Sergei L. Dudarev

Bio: Sergei L. Dudarev is an academic researcher from Culham Centre for Fusion Energy. The author has contributed to research in topics: Dislocation & Vacancy defect. The author has an hindex of 54, co-authored 263 publications receiving 17727 citations. Previous affiliations of Sergei L. Dudarev include University of Oxford & United Kingdom Atomic Energy Authority.

Electron-energy-loss spectra and the structural stability of nickel oxide: An LSDA+U study

Abstract: We demonstrate how by taking better account of electron correlations in the $3d$ shell of metal ions in nickel oxide it is possible to improve the description of both electron energy loss spectra and parameters characterizing the structural stability of the material compared with local spin density functional theory.

Multiscale modeling of crowdion and vacancy defects in body-centered-cubic transition metals

Abstract: We investigate the structure and mobility of single self-interstitial atom and vacancy defects in body-centered-cubic transition metals forming groups 5B (vanadium, niobium, and tantalum) and 6B (chromium, molybdenum, and tungsten) of the Periodic Table. Density-functional calculations show that in all these metals the axially symmetric self-interstitial atom configuration has the lowest formation energy. In chromium, the difference between the energies of the and the self-interstitial configurations is very small, making the two structures almost degenerate. Local densities of states for the atoms forming the core of crowdion configurations exhibit systematic widening of the "local" d band and an upward shift of the antibonding peak. Using the information provided by electronic structure calculations, we derive a family of Finnis-Sinclair-type interatomic potentials for vanadium, niobium, tantalum, molybdenum, and tungsten. Using these potentials, we investigate the thermally activated migration of self-interstitial atom defects in tungsten. We rationalize the results of simulations using analytical solutions of the multistring Frenkel-Kontorova model describing nonlinear elastic interactions between a defect and phonon excitations. We find that the discreteness of the crystal lattice plays a dominant part in the picture of mobility of defects. We are also able to explain the origin of the non-Arrhenius diffusion of crowdions and to show that at elevated temperatures the diffusion coefficient varies linearly as a function of absolute temperature.

Self-interstitial atom defects in bcc transition metals: Group-specific trends

Abstract: We present an investigation of systematic trends for the self-interstitial atom (SIA) defect behavior in body-centered cubic (bcc) transition metals using density-functional calculations. In all the nonmagnetic bcc metals the most stable SIA defect configuration has the $⟨111⟩$ symmetry. Metals in group 5B of the periodic table (V, Nb, Ta) have significantly different energies of formation of the $⟨111⟩$ and $⟨110⟩$ SIA configurations, while for the group 6B metals (Cr, Mo, W) the two configurations are linked by a soft bending mode. The relative energies of SIA defects in the nonmagnetic bcc metals are fundamentally different from those in ferromagnetic bcc $\ensuremath{\alpha}$-Fe. The systematic trend exhibited by the SIA defect structures in groups 5B and 6B transition metals correlates with the observed thermally activated mobility of SIA defects.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

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

Abstract: 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。

Advanced capabilities for materials modelling with Quantum ESPRESSO.

Abstract: Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software

Electronic excitations: density-functional versus many-body Green's-function approaches

Abstract: Electronic excitations lie at the origin of most of the commonly measured spectra. However, the first-principles computation of excited states requires a larger effort than ground-state calculations, which can be very efficiently carried out within density-functional theory. On the other hand, two theoretical and computational tools have come to prominence for the description of electronic excitations. One of them, many-body perturbation theory, is based on a set of Green’s-function equations, starting with a one-electron propagator and considering the electron-hole Green’s function for the response. Key ingredients are the electron’s self-energy S and the electron-hole interaction. A good approximation for S is obtained with Hedin’s GW approach, using density-functional theory as a zero-order solution. First-principles GW calculations for real systems have been successfully carried out since the 1980s. Similarly, the electron-hole interaction is well described by the Bethe-Salpeter equation, via a functional derivative of S. An alternative approach to calculating electronic excitations is the time-dependent density-functional theory (TDDFT), which offers the important practical advantage of a dependence on density rather than on multivariable Green’s functions. This approach leads to a screening equation similar to the Bethe-Salpeter one, but with a two-point, rather than a four-point, interaction kernel. At present, the simple adiabatic local-density approximation has given promising results for finite systems, but has significant deficiencies in the description of absorption spectra in solids, leading to wrong excitation energies, the absence of bound excitonic states, and appreciable distortions of the spectral line shapes. The search for improved TDDFT potentials and kernels is hence a subject of increasing interest. It can be addressed within the framework of many-body perturbation theory: in fact, both the Green’s functions and the TDDFT approaches profit from mutual insight. This review compares the theoretical and practical aspects of the two approaches and their specific numerical implementations, and presents an overview of accomplishments and work in progress.

Advanced capabilities for materials modelling with Quantum ESPRESSO

Abstract: Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.