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

https://www.pci.uni-heidelberg.de/tc/usr/mctdh/lit/rev.pdf

The multiconfiguration time-dependent Hartree (MCTDH) method: a highly efficient algorithm for propagating wavepackets

: 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

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Density functional theory for transition metals and transition metal chemistry

Materials research has driven the development of modern nano-electronic devices. In particular, research in magnetic thin films has revolutionized the development of spintronic devices1,2 because identifying new magnetic materials is key to better device performance and design. Van der Waals crystals retain their chemical stability and structural integrity down to the monolayer and, being atomically thin, are readily tuned by various kinds of gate modulation3,4. Recent experiments have demonstrated that it is possible to obtain two-dimensional ferromagnetic order in insulating Cr2Ge2Te6 (ref. 5) and CrI3 (ref. 6) at low temperatures. Here we develop a device fabrication technique and isolate monolayers from the layered metallic magnet Fe3GeTe2 to study magnetotransport. We find that the itinerant ferromagnetism persists in Fe3GeTe2 down to the monolayer with an out-of-plane magnetocrystalline anisotropy. The ferromagnetic transition temperature, Tc, is suppressed relative to the bulk Tc of 205 kelvin in pristine Fe3GeTe2 thin flakes. An ionic gate, however, raises Tc to room temperature, much higher than the bulk Tc. The gate-tunable room-temperature ferromagnetism in two-dimensional Fe3GeTe2 opens up opportunities for potential voltage-controlled magnetoelectronics7-11 based on atomically thin van der Waals crystals.

Gate-tunable Room-temperature Ferromagnetism in Two-dimensional Fe 3 GeTe 2

Extending our previous studies for the H2+OH reaction in five mathematical dimensions (5D) [J. Chem. Phys. 99, 5615 (1993); 100, 2697 (1994)], we present in this paper a full‐dimensional (6D) dynamics study for the title reaction. The 6D treatment uses the time‐dependent wave‐packet approach and employs discrete variable representations for three radial coordinates and coupled angular momentum basis functions for three angular coordinates. The present 6D study employs an energy projection method to extract reaction probabilities for a whole range of energies from a single wave‐packet propagation, while previous studies produced only energy‐averaged reaction probability from a single wave‐packet propagation. The application of the energy‐projection method allows us to efficiently map out the energy dependence of the reaction probability on a fine grid which revealed surprisingly sharp resonancelike features at low collision energies on the Schatz–Elgersma potential surface. Our calculation shows that the potential‐averaged 5D treatment can produce reaction probabilities essentially indistinguishable from the full‐dimensional result. We also report initial state‐selected reaction cross sections and rate constants which are in good agreement with our previous calculations. The effect of OH vibration on H2+OH reaction is examined in the present study and our calculation shows that the OH vibration can enhance the rate constant by about a factor of 1.7 in good agreement with the experimental estimate of about 1.5.

Full‐dimensional time‐dependent treatment for diatom–diatom reactions: The H2+OH reaction

We show in this paper a time‐dependent (TD) quantum wave packet calculation for the combustion reaction H+O2 using the DMBE IV (double many‐body expansion) potential energy surface which has a deep well and supports long‐lived resonances. The reaction probabilities from the initial states of H+O2(3Σ−g) (v=0–3, j=1) for total angular momentum J=0 are obtained for scattering energies from threshold up to 2.5 eV, which show numerous resonance features. Our results show that, by carrying out the wave packet propagation to several picoseconds, one can resolve essentially all the resonance features for this reaction. The present TD results are in good agreement with other time‐independent calculations. A particular advantage of the time‐dependent approach to this reaction is that resonance structures—strong energy dependence of the reaction probability—can be mapped out in a single wave packet propagation without having to repeat scattering calculations for hundreds of energies. We also report calculations of some low‐lying vibrational energies of the hydroperoxyl radical HO2(2A‘) and their spectroscopic assignments. The vibrational frequencies of HO2(2A‘) on the DMBE IV potential energy surface are lower than experimental values, indicating the need to further improve the accuracy of the potential energy surface.

Quantum reactive scattering with a deep well: Time‐dependent calculation for H+O2 reaction and bound state characterization for HO2

A full quantum dynamical study of the reactions of a hydrogen atom with water, on an accurate ab initio potential energy surface, is reported. The theoretical results are compared with available experimental data for the exchange and abstraction reactions in H + D2O and H + H2O. Clear agreement between theory and experiment is revealed for available thermal rate coefficients and the effects of vibrational excitation of the reactants. The excellent agreement between experiment and theory on integral cross sections for the exchange reaction is unprecedented beyond atom-diatom reactions. However, the experimental cross sections for abstraction are larger than the theoretical values by more than a factor of 10. Further experiments are required to resolve this.

https://science.sciencemag.org/content/sci/290/5493/961.full.pdf

First-Principles Theory for the H + H2O, D2O Reactions

A time‐dependent wave packet method has been employed to compute initial state‐specific total reaction probabilities for the benchmark reaction H2+OH→H2O+H on the modified Schatz–Elgersman potential energy surface which is derived from ab initio data In our quantum treatment, the OH bond length is fixed but the remaining five degrees of freedom are treated exactly in the wave packet calculation Initial state‐specific total reaction probabilities for the title reaction are presented for total angular momentum J=0 and the effects of reagents rotation and H2 vibration on reaction are examined

Accurate quantum calculation for the benchmark reaction H2+OH→H2O +H in five‐dimensional space: Reaction probabilities for J=0

A time‐dependent wave packet method has been developed to study atom–triatom ABC+D→AB+CD reactions in full six dimensions (6D). The approach employs a body‐fixed coupled angular momentum basis for three angular coordinates, and three 1D bases for three radial coordinates. It permits the calculation of diatom AB vibrational state resolved total reaction probability for an initial rovibrational state of the triatom ABC. The approach is applied to study the H+H2O→H2+OH reaction on the modified Schatz–Elgersman potential energy surface. Initial state‐selected total reaction probabilities are presented for initial ground and several vibrationally excited states of H2O for total angular momentum J=0, along with the final OH vibrational state distributions. We also report the cross sections for reaction from the initial ground vibrational and the first bending excited states of H2O. Comparisons are made between our results and those from other theoretical calculations and experiments.

Dong H. Zhang

Papers

Full‐dimensional time‐dependent treatment for diatom–diatom reactions: The H2+OH reaction

Quantum reactive scattering with a deep well: Time‐dependent calculation for H+O2 reaction and bound state characterization for HO2

First-Principles Theory for the H + H2O, D2O Reactions

Accurate quantum calculation for the benchmark reaction H2+OH→H2O +H in five‐dimensional space: Reaction probabilities for J=0

A six dimensional quantum study for atom–triatom reactions: The H+H2O→H2+OH reaction