This article reviews the basic theoretical aspects of graphene, a one-atom-thick allotrope of carbon, with unusual two-dimensional Dirac-like electronic excitations. The Dirac electrons can be controlled by application of external electric and magnetic fields, or by altering sample geometry and/or topology. The Dirac electrons behave in unusual ways in tunneling, confinement, and the integer quantum Hall effect. The electronic properties of graphene stacks are discussed and vary with stacking order and number of layers. Edge (surface) states in graphene depend on the edge termination (zigzag or armchair) and affect the physical properties of nanoribbons. Different types of disorder modify the Dirac equation leading to unusual spectroscopic and transport properties. The effects of electron-electron and electron-phonon interactions in single layer and multilayer graphene are also presented.

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The electronic properties of graphene

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

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 present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.

Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium.

The ultimate aim of any detection method is to achieve such a level of sensitivity that individual quanta of a measured entity can be resolved. In the case of chemical sensors, the quantum is one atom or molecule. Such resolution has so far been beyond the reach of any detection technique, including solid-state gas sensors hailed for their exceptional sensitivity1, 2, 3, 4. The fundamental reason limiting the resolution of such sensors is fluctuations due to thermal motion of charges and defects5, which lead to intrinsic noise exceeding the sought-after signal from individual molecules, usually by many orders of magnitude. Here, we show that micrometre-size sensors made from graphene are capable of detecting individual events when a gas molecule attaches to or detaches from graphene's surface. The adsorbed molecules change the local carrier concentration in graphene one by one electron, which leads to step-like changes in resistance. The achieved sensitivity is due to the fact that graphene is an exceptionally low-noise material electronically, which makes it a promising candidate not only for chemical detectors but also for other applications where local probes sensitive to external charge, magnetic field or mechanical strain are required.

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Detection of individual gas molecules adsorbed on graphene

The recent development of the “scanning tunneling microscope” (STM) by Binnig et al. [8.1–5] has made possible the direct real-space imaging of surface topography. In this technique, a metal tip is scanned along the surface while ad justing its height to maintain constant vacuum tunneling current. The result is essentially a contour map of the surface. This contribution reviews the the ory [8.6–8] of STM, with illustrative examples. Because the microscopic structure of the tip is unknown, the tip wave functions are modeled as s-wave functions in the present approach [8.6, 7]. This approximation works best for small effective tip size. The tunneling current is found to be proportional to the surface local density of states (at the Fermi level), evaluated at the position of the tip. The effective resolution is roughly [2A(R+d)]1/2, where R is the effective tip radius and d is the gap distance. When applied to the 2x1 and 3x1 reconstructions of the Au(l10) surface, the theory gives excellent agreement with experiment [8.4] if a 9 A tip radius is assumed. For dealing with more complex or aperiodic surfaces, a crude but convenient calculational technique based on atom charge superposition is introduced; it reproduces the Au(l10) results reasonably well. This method is used to test the structure-sensitivity of STM. The Au(l10) image is found to be rather insensitive to the position of atoms beyond the first atomic layer.

Theory of the scanning tunneling microscope

A general form is proposed for an empirical interatomic potential for multicomponent systems. This form interpolates between potentials for the respective elements to treat heteronuclear bonds. The approach is applied to C-Si and Si-Ge systems. In particular, the properties of SiC and its defects are well described.

Modeling solid-state chemistry: Interatomic potentials for multicomponent systems

Empirical interatomic potentials permit the calculation of structural properties and energetics of complex systems. A new approach for constructing such potentials, by explicitly incorporating the dependence of bond order on local environment, permits an improved description of covalent materials. In particular, a new potential for silicon is presented, along with results of extensive tests which suggest that this potential provides a rather realistic description of silicon. The limitations of the potential are discussed in detail.

New empirical approach for the structure and energy of covalent systems

A theory is presented for vacuum tunneling between a real solid surface and a model probe with a locally spherical tip, applicable to the recently developed "scanning tunneling microscope." Calculations for 2\ifmmode\times\else\texttimes\fi{}1 and 3\ifmmode\times\else\texttimes\fi{}1 reconstructions of Au(110) are in excellent agreement with recent experimental results, if an effective radius of curvature of 9 \AA{} is assumed for the tip.

https://link.aps.org/pdf/10.1103/PhysRevLett.50.1998

Theory and Application for the Scanning Tunneling Microscope

An empirical interatomic potential is introduced, which gives a convenient and relatively accurate description of the structural properties and energetics of carbon, including elastic properties, phonons, polytypes, and defects and migration barriers in diamond and graphite. The potential is applied to study amorphous carbon formed in three different ways. Two resulting structures are similar to experimental $a\ensuremath{-}\mathrm{C}$, but another more diamondlike form has essentially identical energy. The liquid is also found to have unexpected properties.

Jerry Tersoff

Papers

Theory of the scanning tunneling microscope

Modeling solid-state chemistry: Interatomic potentials for multicomponent systems

New empirical approach for the structure and energy of covalent systems

Theory and Application for the Scanning Tunneling Microscope

Empirical interatomic potential for carbon, with application to amorphous carbon