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

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

Cell motility in viscous fluids is ubiquitous and affects many biological processes, including reproduction, infection and the marine life ecosystem. Here we review the biophysical and mechanical principles of locomotion at the small scales relevant to cell swimming, tens of micrometers and below. At this scale, inertia is unimportant and the Reynolds number is small. Our emphasis is on the simple physical picture and fundamental flow physics phenomena in this regime. We first give a brief overview of the mechanisms for swimming motility, and of the basic properties of flows at low Reynolds number, paying special attention to aspects most relevant for swimming such as resistance matrices for solid bodies, flow singularities and kinematic requirements for net translation. Then we review classical theoretical work on cell motility, in particular early calculations of swimming kinematics with prescribed stroke and the application of resistive force theory and slender-body theory to flagellar locomotion. After examining the physical means by which flagella are actuated, we outline areas of active research, including hydrodynamic interactions, biological locomotion in complex fluids, the design of small-scale artificial swimmers and the optimization of locomotion strategies. (Some figures in this article are in colour only in the electronic version) This article was invited by Christoph Schmidt.

/pdf/the-hydrodynamics-of-swimming-microorganisms-bonwl3c7w2.pdf

The hydrodynamics of swimming microorganisms

Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

http://absimage.aps.org/image/MAR08/MWS_MAR08-2008-020581.pdf

The Genomic Code for Nucleosome Positioning

Theory of polyelectrolytes in solutions and at surfaces

Dilute or semidilute solutions of polyelectrolytes show below a critical temperature the phenomenon of counterion condensation. This effect leads (a) to a decrease of the effective total charge of the macroion and (b) to a counterion-induced attraction between different parts of the chain. In this paper we provide simple scaling arguments that allow one to calculate the chain size and the effective total charge as a function of temperature, solvent quality etc. Especially we show that effect (a) alone leads to a continuous reduction of the chain size with decreasing temperature. Due to a feedback-type mechanism effect (b) amplifies this collapse process in such a way that it is reminiscent of a first-order phase transition.

https://wwwhome.lorentz.leidenuniv.nl/~schiessel/Documents/macromolecules98.pdf

Counterion-Condensation-Induced Collapse of Highly Charged Polyelectrolytes

/pdf/topical-review-the-physics-of-chromatin-jjti3kps4x.pdf

TOPICAL REVIEW: The physics of chromatin

Recently fractional calculus has become an important tool in the analysis of slow relaxation phenomena, such as stress-strain relationships in polymeric materials. In the rheological constitutive equations this implies the replacement of the first-order derivatives by fractional derivatives. Here we show that such procedures have hierarchical mechanical analogues. We focus on the generalized dashpot and the generalized Maxwell model and display the corresponding arrangements. Our models allow a transparent interpretation of the parameters which enter the fractional equations, and reveal that the internal dynamics are hierarchically constrained.

https://iopscience.iop.org/article/10.1088/0305-4470/26/19/034/pdf

Hierarchical analogues to fractional relaxation equations

Recent progress has been made in the understanding of the physical properties of chromatin—the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of the hierarchy of DNA folding into the chromatin complex. (i) The nucleosome, the chromatin repeating unit consisting of a globular aggregate of eight histone proteins with the DNA wrapped around it: its overcharging, the DNA unwrapping transition, the ‘sliding’ of the octamer along the DNA. (ii) The 30 nm chromatin fibre, the necklace-lik es tructure of nucleosomes connected via linker DNA: its geometry, its mechanical properties under stretching and its response to changing ioni cc onditions. I will stress that chromatin combines two seemingly contradictory features: (1) high compaction of DNA within the nuclear envelope and, at the same time, (2) accessibility to genes, promoter regions and gene regulatory sequences. Contents

/pdf/the-physics-of-chromatin-js4sbt433i.pdf

The physics of chromatin.

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem arises in the case of globular aggregates of proteins (histones) that are wound by DNA in the chromosomes of plants and animals; these beads (nucleosomes) are multiply wrapped and yet are able to reposition themselves over long distances, while remaining bound by the DNA chain.

/pdf/polymer-reptation-and-nucleosome-repositioning-4d58rwlb1h.pdf

Helmut Schiessel

Papers

Counterion-Condensation-Induced Collapse of Highly Charged Polyelectrolytes

TOPICAL REVIEW: The physics of chromatin

Hierarchical analogues to fractional relaxation equations

The physics of chromatin.

Polymer reptation and nucleosome repositioning.