There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

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CHARMM: the biomolecular simulation program.

A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: ...

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Secondary organic aerosol (SOA) accounts for a significant fraction of ambient tropospheric aerosol and a detailed knowledge of the formation, properties and transformation of SOA is therefore required to evaluate its impact on atmospheric processes, climate and human health. The chemical and physical processes associated with SOA formation are complex and varied, and, despite considerable progress in recent years, a quantitative and predictive understanding of SOA formation does not exist and therefore represents a major research challenge in atmospheric science. This review begins with an update on the current state of knowledge on the global SOA budget and is followed by an overview of the atmospheric degradation mechanisms for SOA precursors, gas-particle partitioning theory and the analytical techniques used to determine the chemical composition of SOA. A survey of recent laboratory, field and modeling studies is also presented. The following topical and emerging issues are highlighted and discussed in detail: molecular characterization of biogenic SOA constituents, condensed phase reactions and oligomerization, the interaction of atmospheric organic components with sulfuric acid, the chemical and photochemical processing of organics in the atmospheric aqueous phase, aerosol formation from real plant emissions, interaction of atmospheric organic components with water, thermodynamics and mixtures in atmospheric models. Finally, the major challenges ahead in laboratory, field and modeling studies of SOA are discussed and recommendations for future research directions are proposed.

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The formation, properties and impact of secondary organic aerosol: current and emerging issues

The potential energy surface of the first excited state of the water-argon complex is explored at a multireference perturbation theory level as an initial step of the project aimed at the study and control of photodissociation in H2O-Arn (n = 1, 2, ..., 12) clusters. Ab initio calculations, which will serve as a basis for the construction of an analytical force field for dynamical simulations, reveal the anisotropy of the excited state surface and weak potential coupling between intermolecular and intramolecular degrees of freedom. The importance of the "cage effect" is demonstrated.

Water Photolysis in Rare Gas Environment: The CASPT2 Excited State H2O(A)-Ar Potential

We have studied several microhydrated (H 2 O) n ·NO + ·H 2 S structures ( n = 1–3) and their fragments using wave-function based approach (coupled-clusters including single, double and non-iterative triple substitutions – CCSD(T) and second-order perturbation theory – MP2) and also employing density functional theory (with BLYP and ωB97XD functional). MP2 energetics is very close to CCSD(T) one. Both functionals provide reasonable binding energies compared to MP2, the ωB97XD being superior to BLYP. The exploratory ab initio molecular dynamics performed on four- and five-body clusters revealed that the hydrogen bonds network and cooperativity in these systems play a crucial role in the proton transfer from H 2 S·NO + to H 2 O and its conversion to thionitrous acid.

Effects of micro-hydration in proton transfer from H2S·NO+ complex to water: Ab initio and molecular dynamics study

Molecular-Level Organization of the Tear Film Lipid Layer: A Molecular Dynamics Simulation Study

Gray-Weale and Beattie's rationalization of the neg. charge obsd. on the surface of water in terms of accumulation of OH- is based on the supposedly uniquely large dielec. decrement of hydroxide solns. [A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994]. We challenge this rationalization and point to another ion, namely fluoride, which has a comparable dielec. decrement and size and which is repelled from the surface of water.

An explanation for the charge on water's surface, by A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994. Comment

Traditionally, the surfaces of aqueous electrolytes are described as inactive and practically devoid of ions [1, 2] Indeed, this has turned out to be true for non - polarizable ions, as alkali cations and small anions, as fluoride as well However, due to polarization interactions singly charged anions, with the heavy halides as particular examples, exhibit a propensity for the water / air (vacuum) interface This was first suggested in order to rationalize the occurrence of chemical reactions on aqueous interfaces, sea - salt particles, ocean surfaces etc This initiated MD calculations using polarizable potentials They suggest that highly polarisable anions can indeed be preferentially adsorbed at the outermost liquid layer In this description, the ions are polarized by the anisotropy of the interface, creating an induced dipole that is stronger than in the bulk The interaction between the polarized ions and the surrounding water molecules compensates for the reduced solvation available at the surface This has triggered a number of laboratory studies, applying mainly non - linear optical probes Battelle operates Pacific Northwest National Laboratory for the US Department of Energy

Pavel Jungwirth

Papers

Water Photolysis in Rare Gas Environment: The CASPT2 Excited State H2O(A)-Ar Potential

Effects of micro-hydration in proton transfer from H2S·NO+ complex to water: Ab initio and molecular dynamics study

Molecular-Level Organization of the Tear Film Lipid Layer: A Molecular Dynamics Simulation Study

An explanation for the charge on water's surface, by A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994. Comment

Segregation of salt ions at amorphous solid and liquid surfaces