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第五章 物力作用过程与机制 从隶质层面上讨论了隶质活动方式主要是旋转和位移，论述了以核簇物力矢量主导下所致的相互吸引、相互排斥以及谷穴吸引这三种物力作用过程及内在机制。从粒子的相邻关系上，以隶质旋移所致的主动物力矢量改变的特征，讨论了物力冲击、峰丘斥动以及旋移联动这三种物力作用过程及其效应机制，进一步论证和解述了造物进化论及物有斥引力论的基本概念和原则
Virus Replication as a Phenotypic Version of Polynucleotide Evolution
Viral evolution Branching processes Phenotypic model
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2012/5/3
In this paper we revisit and adapt to viral evolution an approach based on the theory of branching process advanced by Demetrius, Schuster and Sigmund ("Polynucleotide evolution and branching processe...
Supplementary information for "Selective sweeps in growing microbial colonies"
Supplementary information Selective sweeps growing microbial colonies Populations and Evolution
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2012/5/2
This is supplementary information for arXiv:1204.4896, which also appeared in Physical Biology 9, 026008 (2012). Main text abstract: Evolutionary experiments with microbes are a powerful tool to study...
Low-dimensional clustering detects incipient dominant influenza strain clusters
clustering H1N1 H3N2 influenza
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2012/5/2
Influenza has been circulating in the human population and has caused three pandemics in the last century (1918 H1N1, 1957 H2N2, 1968 H3N2). The 2009 A(H1N1) was classified by the World Health Organiz...
A Novel Sequence-Based Antigenic Distance Measure for H1N1, with Application to Vaccine Effectiveness and the Selection of Vaccine Strains
Influenza Vaccine effectiveness Antigenic distance pepitope Antigenic drift
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2012/5/2
H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating virus strains help res...
Evolutionary branching in a stochastic population model with distinct mutational steps
Evolutionary branching genetic drift selection adaptation
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2012/5/2
Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life caree...
We consider the evolution of large but finite populations on arbitrary fitness landscapes. We describe the evolutionary process by a Markov, Moran process. We show that to $\mathcal O(1/N)$, the time-...
Quantifying Selection and Diversity in Viruses by Entropy Methods, with Application to the Hemagglutinin of H3N2 Influenza
Quantifying Selection and Diversity Viruses Entropy Methods Hemagglutinin of H3N2 Influenza Populations and Evolution
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2012/5/2
Many viruses evolve rapidly. For example, hemagglutinin of the H3N2 influenza A virus evolves to escape antibody binding. This evolution of the H3N2 virus means that people who have previously been ex...
A Multi-Scale Model for Correlation in B Cell VDJ Usage of Zebrafish
Multi-Scale Model Correlation B Cell VDJ Usage of Zebrafish Populations and Evolution
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2012/5/2
The zebrafish (\emph{Danio rerio}) is one of the model animals for study of immunology because the dynamics in the adaptive immune system of zebrafish are similar to that in higher animals. In this wo...
The Emergence of Modularity in Biological Systems
Emergence of Modularity Biological Systems Populations and Evolution
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2012/5/2
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biolo...
Epidemics on a stochastic model of temporal network
Epidemics stochastic model of temporal network Populations and Evolution
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2012/5/2
Contacts between individuals serve as pathways where infections may propagate. These contact patterns can be represented by network structures. Static structures have been the common modeling paradigm...
Universal pacemaker of genome evolution
Universal pacemaker of genome evolution Populations and Evolution
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2012/5/2
Molecular clock (MC) is a central concept of molecular evolution according to which each gene evolves at a characteristic, near constant rate. Numerous evolutionary studies have demonstrated the valid...
Robustness Against Extinction by Stochastic Sex Determination in Small Populations
Robustness Against Extinction Stochastic Sex Determination Small Populations Populations and Evolution
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2012/5/2
Sexually reproducing populations with small number of individuals may go extinct by stochastic fluctuations in sex determination, causing all their members to become male or female in a generation. In...
Selective sweeps in growing microbial colonies
Selective sweeps growing microbial colonies Populations and Evolution
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2012/5/2
Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a ch...
Species tree inference by the STAR method, and generalizations
Species tree inference STAR method generalizations Populations and Evolution
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2012/5/2
The multispecies coalescent model describes the generation of gene trees from a rooted metric species tree, and thus provides a framework for the inference of species trees from sampled gene trees. We...