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

Coherence phenomena arise from interference, or the addition, of wave-like amplitudes with fixed phase differences. Although coherence has been shown to yield transformative ways for improving function, advances have been confined to pristine matter and coherence was considered fragile. However, recent evidence of coherence in chemical and biological systems suggests that the phenomena are robust and can survive in the face of disorder and noise. Here we survey the state of recent discoveries, present viewpoints that suggest that coherence can be used in complex chemical systems, and discuss the role of coherence as a design element in realizing function.

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Using coherence to enhance function in chemical and biophysical systems

The journal of physical chemistry letters

Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental assumptions and questions in the field, identify basic design principles and develop a key underlying theme – the dynamics of quantum dynamical networks in the presence of an environment and the fruitful interplay that the two may enter. At the hand of three biological phenomena whose understanding is held to require quantum mechanical processes, namely excitation and charge transfer in photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for quantum biology.

Vibrations, quanta and biology

New free-electron laser and high-harmonic generation X-ray light sources are capable of supplying pulses short and intense enough to perform resonant nonlinear time-resolved experiments in molecules. Valence-electron motions can be triggered impulsively by core excitations and monitored with high temporal and spatial resolution. We discuss possible experiments that employ attosecond X-ray pulses to probe the quantum coherence and correlations of valence electrons and holes, rather than the charge density alone, building on the analogy with existing studies of vibrational motions using femtosecond techniques in the visible regime.

Multidimensional Attosecond Resonant X-Ray Spectroscopy of Molecules: Lessons from the Optical Regime

We report simulations of X-ray absorption near edge structure (XANES), resonant inelastic X-ray scattering (RIXS) and 1D stimulated X-ray Raman spectroscopy (SXRS) signals of cysteine at the oxygen, nitrogen, and sulfur K and L2,3 edges. Comparison of the simulated XANES signals with experiment shows that the restricted window time-dependent density functional theory is more accurate and computationally less expensive than the static exchange method. Simulated RIXS and 1D SXRS signals give some insights into the correlation of different excitations in the molecule.

/pdf/core-and-valence-excitations-in-resonant-x-ray-spectroscopy-2dvhyjzect.pdf

Core and valence excitations in resonant X-ray spectroscopy using restricted excitation window time-dependent density functional theory.

A compact correlation-function expression for time-resolved stimulated Raman signals, generated by combining a spectrally narrow (picosecond) with a broad (femtosecond) pulse, is derived using a closed time path loop diagrammatic technique that represents forward and backward time evolution of the vibrational wave function. We show that even though the external spectral and temporal parameters of the pulses may be independently controlled, the effective temporal and spectral resolution of the experiment may not exceed the fundamental bandwidth limitation.

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Communication: Comment on the effective temporal and spectral resolution of impulsive stimulated Raman signals

Expressions for the two-dimensional stimulated x-ray Raman spectroscopy (2D-SXRS) signal obtained using attosecond x-ray pulses are derived. The 1D- and 2D-SXRS signals are calculated for trans-N-methyl acetamide (NMA) with broad bandwidth (181 as, 14.2 eV FWHM) pulses tuned to the oxygen and nitrogen K-edges. Crosspeaks in 2D signals reveal electronic Franck-Condon overlaps between valence orbitals and relaxed orbitals in the presence of the core-hole.

/pdf/two-dimensional-stimulated-resonance-raman-spectroscopy-of-40twxhxksb.pdf

Two-dimensional stimulated resonance Raman spectroscopy of molecules with broadband x-ray pulses.

Expressions for the two-dimensional Stimulated x-ray Raman Spectroscopy (2D-SXRS) signal obtained using attosecond x-ray pulses are derived. The 1D- and 2D-SXRS signals are calculated for trans-N-methyl acetamide (NMA) with broad bandwidth (FWHM ~14.2eV, 181 as) pulses tuned to the oxygen and nitrogen K-edges. Crosspeaks in 2D signals reveal electronic Franck-Condon overlaps between valence orbitals and relaxed orbitals in the presence of the core hole.

/pdf/two-dimensional-stimulated-resonance-raman-spectroscopy-of-4fxtrney4v.pdf

Jason D. Biggs

Papers

Multidimensional Attosecond Resonant X-Ray Spectroscopy of Molecules: Lessons from the Optical Regime

Core and valence excitations in resonant X-ray spectroscopy using restricted excitation window time-dependent density functional theory.

Communication: Comment on the effective temporal and spectral resolution of impulsive stimulated Raman signals

Two-dimensional stimulated resonance Raman spectroscopy of molecules with broadband x-ray pulses.

Two-Dimensional Stimulated Resonance Raman Spectroscopy of Molecules with Broadband X-ray Pulses