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

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

https://www.pnas.org/content/pnas/99/20/12562.full.pdf

Escaping free-energy minima

A method is proposed for carrying out molecular dynamics simulations of processes that involve electronic transitions. The time dependent electronic Schrodinger equation is solved self‐consistently with the classical mechanical equations of motion of the atoms. At each integration time step a decision is made whether to switch electronic states, according to probabilistic ‘‘fewest switches’’ algorithm. If a switch occurs, the component of velocity in the direction of the nonadiabatic coupling vector is adjusted to conserve energy. The procedure allows electronic transitions to occur anywhere among any number of coupled states, governed by the quantum mechanical probabilities. The method is tested against accurate quantal calculations for three one‐dimensional, two‐state models, two of which have been specifically designed to challenge any such mixed classical–quantal dynamical theory. Although there are some discrepancies, initial indications are encouraging. The model should be applicable to a wide variety of gas‐phase and condensed‐phase phenomena occurring even down to thermal energies.

/pdf/molecular-dynamics-with-electronic-transitions-39jwikyow5.pdf

Molecular dynamics with electronic transitions

12.2.2. Four-Wave Mixing (FWM) 4849 12.2.3. Dye Aggregation 4850 12.2.4. Optoelectronic Nanodevices 4850 12.3. Sensor 4851 12.3.1. Chemical Sensor 4851 12.3.2. Biological Sensor 4851 12.4. Catalysis 4852 13. Conclusion and Perspectives 4852 14. Abbreviations 4853 15. Acknowledgements 4854 16. References 4854 * Corresponding author E-mail: tpal@chem.iitkgp.ernet.in. † Raidighi College. § Indian Institute of Technology. 4797 Chem. Rev. 2007, 107, 4797−4862

Interparticle Coupling Effect on the Surface Plasmon Resonance of Gold Nanoparticles: From Theory to Applications

▪ Abstract Proton-coupled electron transfer (PCET) is an important mechanism for charge transfer in a wide variety of systems including biology- and materials-oriented venues. We review several are...

/pdf/proton-coupled-electron-transfer-3oyvp0w9qd.pdf

Proton-Coupled Electron Transfer

An extension of the classical trajectory approach is proposed that may be useful in treating many types of nonadiabatic molecular collisions. Nuclei are assumed to move classically on a single potential energy surface until an avoided surface crossing or other region of large nonadiabatic coupling is reached. At such points the trajectory is split into two branches, each of which follows a different potential surface. The validity of this model as applied to the HD2+ system is assessed by numerical integration of the appropriate semiclassical equations. A 3d “trajectory surface hopping” treatment of the reaction of H+ with D2 at a collision energy of 4 eV is reported. The excellent agreement with experiment is an encouraging indication of the potential usefulness of this approach.

Trajectory Surface Hopping Approach to Nonadiabatic Molecular Collisions: The Reaction of H+ with D2

We apply ‘‘molecular dynamics with quantum transitions’’ (MDQT), a surface‐hopping method previously used only for electronic transitions, to proton transfer in solution, where the quantum particle is an atom. We use full classical mechanical molecular dynamics for the heavy atom degrees of freedom, including the solvent molecules, and treat the hydrogen motion quantum mechanically. We identify new obstacles that arise in this application of MDQT and present methods for overcoming them. We implement these new methods to demonstrate that application of MDQT to proton transfer in solution is computationally feasible and appears capable of accurately incorporating quantum mechanical phenomena such as tunneling and isotope effects. As an initial application of the method, we employ a model used previously by Azzouz and Borgis to represent the proton transfer reaction AH–B■A−–H+B in liquid methyl chloride, where the AH–B complex corresponds to a typical phenol–amine complex. We have chosen this model, in part, because it exhibits both adiabatic and diabatic behavior, thereby offering a stringent test of the theory. MDQT proves capable of treating both limits, as well as the intermediate regime. Up to four quantum states were included in this simulation, and the method can easily be extended to include additional excited states, so it can be applied to a wide range of processes, such as photoassisted tunneling. In addition, this method is not perturbative, so trajectories can be continued after the barrier is crossed to follow the subsequent dynamics.

/pdf/proton-transfer-in-solution-molecular-dynamics-with-quantum-vngslkmpv7.pdf

Proton transfer in solution: Molecular dynamics with quantum transitions

We present a unified derivation of the mean-field (Ehrenfest) and surface-hopping approaches to mixed quantum–classical dynamics that elucidates the underlying approximations of the methods and their strengths and weaknesses. We then report a quantitative test of alternative mixed quantum–classical methods against accurate quantum mechanical calculations for a simple one-dimensional curve-crossing model. We conclude that, for this model, surface-hopping with the adiabatic representation is decidedly superior to either mean-field or surface-hopping with the diabatic representation.

http://www.univie.ac.at/columbus/workshops/rio2005/LECTURES/BARBATTI/PAPERS/tully_suface_hopping.pdf

Mixed quantum–classical dynamics

Nonadiabatic dynamics—nuclear motion evolving on multiple potential energy surfaces—has captivated the interest of chemists for decades. Exciting advances in experimentation and theory have combined to greatly enhance our understanding of the rates and pathways of nonadiabatic chemical transformations. Nevertheless, there is a growing urgency for further development of theories that are practical and yet capable of reliable predictions, driven by fields such as solar energy, interstellar and atmospheric chemistry, photochemistry, vision, single molecule electronics, radiation damage, and many more. This Perspective examines the most significant theoretical and computational obstacles to achieving this goal, and suggests some possible strategies that may prove fruitful.

John C. Tully

Papers

Molecular dynamics with electronic transitions

Trajectory Surface Hopping Approach to Nonadiabatic Molecular Collisions: The Reaction of H+ with D2

Proton transfer in solution: Molecular dynamics with quantum transitions

Mixed quantum–classical dynamics

Perspective: Nonadiabatic dynamics theory.