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 unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

It is shown that the ordinary semiclassical theory of the absorption of light by exciton states is not completely satisfactory (in contrast to the case of absorption due to interband transitions). A more complete theory is developed. It is shown that excitons are approximate bosons, and, in interaction with the electromagnetic field, the exciton field plays the role of the classical polarization field. The eigenstates of the system of crystal and radiation field are mixtures of photons and excitons. The ordinary one-quantum optical lifetime of an excitation is infinite. Absorption occurs only when "three-body" processes are introduced. The theory includes "local field" effects, leading to the Lorentz local field correction when it is applicable. A Smakula equation for the oscillator strength in terms of the integrated absorption constant is derived.

a Quantum-Mechanical Theory of the Contribution of Excitons to the Complex Dielectric Constant of Crystals.

Light–matter coupling with strength comparable to the bare transition frequencies of the system is called ultrastrong. This Review surveys how experiments have realized ultrastrong coupling in the past decade, the new phenomena predicted in this regime and the applications it enables. Ultrastrong coupling between light and matter has, in the past decade, transitioned from a theoretical idea to an experimental reality. It is a new regime of quantum light–matter interaction, which goes beyond weak and strong coupling to make the coupling strength comparable to the transition frequencies in the system. The achievement of weak and strong coupling has led to increased control of quantum systems and to applications such as lasers, quantum sensing, and quantum information processing. Here we review the theory of quantum systems with ultrastrong coupling, discussing entangled ground states with virtual excitations, new avenues for nonlinear optics, and connections to several important physical models. We also overview the multitude of experimental setups, including superconducting circuits, organic molecules, semiconductor polaritons, and optomechanical systems, that have now achieved ultrastrong coupling. We conclude by discussing the many potential applications that these achievements enable in physics and chemistry.

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Ultrastrong coupling between light and matter

A laser frequency comb is a broad spectrum composed of equidistant narrow lines. Initially invented for frequency metrology, such combs enable new approaches to spectroscopy over broad spectral bandwidths, of particular relevance to molecules. The performance of existing spectrometers — such as crossed dispersers employing, for example, virtual imaging phase array etalons, or Michelson-based Fourier transform interferometers — can be dramatically enhanced with optical frequency combs. A new class of instruments, such as dual-comb spectrometers without moving parts, enables fast and accurate measurements over broad spectral ranges. The direct self-calibration of the frequency scale of the spectra within the accuracy of an atomic clock and the negligible contribution of the instrumental line-shape will enable determinations of all spectral parameters with high accuracy for stringent comparisons with theories in atomic and molecular physics. Chip-scale frequency comb spectrometers promise integrated devices for real-time sensing in analytical chemistry and biomedicine. This Review gives a summary of the developments in the emerging and rapidly advancing field of atomic and molecular broadband spectroscopy with frequency combs. Frequency comb spectroscopy is a recent field of research that has blossomed in the past five years. This Review discusses developments in the emerging and rapidly advancing field of atomic and molecular broadband spectroscopy with frequency combs.

Frequency comb spectroscopy

Molecular potential energy surfaces can be actively manipulated by light. This is usually done by strong classical laser light but was recently demonstrated for the quantum field in an optical cavity. The photonic vacuum state of a localized cavity mode can be strongly mixed with the molecular degrees of freedom to create hybrid field-matter states known as polaritons. We simulate the avoided crossing of sodium iodide in a cavity by incorporating the quantized cavity field into the nuclear wave packet dynamics calculation. The quantized field is represented on a numerical grid in quadrature space, thus avoiding the limitations set by the rotating wave approximation (RWA) when the field is expanded in Fock space. This approach allows the investigation of cavity couplings in the vicinity of naturally occurring avoided crossings and conical intersections, which is too expensive in the fock space expansion when the RWA does not apply. Numerical results show how the branching ratio between the covalent and ion...

Cavity Femtochemistry: Manipulating Nonadiabatic Dynamics at Avoided Crossings.

Strong coupling of molecules to the vacuum field of micro cavities can modify the potential energy surfaces thereby opening new photophysical and photochemical reaction pathways. While the influence of laser fields is usually described in terms of classical field, coupling to the vacuum state of a cavity has to be described in terms of dressed photon-matter states (polaritons) which require quantized fields. We present a derivation of the non-adiabatic couplings for single molecules in the strong coupling regime suitable for the calculation of the dressed state dynamics. The formalism allows to use quantities readily accessible from quantum chemistry codes like the adiabatic potential energy surfaces and dipole moments to carry out wave packet simulations in the dressed basis. The implications for photochemistry are demonstrated for a set of model systems representing typical situations found in molecules.

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Non-adiabatic dynamics of molecules in optical cavities

Conical intersections (CIs) dominate the pathways and outcomes of virtually all photophysical and photochemical molecular processes. Despite extensive experimental and theoretical effort, CIs have not been directly observed yet and the experimental evidence is being inferred from fast reaction rates and some vibrational signatures. We show that short x-ray (rather than optical) pulses can directly detect the passage through a CI with the adequate temporal and spectral sensitivity. The technique is based on a coherent Raman process that employs a composite femtosecond or attosecond x-ray pulse to detect the electronic coherences (rather than populations) that are generated as the system passes through the CI.

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Catching Conical Intersections in the Act: Monitoring Transient Electronic Coherences by Attosecond Stimulated X-Ray Raman Signals

Crossings of electronic potential energy surfaces in nuclear configuration space, known as conical intersections, determine the rates and outcomes of a large class of photochemical molecular processes. Much theoretical progress has been made in computing strongly coupled electronic and nuclear motions at different levels, but how to incorporate them in different spectroscopic signals and the approximations involved are less established. This will be the focus of the present review. We survey a wide range of time-resolved spectroscopic techniques which span from the infrared to the X-ray regimes and can be used for probing the nonadiabatic dynamics in the vicinity of conical intersections. Transient electronic and vibrational probes and their theoretical signal calculations are classified by their information content. This includes transient vibrational spectroscopic methods (transient infrared and femtosecond off-resonant stimulated Raman), resonant electronic probes (transient absorption and photoelectro...

Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime

Violations of the Born-Oppenheimer approximation (BOA) and the consequent nonadiabatic dynamics have long been an object of intense study. Recently, such dynamics have been induced via strong coupling of the molecule to a high-amplitude (spatially confined) mode of the electromagnetic field in optical cavities. However, the effects of a cavity on a pre-existing avoided crossing or conical intersection are relatively unexplored. The dynamics of molecules dressed by cavity modes are usually calculated by invoking the rotating wave approximation (RWA), which greatly simplifies the calculation but breaks down when the cavity mode frequency is higher than the relevant material frequencies. We develop a protocol for computing curve crossing dynamics in an optical cavity by exploiting a recently-developed method of solving the quantum Rabi model without invoking the RWA. The method is demonstrated for sodium iodide.

Kochise Bennett

Papers

Cavity Femtochemistry: Manipulating Nonadiabatic Dynamics at Avoided Crossings.

Non-adiabatic dynamics of molecules in optical cavities

Catching Conical Intersections in the Act: Monitoring Transient Electronic Coherences by Attosecond Stimulated X-Ray Raman Signals

Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime

Novel photochemistry of molecular polaritons in optical cavities.