability of entire genome sequences and of high-throughput capabilities to determine gene coexpression patterns has shifted the research focus from the study of single proteins or small complexes to that of the entire proteome 1 . In this context, the search for reliable methods for assigning protein function is of primary importance. There are various approaches available for deducing the function of proteins of unknown function using information derived from sequence similarity or clustering patterns of coregulated genes 2,3 , phylogenetic profiles 4 , protein-protein interactions (refs. 5‐8 and Samanta, M.P. and Liang, S., unpublished data), and protein complexes 9,10 . Here we propose the assignment of proteins to functional classes on the basis of their network of physical interactions as determined by minimizing the number of protein interactions among different functional categories. Function assignment is proteome-wide and is determined by the global connectivity pattern of the protein network. The approach results in multiple functional assignments, a consequence of the existence of multiple equivalent solutions. We apply the method to analyze the yeast Saccharomyces cerevisiae protein-protein interaction network 5 .

Global protein function prediction in protein-protein interaction networks

Abstract: The determination of protein functions is one of the most challenging problems of the post-genomic era. The sequencing of entire genomes and the possibility to access gene's co-expression patterns has moved the attention from the study of single proteins or small complexes to that of the entire proteome. In this context, the search for reliable methods for proteins' function assignment is of uttermost importance. Previous approaches to deduce the unknown function of a class of proteins have exploited sequence similarities or clustering of co-regulated genes, phylogenetic profiles, protein-protein interactions, and protein complexes. We propose to assign functional classes to proteins from their network of physical interactions, by minimizing the number of interacting proteins with different categories. The function assignment is made on a global scale and depends on the entire connectivity pattern of the protein network. Multiple functional assignments are made possible as a consequence of the existence of multiple equivalent solutions. The method is applied to the yeast Saccharomices Cerevisiae protein-protein interaction network. Robustness is tested in presence of a high percentage of unclassified proteins and under deletion/insertion of interactions.

Emergence of Scaling in Random Networks

Abstract: Systems as diverse as genetic networks or the World Wide Web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This feature was found to be a consequence of two generic mechanisms: (i) networks expand continuously by the addition of new vertices, and (ii) new vertices attach preferentially to sites that are already well connected. A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Statistical mechanics of complex networks

Abstract: The emergence of order in natural systems is a constant source of inspiration for both physical and biological sciences. While the spatial order characterizing for example the crystals has been the basis of many advances in contemporary physics, most complex systems in nature do not offer such high degree of order. Many of these systems form complex networks whose nodes are the elements of the system and edges represent the interactions between them. Traditionally complex networks have been described by the random graph theory founded in 1959 by Paul Erdohs and Alfred Renyi. One of the defining features of random graphs is that they are statistically homogeneous, and their degree distribution (characterizing the spread in the number of edges starting from a node) is a Poisson distribution. In contrast, recent empirical studies, including the work of our group, indicate that the topology of real networks is much richer than that of random graphs. In particular, the degree distribution of real networks is a power-law, indicating a heterogeneous topology in which the majority of the nodes have a small degree, but there is a significant fraction of highly connected nodes that play an important role in the connectivity of the network. The scale-free topology of real networks has very important consequences on their functioning. For example, we have discovered that scale-free networks are extremely resilient to the random disruption of their nodes. On the other hand, the selective removal of the nodes with highest degree induces a rapid breakdown of the network to isolated subparts that cannot communicate with each other. The non-trivial scaling of the degree distribution of real networks is also an indication of their assembly and evolution. Indeed, our modeling studies have shown us that there are general principles governing the evolution of networks. Most networks start from a small seed and grow by the addition of new nodes which attach to the nodes already in the system. This process obeys preferential attachment: the new nodes are more likely to connect to nodes with already high degree. We have proposed a simple model based on these two principles wich was able to reproduce the power-law degree distribution of real networks. Perhaps even more importantly, this model paved the way to a new paradigm of network modeling, trying to capture the evolution of networks, not just their static topology.

The Structure and Function of Complex Networks

Abstract: Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201