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

Link prediction in complex networks has attracted increasing attention from both physical and computer science communities. The algorithms can be used to extract missing information, identify spurious interactions, evaluate network evolving mechanisms, and so on. This article summaries recent progress about link prediction algorithms, emphasizing on the contributions from physical perspectives and approaches, such as the random-walk-based methods and the maximum likelihood methods. We also introduce three typical applications: reconstruction of networks, evaluation of network evolving mechanism and classification of partially labeled networks. Finally, we introduce some applications and outline future challenges of link prediction algorithms.

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Link prediction in complex networks: A survey

Close to a transition between different phases a substance can show universal behavior that is independent of the microscopic details and is characterized by power law correlations and critical exponents. In this Colloquium the concepts of criticality and universality are discussed when applied to biological systems and suggest that in some cases these systems can extract functional advantages close to criticality.

Colloquium : Criticality and dynamical scaling in living systems

This review reports on the research done during past years on violations of the fluctuation–dissipation theorem (FDT) in glassy systems. It is focused on the existence of a quasi-fluctuation–dissipation theorem (QFDT) in glassy systems and the current supporting knowledge gained from numerical simulation studies. It covers a broad range of non-stationary aging and stationary driven systems such as structural glasses, spin glasses, coarsening systems, ferromagnetic models at criticality, trap models, models with entropy barriers, kinetically constrained models, sheared systems and granular media. The review is divided into four main parts: (1) an introductory section explaining basic notions related to the existence of the FDT in equilibrium and its possible extension to the glassy regime (QFDT), (2) a description of the basic analytical tools and results derived in the framework of some exactly solvable models, (3) a detailed report of the current evidence in favour of the QFDT and (4) a brief digression on the experimental evidence in its favour. This review is intended for inexpert readers who want to learn about the basic notions and concepts related to the existence of the QFDT as well as for the more expert readers who may be interested in more specific results.

http://iopscience.iop.org/article/10.1088/0305-4470/36/21/201/pdf

Violation of the fluctuation–dissipation theorem in glassy systems: basic notions and the numerical evidence

Two interface effects: Exchange bias and magnetic proximity

We solve the Langevin dynamics of d-dimensional ferromagnetic spherical models with interactions that decay with distance as r−(d+σ). The long time dynamics of correlations and responses are studied in detail in the different dynamical regimes and the validity of fluctuation–dissipation relations (or its violation) are shown. In particular, we show that the fluctuation–dissipation ratio X(t+tw,tw) is asymptotically a function only of the waiting time tw in the aging regime and that X→0 as tw→∞. The results are valid in any finite dimension d and for 0<σ<2 where short-range behavior is recovered. We also solve the T=0 Cahn–Hilliard dynamics of this model (conserved order parameter). An analysis of the multiscaling behavior of the autocorrelation function is presented.

Dynamics of ferromagnetic spherical spin models with power law interactions: exact solution

Although most networks in nature exhibit complex topologies, the origins of such complexity remain unclear. We propose a general evolutionary mechanism based on global stability. This mechanism is incorporated into a model of a growing network of interacting agents in which each new agent’s membership in the network is determined by the agent’s effect on the network’s global stability. It is shown that out of this stability constraint complex topological properties emerge in a self-organized manner, offering an explanation for their observed ubiquity in biological networks.

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Emergent self-organized complex network topology out of stability constraints

We performed Monte Carlo simulations of a bilayer system composed of two thin films, one ferromagnetic (FM) and the other antiferromagnetic (AFM). Two lattice structures for the films were considered: simple cubic and body centered cubic (bcc). We imposed an uncompensated interfacial spin structure in both lattice structures; in particular we emulated an FeF2–FM system in the case of the bcc lattice. Our analysis focused on the incidence of the interfacial strength interactions between the films, Jeb, and the effect of thermal fluctuations on the bias field, HEB. We first performed Monte Carlo simulations on a microscopic model based on classical Heisenberg spin variables. To analyze the simulation results we also introduced a simplified model that assumes coherent rotation of spins located on the same layer parallel to the interface. We found that, depending on the AFM film anisotropy to exchange ratio, the bias field is controlled either by the intrinsic pinning of a domain wall parallel to the interface or by the stability of the first AFM layer (quasi-domain wall) near the interface.

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The exchange bias phenomenon in uncompensated interfaces: theory and Monte Carlo simulations

In this work we study the effects of introducing long-range interactions in the Bak–Sneppen (BS) model of biological evolution. We analyze a recently proposed version of the BS model where the interactions decay as r − α ; in this way, the first nearest neighbors model is recovered in the limit α →∞, and the random neighbors version for α =0. We study the space and time correlations and analyze how the critical behavior of the system changes with the parameter α . We also study the sensibility to initial conditions of the model using the spreading of damage technique. We found that the system displays several distinct critical regimes as α is varied from α =0 to α →∞.

Self-organized criticality in a model of biological evolution with long range interactions

The far-from-equilibrium low-temperature dynamics of ultrathin magnetic films is analyzed by using Monte Carlo numerical simulations on a two-dimensional Ising model with competing exchange (J 0 ) and dipolar (J d ) interactions. In particular, we focus our attention on the low-temperature region of the (δ,T) phase diagram (where δ=J 0 /J d ) for the range of values of S where striped phases with widths h=I (h I ) and h=2 (h2) are present. The presence of metastable states of the phase h2 in the region where the phase h 1 is the thermodynamically stable one and vice versa was established recently. In this work we show that the presence of these metastable states appears as a blocking mechanism that slows the dynamics of magnetic domain growth when the system is quenched from a high-temperature state to a low-temperature state in the region of metastability.

Francisco A. Tamarit

Papers

Dynamics of ferromagnetic spherical spin models with power law interactions: exact solution

Emergent self-organized complex network topology out of stability constraints

The exchange bias phenomenon in uncompensated interfaces: theory and Monte Carlo simulations

Self-organized criticality in a model of biological evolution with long range interactions

Slow dynamics in a two-dimensional Ising model with competing interactions