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

We provide a broad review of fundamental electronic properties of two-dimensional graphene with the emphasis on density and temperature dependent carrier transport in doped or gated graphene structures. A salient feature of our review is a critical comparison between carrier transport in graphene and in two-dimensional semiconductor systems (e.g. heterostructures, quantum wells, inversion layers) so that the unique features of graphene electronic properties arising from its gap- less, massless, chiral Dirac spectrum are highlighted. Experiment and theory as well as quantum and semi-classical transport are discussed in a synergistic manner in order to provide a unified and comprehensive perspective. Although the emphasis of the review is on those aspects of graphene transport where reasonable consensus exists in the literature, open questions are discussed as well. Various physical mechanisms controlling transport are described in depth including long- range charged impurity scattering, screening, short-range defect scattering, phonon scattering, many-body effects, Klein tunneling, minimum conductivity at the Dirac point, electron-hole puddle formation, p-n junctions, localization, percolation, quantum-classical crossover, midgap states, quantum Hall effects, and other phenomena.

/pdf/electronic-transport-in-two-dimensional-graphene-32oou47sy4.pdf

Electronic transport in two-dimensional graphene

Molecular self-assembly offers a 'bottom-up' route to fabrication with subnanometre precision of complex structures from simple components. DNA has proved to be a versatile building block for programmable construction of such objects, including two-dimensional crystals, nanotubes, and three-dimensional wireframe nanopolyhedra. Templated self-assembly of DNA into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase 'scaffold strand' that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide 'staple strands'. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes-monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross-with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometre scale.

/pdf/self-assembly-of-dna-into-nanoscale-three-dimensional-shapes-2g73511y4b.pdf

Self-assembly of DNA into nanoscale three-dimensional shapes

Superstring theoryをめぐって(放談室)

http://thefauve.hwa.ucsd.edu/~thwa/pub/therm1.pdf

Transcriptional regulation by the numbers: models.

The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene expression in a bacterium or its precise location within a developing embryo, the natural language for these experiments is that of numbers. Such quantitative data demands quantitative models. We review a class of models ("thermodynamic models") which exploit statistical mechanics to compute the probability that RNA polymerase is at the appropriate promoter. This provides a mathematically precise elaboration of the idea that activators are agents of recruitment which increase the probability that RNA polymerase will be found at the promoter of interest. We discuss a framework which describes the interactions of repressors, activators, helper molecules and RNA polymerase using the concept of effective concentrations, expressed in terms of a function we call the "regulation factor". This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell. In a companion paper [1], these ideas are applied to several case studies which illustrate the use of the general formalism.

Transcriptional Regulation by the Numbers 1: Models

https://www.theorie.physik.uni-muenchen.de/lsfrey/publications/articles/Bintu_CurrOpinGenDev_2005b.pdf

Transcriptional regulation by the numbers: applications.

Part I The Facts of Life 1. Why: Biology By the Numbers 2. What and Where: Construction Plans for Cells and Organisms 3. When: Stopwatches at Many Scales 4. Who: "Bless the Little Beasties" Part II Life at Rest 5. Mechanical and Chemical Equilibrium in the Living Cell 6. Entropy Rules! 7. Two-State Systems: From Ion Channels to Cooperative Binding 8. Random Walks and the Structure of Macromolecules 9. Electrostatics for Salty Solutions 10. Beam Theory: Architecture for Cells and Skeletons 11. Biological Membranes: Life in Two Dimensions Part III Life in Motion 12. The Mathematics of Water 13. A Statistical View of Biological Dynamics 14. Life in Crowded and Disordered Environments 15. Rate Equations and Dynamics in the Cell 16. Dynamics of Molecular Motors 17. Biological Electricity and the Hodgkin-Huxley Model Part IV The Meaning of Life 18. Sequences, Specificity and Evolution 19. Network Organization in Space and Time 20. Whither Physical Biology

https://physicstoday.scitation.org/doi/pdf/10.1063/1.3206095

Physical Biology of the Cell

https://www.seas.upenn.edu/~purohit/mypapers/mybiophys.pdf

Jane Kondev

Papers

Transcriptional regulation by the numbers: models.

Transcriptional Regulation by the Numbers 1: Models

Transcriptional regulation by the numbers: applications.

Physical Biology of the Cell

Forces during bacteriophage DNA packaging and ejection.