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

Over the last forty years many computer simulations of water have been performed using rigid non-polarizable models. Since these models describe water interactions in an approximate way it is evident that they cannot reproduce all of the properties of water. By now many properties for these kinds of models have been determined and it seems useful to compile some of these results and provide a critical view of the successes and failures. In this paper a test is proposed in which 17 properties of water, from the vapour and liquid to the solid phases, are taken into account to evaluate the performance of a water model. A certain number of points between zero (bad agreement) and ten (good agreement) are given for the predictions of each model and property. We applied the test to five rigid non-polarizable models, TIP3P, TIP5P, TIP4P, SPC/E and TIP4P/2005, obtaining an average score of 2.7, 3.7, 4.7, 5.1, and 7.2 respectively. Thus although no model reproduces all properties, some models perform better than others. It is clear that there are limitations for rigid non-polarizable models. Neglecting polarizability prevents an accurate description of virial coefficients, vapour pressures, critical pressure and dielectric constant. Neglecting nuclear quantum effects prevents an accurate description of the structure, the properties of water below 120 K and the heat capacity. It is likely that for rigid non-polarizable models it may not be possible to increase the score in the test proposed here beyond 7.6. To get closer to experiment, incorporating polarization and nuclear quantum effects is absolutely required even though a substantial increase in computer time should be expected. The test proposed here, being quantitative and selecting properties from all phases of water can be useful in the future to identify progress in the modelling of water.

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Simulating water with rigid non-polarizable models: a general perspective

Fluid phase equilibria

The performance of several popular water models (TIP3P, TIP4P, TIP5P and TIP4P/2005) is analyzed. For that purpose the predictions for ten different properties of water are investigated, namely: 1. vapour–liquid equilibria (VLE) and critical temperature; 2. surface tension; 3. densities of the different solid structures of water (ices); 4. phase diagram; 5. melting-point properties; 6. maximum in the density of water at room pressure and thermal coefficients α and κT; 7. structure of liquid water and ice; 8. equation of state at high pressures; 9. self-diffusion coefficient; 10. dielectric constant. For each property, the performance of each model is analyzed in detail with a critical discussion of the possible reason of the success or failure of the model. A final judgement on the quality of these models is provided. TIP4P/2005 provides the best description of almost all properties of the list, the only exception being the dielectric constant. In second position, TIP5P and TIP4P yield a similar performance overall, and the last place with the poorest description of the water properties is provided by TIP3P. The ideas leading to the proposal and design of the TIP4P/2005 are also discussed in detail. TIP4P/2005 is probably close to the best description of water that can be achieved with a non-polarizable model described by a single Lennard-Jones (LJ) site and three charges.

What ice can teach us about water interactions: a critical comparison of the performance of different water models.

First-principles calculations are performed to investigate the interaction of physisorbed small molecules, including CO, H2, H2O, NH3, NO, NO2, and O2, with phosphorene, and their energetics, charge transfer, and magnetic moment are evaluated on the basis of dispersion-corrected density functional theory. Our calculations reveal that CO, H2, H2O, and NH3 molecules act as a weak donor, whereas O2 and NO2 act as a strong acceptor. While the NO molecule donates electrons to graphene, it receives electrons from phosphorene. Among all the investigated molecules, NO2 has the strongest interaction through hybridizing its frontier orbitals with the 3p orbital of phosphorene. The nontrivial and distinct charge transfer occurring between phosphorene and these physisorbed molecules not only renders phosphorene promising for application as a gas sensor but also provides an effective route for modulating the polarity and density of carriers in phosphorene. In addition, the intermediate binding energy of hydrogen molec...

Energetics, Charge Transfer, and Magnetism of Small Molecules Physisorbed on Phosphorene

https://www-wales.ch.cam.ac.uk/pdf/CPL.415.302.2005.pdf

Global minima for water clusters (H2O)n, n ⩽ 21, described by a five-site empirical potential

We present crystalline structures for 60-, 256-, and 320-atom supercells of binary Lennard-Jones solids. These structures, based on cubic close packing, are much lower in energy than the disordered structures usually considered for this model glass former. We present a disconnectivity graph for a database of minima and transition states for the 320-atom system, which has been simplified using a grouping technique based on the canonical rate constants.

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Crystals of binary Lennard-Jones solids

Likely candidates for the global potential energy minima of C60(H2O)n clusters with n < or = 21 are found using basin-hopping global optimization. The potential energy surfaces are constructed using the TIP4P intermolecular potential for the water molecules, a Lennard-Jones water-fullerene potential, and a water-fullerene polarization potential, which depends on the first few nonvanishing C60 multipole polarizabilities. This combination produces a rather hydrophobic water-fullerene interaction. As a consequence, the water component of the lowest C60(H2O)n minima is quite closely related to low-lying minima of the corresponding TIP4P (H2O)n clusters. In most cases, the geometrical substructure of the water molecules in the C60(H2O)n global minimum coincides with that of the corresponding free water cluster. Exceptions occur when the interaction with C60 induces a change in geometry. This qualitative picture does not change significantly if we use the TIP3P model for the water-water interaction. Structures such as C60@(H2O)60, in which the water molecules surround the C60 fullerene, correspond to local minima with much higher potential energies. For such a structure to become the global minimum, the magnitude of the water-fullerene interaction must be increased to an unphysical value.

Global potential energy minima of C60(H2O)n clusters.

We present candidate structures for the global minima of N-atom rare gas clusters containing one additional alkali metal ion, LJNM. Lennard-Jones and Mason–Schamp potentials are used to represent the rare gas–rare gas and rare gas–alkali metal ion interactions, respectively. Results are presented for parameters appropriate to both Ar–K+ and Xe–Cs+ systems. When the ion is closer in size to the rare gas atoms (for XeNCs+) the global minima tend to be based on icosahedral packing. However, when the ion is relatively small (for ArNK+) the global minima below a certain size threshold are based on structures where the ion has lower coordination numbers. For larger clusters the global minima are again based on icosahedral packing. The latter structures can be found with minimal computational effort using the known global minima for clusters bound by Lennard-Jones or Morse potentials, substituting one atom at a time by the ion and minimizing.

/pdf/global-minima-for-rare-gas-clusters-containing-one-alkali-1gfk8iaxwa.pdf

Global minima for rare gas clusters containing one alkali metal ion

http://www-wales.ch.cam.ac.uk/pdf/CPL.412.23.2005.pdf

Javier Hernández-Rojas

Papers

Global minima for water clusters (H2O)n, n ⩽ 21, described by a five-site empirical potential

Crystals of binary Lennard-Jones solids

Global potential energy minima of C60(H2O)n clusters.

Global minima for rare gas clusters containing one alkali metal ion

Global minima and energetics of Li+(H2O)n and Ca2+(H2O)n clusters for n ⩽ 20