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 jellium model of simple metal clusters has enjoyed remarkable empirical success, leading to many theoretical questions. In this review, we first survey the hierarchy of theoretical approximations leading to the model. We then describe the jellium model in detail, including various extensions. One important and useful approximation is the local-density approximation to exchange and correlation effects, which greatly simplifies self-consistent calculations of the electronic structure. Another valuable tool is the semiclassical approximation to the single-particle density matrix, which gives a theoretical framework to connect the properties of large clusters with the bulk and macroscopic surface properties. The physical properties discussed in this review are the ground-state binding energies, the ionization potentials, and the dipole polarizabilities. We also treat the collective electronic excitations from the point of view of the cluster response, including some useful sum rules.

/pdf/the-physics-of-simple-metal-clusters-self-consistent-jellium-3u9wf8r66h.pdf

The physics of simple metal clusters: self-consistent jellium model and semiclassical approaches

Atomic-level structure and structure–property relationship in metallic glasses

A density functional theory-based algorithm for periodic and non-periodic ab initio calculations is presented. This scheme uses pseudopotentials in order to integrate out the core electrons from the problem. The valence pseudo-wavefunctions are expanded in Gaussian-type orbitals and the density is represented in a plane wave auxiliary basis. The Gaussian basis functions make it possible to use the efficient analytical integration schemes and screening algorithms of quantum chemistry. Novel recursion relations are developed for the calculation of the matrix elements of the density-dependent Kohn-Sham self-consistent potential. At the same time the use of a plane wave basis for the electron density permits efficient calculation of the Hartree energy using fast Fourier transforms, thus circumventing one of the major bottlenecks of standard Gaussian based calculations. Furthermore, this algorithm avoids the fitting procedures that go along with intermediate basis sets for the charge density. The performance a...

A hybrid Gaussian and plane wave density functional scheme

We propose a new effective Monte Carlo (MC) procedure for direct calculation of the free energy in a single MC run. The partition function of the expanded ensemble is introduced including a sum of canonical partition functions with a set of temperatures and additive factors (modification). Random walk in the space of both particle coordinates and temperatures provides calculation of free energy in a wide range of T. The method was applied to a primitive model of electrolyte including the region of low temperatures. In similar way other variants of expanded ensembles are constructed (e.g., over the number of particles N or volume V). Its facilities in quantum statistics (path integral Monte Carlo) and some other applications are also discussed.

New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles

Electron attachment and localization in small water clusters (H2O)n (n=8–128) is studied using path‐integral molecular dynamics simulations. The electron‐water molecule interaction is described via a pseudopotential which includes Coulomb, polarization, exclusion and exchange contributions. Different electron localization modes are found depending on cluster size. For small and intermediate size clusters (n=8–32), the energetically favored localization mode involves a surface state and the calculated excess electron binding energies are in agreement with experimentally measured values. In larger clusters, n=64, 128, internal localization (solvation) is energetically favored. In both cases the localization of the excess electron is accompanied by large cluster molecular reorganization. The cluster size dependence of the localization mode, the energetics, structure, and excess electron distributions in the negative molecular anions (H2O)−n, and the dependence on temperature are explored.

Electron localization in water clusters. II. Surface and internal states

A local pseudopotential for the interaction of an electron with a water molecule in the electronic ground state is developed The potential contains Coulomb, adiabatic polarization, exclusion, and exchange contributions The potential is suitable for a description of excess electron states in water clusers, and for studies of electron solvation in water Quantum path integral molecular dynamics simulations of electron localization in water clusters employing this potential yield results in agreement with available experimental data and all‐electron quantum chemical calculations

Electron localization in water clusters. I. Electron--water pseudopotential

Hydration of sodium in water clusters, Na(H 2 O) n , 1≤n≤8, is investigated using nonlocal pseudopotentials and local-spin-density functional theory, with exchange-correlation gradient corrections: Addition of water molecules to an Na atom results in a successive decrease in the ionization potential, with a marked reduced variation for n>4. This reflects the formation of a molecular shell about the Na for n∼4, accompanied by expulsion of the metal valence electron from the hydration cavity and its delocalization in a «surface Rydberg-like state»

Hydration of sodium in water clusters.

Molecular-dynamics simulations and in situ experimental observations of the melting and equilibrium structure of the crystalline Si(100)-melt interface are described. The equilibrium interface is structured, exhibiting facets established on (111) planes.

/pdf/faceting-at-the-silicon-100-crystal-melt-interface-theory-26h4mb808r.pdf

Faceting at the silicon (100) crystal-melt interface: Theory and experiment.

The dynamics and spectra of negatively charged water clusters, containing a single excess electron, are investigated. In our calculations the atomic water constituents of the clusters are treated classically while the excess electron is described quantum mechanically using the fast Fourier transform algorithm to solve the Schrodinger equation. Information about ground and excited electronic states corresponding to the equilibrium, finite temperature, ground‐state ensemble configurations can be obtained by solving for these states for given nuclear configurations generated via quantum mechanical path‐integral molecular dynamics simulations. As an alternative, more efficient way, we introduce the adiabatic simulation method which consists of propagating the nuclei in real time while concurrently annealing the electronic wave functions to their correct values corresponding to the instantaneous, dynamically generated nuclear configurations. The resulting trajectories can be used for analyzing nuclear motion i...

R. N. Barnett

Papers

Electron localization in water clusters. II. Surface and internal states

Electron localization in water clusters. I. Electron--water pseudopotential

Hydration of sodium in water clusters.

Faceting at the silicon (100) crystal-melt interface: Theory and experiment.

Dynamics and spectra of a solvated electron in water clusters