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

Triatomic hydrogen positive ion surface crossing effects in chemical reactions based on potential energy surfaces calculation using diatomics-in- molecules approach

/pdf/effects-of-surface-crossing-in-chemical-reactions-the-h3-2mtuc1t58w.pdf

Effects of surface crossing in chemical reactions - The H3 system

A three dimensional generalized Langevin formalism is presented and applied to Ar and Xe interactions with Pt (111). Approximations for the random force and friction terms are proposed which permit realistic description of the motion and response of the surface atoms, including proper correlations among neighboring atoms. A ’’ghost atom’’ technique is developed which provides convenient numerical solution of the generalized Langevin equations in such a way that the fluctuation–dissipation theorem relating the random force and friction is satisfied rigorously. A simple prescription for determining parameters in the random force and friction is outlined. The prescription is applied to a four‐atom active zone to obtain explicit relationships for all parameters, depending only on the bulk and surface Debye frequencies, for fcc (100), (110), and (111), and bcc (100) and (110) surfaces. Calculations of energy accommodation, sticking probabilities, and thermal desorption rates are reported for Ar and Xe on Pt(111). The sensitivity of these properties on the parameters of the random force and friction, i.e., on the phonon spectrum, is examined. The dependence is found to be sufficiently weak to demonstrate convincingly that the generalized Langevin approach with relatively simple parameterization is capable of describing gas–surface dynamics with high accuracy.

Dynamics of gas–surface interactions: 3D generalized Langevin model applied to fcc and bcc surfaces

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2-4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2C=NH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2C=NH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation.

Ab initio Ehrenfest dynamics.

We present an analysis of the equilibrium limits of the two most widely used approaches for simulating the dynamics of molecular systems that combine both quantum and classical degrees of freedom. For a two-level quantum system connected to an infinite number of classical particles, we derive a simple analytical expression for the equilibrium mean energy attained by the self-consistent-field (Ehrenfest) method and show that it deviates substantially from Boltzmann. By contrast, “fewest switches” surface hopping achieves Boltzmann quantum state populations. We verify these analytical results with simulations.

https://www.gc.cuny.edu/CUNY_GC/media/CUNY-Graduate-Center/PDF/ITS/5-22-14%20Workshop%20References/Tully_parandekar-detbal05.pdf

Mixed quantum-classical equilibrium.

A generalization of classical adiabatic molecular dynamics, which we term molecular dynamics with electronic frictions, is described for nuclear motion on a continuum of potential‐energy surfaces, such as for adsorbate dynamics at a metal surface. In this situation, the Born–Oppenheimer approximation fails, since for any molecular motion—such as vibrations, rotations, or translations—there are resonant electronic excitations of the metal. However, such excitations are often highly delocalized, so that the continuum of electronic potential‐energy surfaces on which nuclear motion occurs are all of similar shape, and can be replaced by a single, effective potential. Nonadiabatic energy exchange between nuclear and electronic degrees of freedom is then represented by frictional and fluctuating forces on the nuclei, and no explicit electronic dynamics are required. The friction in general involves memory, although it is shown that the Markov limit in which memory vanishes is likely to be quite broadly applicab...

John C. Tully

Papers

Effects of surface crossing in chemical reactions - The H3 system

Dynamics of gas–surface interactions: 3D generalized Langevin model applied to fcc and bcc surfaces

Ab initio Ehrenfest dynamics.

Mixed quantum-classical equilibrium.

Molecular dynamics with electronic frictions