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

Physical Review B

Associate DIETRICH BELITZ, University of Oregon Editors: Condensed Matter Physics (Theoretical) J. IGNACIO CIRAC, Max-Planck-Institut für Quantenoptik Quantum Information RAYMOND E. GOLDSTEIN, University of Cambridge Biological Physics ARTHUR F. HEBARD, University of Florida Condensed Matter Physics (Experimental) RANDALL D. KAMIEN, University of Pennsylvania Soft Condensed Matter DANIEL KLEPPNER, Massachusetts Institute of Technology Atomic, Molecular, and Optical Physics (Experimental) PAUL G. LANGACKER, Institute for Advanced Study, Princeton University Particle Physics (Theoretical) VERA LÜTH, Stanford University Particle Physics (Experimental) DAVID D. MEYERHOFER, University of Rochester Physics of Plasmas and Matter at High-Energy Density WITOLD NAZAREWICZ, University of Tennessee, Oak Ridge National Laboratory Nuclear Physics JOHN H. SCHWARZ, California Institute of Technology Mathematical Physics FRIEDRICH-KARL THIELEMANN, Universität Basel Astrophysics Senior Assistant Editor: DEBBIE BRODBAR, APS Editorial Office American Physical Society

Reviews of Modern Physics

The Journal of Physical Chemistry Letters

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green’s functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

/pdf/dftb-a-software-package-for-efficient-approximate-density-4x2nsa3iyh.pdf

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

Higher acenes have drawn much attention as promising organic semiconductors with versatile electronic properties. However, the nature of their ground state and electronic excited states is still not fully clear. Their unusual chemical reactivity and instability are the main obstacles for experimental studies, and the potentially prominent diradical character, which might require a multireference description in such large systems, hinders theoretical investigations. Here, we provide a detailed answer with the particle–particle random-phase approximation calculation. The 1 A g ground states of acenes up to decacene are on the closed-shell side of the diradical continuum, whereas the ground state of undecacene and dodecacene tilts more to the open-shell side with a growing polyradical character. The ground state of all acenes has covalent nature with respect to both short and long axes. The lowest triplet state 3 B 2u is always above the singlet ground state even though the energy gap could be vanishingly small in the polyacene limit. The bright singlet excited state 1 B 2u is a zwitterionic state to the short axis. The excited 1 A g state gradually switches from a double-excitation state to another zwitterionic state to the short axis, but always keeps its covalent nature to the long axis. An energy crossing between the 1 B 2u and excited 1 A g states happens between hexacene and heptacene. Further energetic consideration suggests that higher acenes are likely to undergo singlet fission with a low photovoltaic efficiency; however, the efficiency might be improved if a singlet fission into multiple triplets could be achieved.

https://www.pnas.org/content/pnas/113/35/E5098.full.pdf

Nature of ground and electronic excited states of higher acenes

Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear–electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron–proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron–proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF–. The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pK...

Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries

We formulate an adiabatic connection for the exchange-correlation energy in terms of pairing matrix fluctuation. This connection opens new channels for density functional approximations based on pairing interactions. Even the simplest approximation to the pairing matrix fluctuation, the particle-particle random phase approximation (pp-RPA), has some highly desirable properties. It has no delocalization error with a nearly linear energy behavior for systems with fractional charges, describes van der Waals interactions similarly and thermodynamic properties significantly better than particle-hole RPA, and eliminates static correlation error for single-bond systems. Most significantly, the pp-RPA is the first known functional that has an explicit and closed-form dependence on the occupied and unoccupied orbitals and captures the energy derivative discontinuity in strongly correlated systems. These findings illustrate the potential of including pairing interactions within a density functional framework.

/pdf/exchange-correlation-energy-from-pairing-matrix-fluctuation-1fleje3cji.pdf

Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random-phase approximation

Multicomponent density functional theory (DFT) enables the consistent quantum mechanical treatment of both electrons and protons. A major challenge has been the design of electron-proton correlation (epc) functionals that produce even qualitatively accurate proton densities. Herein an electron-proton correlation functional, epc17, is derived analogously to the Colle-Salvetti formalism for electron correlation and is implemented within the nuclear-electronic orbital (NEO) framework. The NEO-DFT/epc17 method produces accurate proton densities efficiently and is promising for diverse applications.

Development of a practical multicomponent density functional for electron-proton correlation to produce accurate proton densities.

The development of approximate exchange-correlation functionals is critical for modern density functional theory. A recent analysis of atomic systems suggested that some modern functionals are straying from the path toward the exact functional because electron densities are becoming less accurate while energies are becoming more accurate since the year 2000. To investigate this trend for more chemically relevant systems, the electron densities in the bonding regions and the atomization energies are analyzed for a series of diatomic molecules with 90 different functionals. For hybrid generalized gradient approximation functionals developed since the year 2000, the errors in densities and atomization energies are decoupled; the accuracy of the energies remains relatively consistent while the accuracy of the densities varies significantly. Such decoupling is not observed for generalized gradient and meta-generalized gradient approximation functionals. Analysis of electron densities in bonding regions is foun...

Yang Yang

Papers

Nature of ground and electronic excited states of higher acenes

Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries

Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random-phase approximation

Development of a practical multicomponent density functional for electron-proton correlation to produce accurate proton densities.

Is the Accuracy of Density Functional Theory for Atomization Energies and Densities in Bonding Regions Correlated