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

Topological photonics is a rapidly emerging field of research in which geometrical and topological ideas are exploited to design and control the behavior of light. Drawing inspiration from the discovery of the quantum Hall effects and topological insulators in condensed matter, recent advances have shown how to engineer analogous effects also for photons, leading to remarkable phenomena such as the robust unidirectional propagation of light, which hold great promise for applications. Thanks to the flexibility and diversity of photonics systems, this field is also opening up new opportunities to realize exotic topological models and to probe and exploit topological effects in new ways. This article reviews experimental and theoretical developments in topological photonics across a wide range of experimental platforms, including photonic crystals, waveguides, metamaterials, cavities, optomechanics, silicon photonics, and circuit QED. A discussion of how changing the dimensionality and symmetries of photonics systems has allowed for the realization of different topological phases is offered, and progress in understanding the interplay of topology with non-Hermitian effects, such as dissipation, is reviewed. As an exciting perspective, topological photonics can be combined with optical nonlinearities, leading toward new collective phenomena and novel strongly correlated states of light, such as an analog of the fractional quantum Hall effect.

Topological Photonics

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (Some figures may appear in colour only in the online journal) This article was invited by Erwin Frey.

/pdf/stochastic-thermodynamics-fluctuation-theorems-and-molecular-2epwyvmpf0.pdf

Stochastic thermodynamics, fluctuation theorems and molecular machines

The Haldane model on a honeycomb lattice is a paradigmatic example of a Hamiltonian featuring topologically distinct phases of matter. It describes a mechanism through which a quantum Hall effect can appear as an intrinsic property of a band structure, rather than being caused by an external magnetic field. Although physical implementation has been considered unlikely, the Haldane model has provided the conceptual basis for theoretical and experimental research exploring topological insulators and superconductors. Here we report the experimental realization of the Haldane model and the characterization of its topological band structure, using ultracold fermionic atoms in a periodically modulated optical honeycomb lattice. The Haldane model is based on breaking both time-reversal symmetry and inversion symmetry. To break time-reversal symmetry, we introduce complex next-nearest-neighbour tunnelling terms, which we induce through circular modulation of the lattice position. To break inversion symmetry, we create an energy offset between neighbouring sites. Breaking either of these symmetries opens a gap in the band structure, which we probe using momentum-resolved interband transitions. We explore the resulting Berry curvatures, which characterize the topology of the lowest band, by applying a constant force to the atoms and find orthogonal drifts analogous to a Hall current. The competition between the two broken symmetries gives rise to a transition between topologically distinct regimes. By identifying the vanishing gap at a single Dirac point, we map out this transition line experimentally and quantitatively compare it to calculations using Floquet theory without free parameters. We verify that our approach, which allows us to tune the topological properties dynamically, is suitable even for interacting fermionic systems. Furthermore, we propose a direct extension to realize spin-dependent topological Hamiltonians.

/pdf/experimental-realization-of-the-topological-haldane-model-2vmtdh71tw.pdf

Experimental realization of the topological Haldane model with ultracold fermions

The dynamics of classical and quantum systems, which are driven by a high-frequency $(\ensuremath{\omega})$ field, is investigated. For classical systems, the motion is separated into a slow part and a fast part. The motion for the slow part is computed perturbatively in powers of ${\ensuremath{\omega}}^{\ensuremath{-}1}$ to the order ${\ensuremath{\omega}}^{\ensuremath{-}4},$ and the corresponding time independent Hamiltonian is calculated. Such an effective Hamiltonian for the corresponding quantum problem is computed to the order ${\ensuremath{\omega}}^{\ensuremath{-}4}$ in a high-frequency expansion. Its spectrum is the quasienergy spectrum of the time dependent quantum system. The classical limit of this effective Hamiltonian is the classical effective time independent Hamiltonian. It is demonstrated that this effective Hamiltonian gives the exact quasienergies and quasienergy states of some simple examples, as well as the lowest resonance of a nontrivial model for an atom trap. The theory that is developed in this paper is useful for the analysis of atomic motion in atom traps of various shapes.

Effective Hamiltonians for periodically driven systems

We analyze the operation of a molecular machine driven by the nonadiabatic variation of external parameters. We derive a formula for the integrated flow from one configuration to another, obtain a "no-pumping theorem" for cyclic processes with thermally activated transitions, and show that in the adiabatic limit the pumped current is given by a geometric expression.

Directed flow in nonadiabatic stochastic pumps.

For closed quantum systems driven away from equilibrium, work is often defined in terms of projective measurements of initial and final energies. This definition leads to statistical distributions of work that satisfy nonequilibrium work and fluctuation relations. While this two-point measurement definition of quantum work can be justified heuristically by appeal to the first law of thermodynamics, its relationship to the classical definition of work has not been carefully examined. In this paper we employ semiclassical methods, combined with numerical simulations of a driven quartic oscillator, to study the correspondence between classical and quantal definitions of work in systems with one degree of freedom. We find that a semiclassical work distribution, built from classical trajectories that connect the initial and final energies, provides an excellent approximation to the quantum work distribution when the trajectories are assigned suitable phases and are allowed to interfere. Neglecting the interferences between trajectories reduces the distribution to that of the corresponding classical process. Hence, in the semiclassical limit, the quantum work distribution converges to the classical distribution, decorated by a quantum interference pattern. We also derive the form of the quantum work distribution at the boundary between classically allowed and forbidden regions, where this distribution tunnels into the forbidden region. Our results clarify how the correspondence principle applies in the context of quantum and classical work distributions, and contribute to the understanding of work and nonequilibrium work relations in the quantum regime.

The quantum-classical correspondence principle for work distributions

The definition of quantum work differs markedly from the definition found in classical mechanics textbooks. Now, by showing that quantum work distributions can be understood as interference patterns between classical trajectories, researchers bridge the gap between classical and quantum notions of work.

https://link.aps.org/pdf/10.1103/PhysRevX.5.031038

Quantum-Classical Correspondence Principle for Work Distributions

Coherent nonlinear optical signals are commonly calculated using a semiclassical approach that assumes a quantum system interacting with classical fields. Compact expressions for the signals are then derived in terms of nonlinear susceptibilities. We present an alternative approach based on a quantum description of both matter and field. The signals are further recast in terms of transition amplitudes, which provide a clearer picture for the underlying molecular processes and may be intuitively represented by closed-time-path-loop diagrams. Unlike the semiclassical approach that treats the signal mode macroscopically using Maxwell’s equations, the present formalism allows for a fully microscopic calculation of the entire process. For example, n + 1 wave mixing appears as a concerted n + 1 photon event and all n + 1 field modes (including the signal) are treated on the same footing. Resonant contributions to nonlinear optical signals that carry useful molecule-specific information are recast as the modulus square of transition amplitudes and are clearly separated from the parametric background. Purely dissipative signals that can be measured using a collinear beam geometry and manipulated by pulse shaping techniques are proposed. The approach is demonstrated by applications to the stimulated Raman and the two-photon absorption components of pump–probe, and to coherent anti-Stokes Raman spectroscopy.

/pdf/ultrafast-nonlinear-optical-signals-viewed-from-the-molecule-3kcdqzipbl.pdf

Saar Rahav

Papers

Effective Hamiltonians for periodically driven systems

Directed flow in nonadiabatic stochastic pumps.

The quantum-classical correspondence principle for work distributions

Quantum-Classical Correspondence Principle for Work Distributions

Ultrafast Nonlinear Optical Signals Viewed from the Molecule’s Perspective: Kramers–Heisenberg Transition-Amplitudes versus Susceptibilities