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

One of the most intriguing and most studied features of photosynthesis is the exquisite efficiency with which energy can be transferred within photosynthetic complexes. A new spectroscopic study confirms earlier hints that quantum effects might be at play, by directly revealing quantum-coherent sharing of electronic excitation across 5-nm-wide photosynthetic proteins from Chroomonas CCMP270 marine algae at room temperature. The observation suggests that distant units within the proteins are 'wired' together by quantum-coherence to enhance light-harvesting efficiency. Photosynthesis makes use of sunlight to convert carbon dioxide into useful biomass and is vital for life on Earth. Crucial components for the photosynthetic process are antenna proteins, which absorb light and transmit the resultant excitation energy between molecules to a reaction centre. The efficiency of these electronic energy transfers has inspired much work on antenna proteins isolated from photosynthetic organisms to uncover the basic mechanisms at play1,2,3,4,5. Intriguingly, recent work has documented6,7,8 that light-absorbing molecules in some photosynthetic proteins capture and transfer energy according to quantum-mechanical probability laws instead of classical laws9 at temperatures up to 180 K. This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures. Here we present two-dimensional photon echo spectroscopy10,11,12,13 measurements on two evolutionarily related light-harvesting proteins isolated from marine cryptophyte algae, which reveal exceptionally long-lasting excitation oscillations with distinct correlations and anti-correlations even at ambient temperature. These observations provide compelling evidence for quantum-coherent sharing of electronic excitation across the 5-nm-wide proteins under biologically relevant conditions, suggesting that distant molecules within the photosynthetic proteins are ‘wired’ together by quantum coherence for more efficient light-harvesting in cryptophyte marine algae.

Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

https://hal-amu.archives-ouvertes.fr/hal-01409053/document

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

Fluctuation theorems (FTs), which describe some universal properties of nonequilibrium fluctuations, are examined from a quantum perspective and derived by introducing a two-point measurement on the system. FTs for closed and open systems driven out of equilibrium by an external time-dependent force, and for open systems maintained in a nonequilibrium steady state by nonequilibrium boundary conditions, are derived from a unified approach. Applications to fermion and boson transport in quantum junctions are discussed. Quantum master equations and Green's functions techniques for computing the energy and particle statistics are presented.

/pdf/nonequilibrium-fluctuations-fluctuation-theorems-and-3gfaffpqze.pdf

Nonequilibrium fluctuations, fluctuation theorems, and counting statistics in quantum systems

Molecular aggregates are abundant in nature; they form spontaneously in concentrated solutions and on surfaces and can be synthesized by supramolecular chemistry techniques.1-3 Assemblies of chromophores play important roles in many biological processes such as light-harvesting and primary * To whom correspondence should be addressed. E-mail: smukamel@uci.edu. † University of California Irvine. ‡ Universität Würzburg. § Charles University. Chem. Rev. 2009, 109, 2350–2408 2350

/pdf/coherent-multidimensional-optical-spectroscopy-of-excitons-21ftj1f9ev.pdf

Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives

The stochastic Liouville equations are employed to investigate the combined signatures of chemical exchange (two-state jump) and spectral diffusion (coupling to an overdamped Brownian oscillator) in the coherent response of an anharmonic vibration to three femtosecond infrared pulses. Simulations reproduce the main features recently observed in the OD stretch of phenol in benzene.

/pdf/stochastic-simulation-of-chemical-exchange-in-two-1t625obq2g.pdf

Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy.

The initial energy transfer steps in photosynthesis occur on ultrafast timescales. We analyze the carotenoid to bacteriochlorophyll energy transfer in LH2 Marichromatium purpuratum as well as in an artificial light-harvesting dyad system by using transient grating and two-dimensional electronic spectroscopy with 10 fs time resolution. We find that Forster-type models reproduce the experimentally observed 60 fs transfer times, but overestimate coupling constants, which lead to a disagreement with both linear absorption and electronic 2D-spectra. We show that a vibronic model, which treats carotenoid vibrations on both electronic ground and excited states as part of the system’s Hamiltonian, reproduces all measured quantities. Importantly, the vibronic model presented here can explain the fast energy transfer rates with only moderate coupling constants, which are in agreement with structure based calculations. Counterintuitively, the vibrational levels on the carotenoid electronic ground state play the central role in the excited state population transfer to bacteriochlorophyll; resonance between the donor-acceptor energy gap and the vibrational ground state energies is the physical basis of the ultrafast energy transfer rates in these systems.

Vibronic coupling explains the ultrafast carotenoid-to-bacteriochlorophyll energy transfer in natural and artificial light harvesters

Center line slope (CLS) analysis in 2D infrared spectroscopy has been extensively used to extract frequency-frequency correlation functions of vibrational transitions. We apply this concept to 2D electronic spectroscopy, where CLS is a measure of electronic gap fluctuations. The two domains, infrared and electronic, possess differences: In the infrared, the frequency fluctuations are classical, often slow and Gaussian. In contrast, electronic spectra are subject to fast spectral diffusion and affected by underdamped vibrational wavepackets in addition to Stokes shift. All these effects result in non-Gaussian peak profiles. Here, we extend CLS-analysis beyond Gaussian line shapes and test the developed methodology on a solvated molecule, zinc phthalocyanine. We find that CLS facilitates the interpretation of 2D electronic spectra by reducing their complexity to one dimension. In this way, CLS provides a highly sensitive measure of model parameters describing electronic-vibrational and electronic-solvent interaction.

František Šanda

Papers

Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives

Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives

Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy.

Vibronic coupling explains the ultrafast carotenoid-to-bacteriochlorophyll energy transfer in natural and artificial light harvesters

Center Line Slope Analysis in Two-Dimensional Electronic Spectroscopy