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.

/pdf/charmm-the-biomolecular-simulation-program-4kexem0xkx.pdf

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.

/pdf/the-formation-properties-and-impact-of-secondary-organic-4x4th6v9ke.pdf

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

We employed density functional theory-based ab initio molecular dynamics simulations to examine the hydration structure of several common alkali and alkali earth metal cations. We found that the commonly used atom pairwise dispersion correction scheme D3, which assigns dispersion coefficients based on the neutral form of the atom rather than its actual oxidation state, leads to inaccuracies in the hydration structures of these cations. We evaluated this effect for lithium, sodium, potassium, and calcium and found that the inaccuracies are particularly pronounced for sodium and potassium compared to the experiment. To remedy this issue, we propose disabling the D3 correction specifically for all cation-including pairs, which leads to a much better agreement with experimental data.

https://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.3c00856

Common Cations Are Not Polarizable: Effects of Dispersion Correction on Hydration Structures from Ab Initio Molecular Dynamics

Aqueous sea salt micro-aerosols play an important role in the heterogenous chemistry of the lower marine troposphere both in polluted and in remote areas. In particular, reactions with gases such as ozone or OH radicals leading to the release of molecular chlorine have been intensely studied, both experimentally and theoretically. Moreover, thin layers of sea water deposited on Arctic ice packs have been discovered to be a major source of reactive bromine species which destroy the surface ozone layer during polar sunrise. There is increasing evidence that the air-water interface is of a key importance in these chemical processes. Despite this, little has been known about the structure and physical properties of aqueous sea salt aerosols at a detailed, molecular level. Here, we summarize results of classical molecular dynamics, Car-Parrinello molecular dynamics and ab initio quantum chemistry calculations on concentrated aqueous sodium chloride and bromide solutions confined to cluster and slab geometries. The main questions addressed by the simulations concern the onset of NaC1 ionic solvation in water clusters, transition from clusters to slabs, structure of solvation layers and degree of ion pairing in concentrated solutions with confined geometries. A key result of the simulations is the observation that polarizable halogen anions (chloride and bromide) are present at the air-water interface of bulk solutions in amounts sufficient for the heterogenous atmospheric chemistry to take place. The calculations also reveal that bromide actually exhibits surfactant activity, i.e. its concentration at the interface is higher than in the bulk. This is in accord with the observed enhanced atmospheric reactivity of aqueous bromide compared to chloride and with SEM experiments on wetting and re-drying of NaCl/NaBr co-crystals.

Physical Properties and Atmospheric Reactivity of Aqueous Sea Salt Micro-Aerosols

We use optical pump-terahertz probe spectroscopy for exploring photoinduced ionization and plasma formation in atmospheric gases. Multiphoton versus strong-field photoionization processes are investigated using variable intensity, polarization and wavelength of the femtosecond optical pump pulses.

Photoionization Mechanisms of Atmospheric Gases Probed by Terahertz Pulses

A chemist realizes that popularity is no measure of strength.

We present new methods for time-dependent quantum mechanical simulations of large polyatomic systems and their applications to photochemical processes in clusters. Two related approaches are discussed: The Classical Separable Potential (CSP) approach, and its extension towards Configuration Interaction (CICSP). The former scheme assumes separability of the vibrational modes of the system, and describes each mode as moving in a mean field due to the other modes. The basic idea, which allows for quantum simulations of hitherto unaccesibly large systems, is that the effective single-mode potentials are obtained from a classical MD simulation that precedes the quantum calculation. The second approach represents an improvement that corrects for correlations between different modes, resulting in a scheme of good accuracy. Applications of the methods are presented for dynamics following photodetachment in a small I−(Ar) 2 cluster (where comparison with numerically exact calculation is possible) and for photoexcitation dynamics and spectroscopy of atomic and molecular impurities in large clusters, such as I 2(Ar) 17 and I 2(Ar) 47 Future directions of method development are suggested in the light of the algorithmic aspects and the applications.

Pavel Jungwirth

Papers

Common Cations Are Not Polarizable: Effects of Dispersion Correction on Hydration Structures from Ab Initio Molecular Dynamics

Physical Properties and Atmospheric Reactivity of Aqueous Sea Salt Micro-Aerosols

Photoionization Mechanisms of Atmospheric Gases Probed by Terahertz Pulses

A chemist realizes that popularity is no measure of strength.

New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems