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

Electronic excitations lie at the origin of most of the commonly measured spectra. However, the first-principles computation of excited states requires a larger effort than ground-state calculations, which can be very efficiently carried out within density-functional theory. On the other hand, two theoretical and computational tools have come to prominence for the description of electronic excitations. One of them, many-body perturbation theory, is based on a set of Green’s-function equations, starting with a one-electron propagator and considering the electron-hole Green’s function for the response. Key ingredients are the electron’s self-energy S and the electron-hole interaction. A good approximation for S is obtained with Hedin’s GW approach, using density-functional theory as a zero-order solution. First-principles GW calculations for real systems have been successfully carried out since the 1980s. Similarly, the electron-hole interaction is well described by the Bethe-Salpeter equation, via a functional derivative of S. An alternative approach to calculating electronic excitations is the time-dependent density-functional theory (TDDFT), which offers the important practical advantage of a dependence on density rather than on multivariable Green’s functions. This approach leads to a screening equation similar to the Bethe-Salpeter one, but with a two-point, rather than a four-point, interaction kernel. At present, the simple adiabatic local-density approximation has given promising results for finite systems, but has significant deficiencies in the description of absorption spectra in solids, leading to wrong excitation energies, the absence of bound excitonic states, and appreciable distortions of the spectral line shapes. The search for improved TDDFT potentials and kernels is hence a subject of increasing interest. It can be addressed within the framework of many-body perturbation theory: in fact, both the Green’s functions and the TDDFT approaches profit from mutual insight. This review compares the theoretical and practical aspects of the two approaches and their specific numerical implementations, and presents an overview of accomplishments and work in progress.

/pdf/electronic-excitations-density-functional-versus-many-body-2tgqd9dfpy.pdf

Electronic excitations: density-functional versus many-body Green's-function approaches

Modern nanotechnology allows one to scale down various important devices (sensors, chips, fibers, etc.) and thus opens up new horizons for their applications. The efficiency of most of them is based on fundamental physical phenomena, such as transport of wave excitations and resonances. Short propagation distances make phase-coherent processes of waves important. Often the scattering of waves involves propagation along different paths and, as a consequence, results in interference phenomena, where constructive interference corresponds to resonant enhancement and destructive interference to resonant suppression of the transmission. Recently, a variety of experimental and theoretical work has revealed such patterns in different physical settings. The purpose of this review is to relate resonant scattering to Fano resonances, known from atomic physics. One of the main features of the Fano resonance is its asymmetric line profile. The asymmetry originates from a close coexistence of resonant transmission and resonant reflection and can be reduced to the interaction of a discrete (localized) state with a continuum of propagation modes. The basic concepts of Fano resonances are introduced, their geometrical and/or dynamical origin are explained, and theoretical and experimental studies of light propagation in photonic devices, charge transport through quantum dots, plasmon scattering in Josephson-junction networks, and matter-wave scattering in ultracold atom systems, among others are reviewed.

/pdf/fano-resonances-in-nanoscale-structures-2c8qeas3bm.pdf

Fano resonances in nanoscale structures

日本物理学会誌及びJournal of the Physical Society of Japanの月刊について

: 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

Molecule-based functional devices on surfaces may take advantage of bistable molecular switches. The conformational dynamics and efficiency of switches are radically different on surfaces compared to the liquid phase. We present a design of molecular layers which enables bistable switching on a surface and, for the first time, demonstrate control of a single switch in a dense and ordered array at the spatial limit. Up and down motion of a central Sn ion through the frame of a phthalocyanine molecule is achieved via resonant electron or hole injection into molecular orbitals.

Pushing and pulling a Sn ion through an adsorbed phthalocyanine molecule.

The point contact of a tunnel tip approaching towards Ag(111) and Cu(111) surfaces is investigated with a low temperature scanning tunneling microscope. A sharp jump to contact, random in nature, is observed in the conductance. After point contact, the tip-apex atom is transferred to the surface, indicating that a one-atom contact is formed during the approach. In sharp contrast, the conductance over single silver and copper adatoms exhibits a smooth and reproducible transition from tunneling to contact regime. Numerical simulations show that this is a consequence of the additional dipolar bonding between the adatom and the surface atoms.

Atom transfer and single-adatom contacts.

The tip of a low-temperature scanning tunneling microscope is brought into contact with individual cobalt atoms adsorbed on Cu(100). A smooth transition from the tunneling regime to contact occurs at a conductance of $G\ensuremath{\approx}{G}_{0}$. Spectroscopy in the contact regime, i.e., at currents in a $\ensuremath{\mu}\mathrm{A}$ range, was achieved and indicated a significant change of the Kondo temperature ${T}_{K}$. Calculations indicate that the proximity of the tip shifts the cobalt $d$ band and thus affects ${T}_{K}$.

Conductance and Kondo effect in a controlled single-atom contact.

The tip of a low-temperature scanning tunneling microscope is approached towards a C60 molecule adsorbed at a pentagon-hexagon bond on Cu(100) to form a tip-molecule contact. The conductance rapidly increases to approximately 0.25 conductance quanta in the transition region from tunneling to contact. Ab-initio calculations within density functional theory and nonequilibrium Green's function techniques explain the experimental data in terms of the conductance of an essentially undeformed C60. The conductance in the transition region is affected by structural fluctuations which modulate the tip-molecule distance.

/pdf/controlled-contact-to-a-c-60-molecule-1y02qoth52.pdf

Controlled contact to a C-60 molecule

Heads or tails? The evolution of structural and electronic properties of tin-phthalocyanine films has been analyzed for sub-monolayer to multilayer coverage using low-temperature scanning tunneling microscopy. Two molecular conformations are observed: randomly dispersed for the first layer, and islands with a single conformation in subsequent layers.

Jörg Kröger

Papers

Pushing and pulling a Sn ion through an adsorbed phthalocyanine molecule.

Atom transfer and single-adatom contacts.

Conductance and Kondo effect in a controlled single-atom contact.

Controlled contact to a C-60 molecule

Structural and electronic properties of ultrathin tin-phthalocyanine films on Ag(111) at the single-molecule level.