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。

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

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

https://www.tau.ac.il/%7Eklafter1/258.pdf

The random walk's guide to anomalous diffusion: a fractional dynamics approach

Statistics for Spatial Data.

A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented, with emphasis on comparisons between theory and quantitative experiments. Examples include patterns in hydrodynamic systems such as thermal convection in pure fluids and binary mixtures, Taylor-Couette flow, parametric-wave instabilities, as well as patterns in solidification fronts, nonlinear optics, oscillatory chemical reactions and excitable biological media. The theoretical starting point is usually a set of deterministic equations of motion, typically in the form of nonlinear partial differential equations. These are sometimes supplemented by stochastic terms representing thermal or instrumental noise, but for macroscopic systems and carefully designed experiments the stochastic forces are often negligible. An aim of theory is to describe solutions of the deterministic equations that are likely to be reached starting from typical initial conditions and to persist at long times. A unified description is developed, based on the linear instabilities of a homogeneous state, which leads naturally to a classification of patterns in terms of the characteristic wave vector q0 and frequency ω0 of the instability. Type Is systems (ω0=0, q0≠0) are stationary in time and periodic in space; type IIIo systems (ω0≠0, q0=0) are periodic in time and uniform in space; and type Io systems (ω0≠0, q0≠0) are periodic in both space and time. Near a continuous (or supercritical) instability, the dynamics may be accurately described via "amplitude equations," whose form is universal for each type of instability. The specifics of each system enter only through the nonuniversal coefficients. Far from the instability threshold a different universal description known as the "phase equation" may be derived, but it is restricted to slow distortions of an ideal pattern. For many systems appropriate starting equations are either not known or too complicated to analyze conveniently. It is thus useful to introduce phenomenological order-parameter models, which lead to the correct amplitude equations near threshold, and which may be solved analytically or numerically in the nonlinear regime away from the instability. The above theoretical methods are useful in analyzing "real pattern effects" such as the influence of external boundaries, or the formation and dynamics of defects in ideal structures. An important element in nonequilibrium systems is the appearance of deterministic chaos. A greal deal is known about systems with a small number of degrees of freedom displaying "temporal chaos," where the structure of the phase space can be analyzed in detail. For spatially extended systems with many degrees of freedom, on the other hand, one is dealing with spatiotemporal chaos and appropriate methods of analysis need to be developed. In addition to the general features of nonequilibrium pattern formation discussed above, detailed reviews of theoretical and experimental work on many specific systems are presented. These include Rayleigh-Benard convection in a pure fluid, convection in binary-fluid mixtures, electrohydrodynamic convection in nematic liquid crystals, Taylor-Couette flow between rotating cylinders, parametric surface waves, patterns in certain open flow systems, oscillatory chemical reactions, static and dynamic patterns in biological media, crystallization fronts, and patterns in nonlinear optics. A concluding section summarizes what has and has not been accomplished, and attempts to assess the prospects for the future.

/pdf/pattern-formation-outside-of-equilibrium-1601b9znum.pdf

Pattern formation outside of equilibrium

Introduction * Scaling and Dimensional Analysis * Power Laws in Statistical Physics * Some Important Questions * Historical Development * Exercises How Phase Transitions Occur In Principle * Review of Statistical Mechanics * The Thermodynamic Limit * Phase Boundaries and Phase Transitions * The Role of Models * The Ising Model * Analytic Properties of the Ising Model * Symmetry Properties of the Ising Model * Existence of Phase Transitions * Spontaneous Symmetry Breaking * Ergodicity Breaking * Fluids * Lattice Gases * Equivalence in Statistical Mechanics * Miscellaneous Remarks * Exercises How Phase Transitions Occur In Practice * Ad Hoc Solution Methods * The Transfer Matrix * Phase Transitions * Thermodynamic Properties * Spatial Correlations * Low Temperature Expansion * Mean Field Theory * Exercises Critical Phenomena in Fluids * Thermodynamics * Two-Phase Coexistence * Vicinity of the Critical Point * Van der Waals Equation * Spatial Correlations * Measurement of Critical Exponents * Exercises Landau Theory * Order Parameters * Common Features of Mean Field Theories * Phenomenological Landau Theory * Continuous Phase Transitions * Inhomogeneous Systems * Correlation Functions * Exercises Fluctuations and the Breakdown of Landau Theory * Breakdown of Microscopic Landau Theory * Breakdown of Phenomenological Landau Theory * The Gaussian Approximation * Critical Exponents * Exercises Scaling in Static, Dynamic and Non-Equilibrium Phenomena * The Static-Scaling Hypothesis * Other Forms of the Scaling Hypothesis * Dynamic Critical Phenomena * Scaling in the Approach to Equilibrium * Summary The Renormalisation Group * Block Spins * Basic Ideas of the Renormalisation Group * Fixed Points * Origin of Scaling * RG in Differential Form * RG for the Two Dimensional Ising Model * First Order Transitions and Non-Critical Properties * RG for the Correlation Function * Crossover Phenomena * Correlations to Scaling * Finite Size Scaling Anomalous Dimensions Far From Equilibrium * Introduction * Similarity Solutions * Anomalous Dimensions in Similarity Solutions * Renormalisation * Perturbation Theory for Barenblatts Equation * Fixed Points * Conclusion Continuous Symmetry * Correlation in the Ordered Phase * Kosterlitz-Thouless Transition Critical Phenomena Near Four Dimensions * Basic Idea of the Epsilon Expansion * RG for the Gaussian Model * RG Beyond the Gaussian Approximation * Feyman Diagrams * The RG Recursion Relations * Conclusion

Lectures On Phase Transitions And The Renormalization Group

The complexity of the world is contrasted with the simplicity of the basic laws of physics. In recent years, considerable study has been devoted to systems that exhibit complex outcomes. This experience has not given us any new laws of physics, but has instead given us a set of lessons about appropriate ways of approaching complex systems.

/pdf/simple-lessons-from-complexity-3slv3pqjyo.pdf

Simple Lessons from Complexity

https://docs.autismresearchcentre.com/papers/2006_Wheelwright_etal_BrainResearch.pdf

Predicting Autism Spectrum Quotient (AQ) from the Systemizing Quotient-Revised (SQ-R) and Empathy Quotient (EQ).

Perturbative renormalization group theory is developed as a unified tool for global asymptotic analysis. With numerous examples, we illustrate its application to ordinary differential equation problems involving multiple scales, boundary layers with technically difficult asymptotic matching, and WKB analysis. In contrast to conventional methods, the renormalization group approach requires neither ad hoc assumptions about the structure of perturbation series nor the use of asymptotic matching. Our renormalization group approach provides approximate solutions which are practically superior to those obtained conventionally, although the latter can be reproduced, if desired, by appropriate expansion of the renormalization group approximant. We show that the renormalization group equation may be interpreted as an amplitude equation, and from this point of view develop reductive perturbation theory for partial differential equations describing spatially extended systems near bifurcation points, deriving both amplitude equations and the center manifold. @S1063651X~96!00506-5#

/pdf/renormalization-group-and-singular-perturbations-multiple-43g7tlnijv.pdf

Renormalization group and singular perturbations: Multiple scales, boundary layers, and reductive perturbation theory

A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing protocols, such as the genetic code. Our proposal is illustrated by using a simplified computer model and placed within the context of a sequence of transitions that early life may have made, before the emergence of vertical descent.

/pdf/collective-evolution-and-the-genetic-code-27ypzbd02i.pdf

Nigel Goldenfeld

Papers

Lectures On Phase Transitions And The Renormalization Group

Simple Lessons from Complexity

Predicting Autism Spectrum Quotient (AQ) from the Systemizing Quotient-Revised (SQ-R) and Empathy Quotient (EQ).

Renormalization group and singular perturbations: Multiple scales, boundary layers, and reductive perturbation theory

Collective evolution and the genetic code