QuantumATK: An integrated platform of electronic and atomic-scale modelling tools

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.Comment: Submitted to Journal of Physics: Condensed Matte

Solution Structure of LC4 Transmembrane Segment of CCR5

CC-chemokine receptor 5 (CCR5) is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1). The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescdence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 binds to the HIV-1 inhibitory peptide LC5 were determined by docking calculations in addition to NMR data. The poses showed the importance of the hydrophobic interface of the assembled structures. The solution structure of LC4 elucidated in the present work provides a structural basis for further studies on the HIV-1 inhibitory function of the LC4 region

Well-posedness for degenerate third order equations with delay and applications to inverse problems

[EN] In this paper, we study well-posedness for the following third-order in time equation with delay <disp-formula idoperators defined on a Banach space X with domains D(A) and D(B) such that t)is the state function taking values in X and u(t): (-, 0] X defined as u(t)() = u(t+) for < 0 belongs to an appropriate phase space where F and G are bounded linear operators. Using operator-valued Fourier multiplier techniques we provide optimal conditions for well-posedness of equation (0.1) in periodic Lebesgue-Bochner spaces Lp(T,X), periodic Besov spaces Bp,qs(T,X) and periodic Triebel-Lizorkin spaces Fp,qs(T,X). A novel application to an inverse problem is given.The first, second and third authors have been supported by MEC, grant MTM2016-75963-P. The second author has been supported by AICO/2016/30. The fourth author has been supported by MEC, grant MTM2015-65825-P.Conejero, JA.; Lizama, C.; Murillo-Arcila, M.; Seoane Sepúlveda, JB. (2019). 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Limiting problems for a nonstandard viscous Cahn--Hilliard system with dynamic boundary conditions

This note is concerned with a nonlinear diffusion problem of phase-field type, consisting of a parabolic system of two partial differential equations, complemented by boundary and initial conditions. The system arises from a model of two-species phase segregation on an atomic lattice and was introduced by Podio-Guidugli in Ric. Mat. 55 (2006), pp.105--118. The two unknowns are the phase parameter and the chemical potential. In contrast to previous investigations about this PDE system, we consider here a dynamic boundary condition for the phase variable that involves the Laplace-Beltrami operator and models an additional nonconserving phase transition occurring on the surface of the domain. We are interested to some asymptotic analysis and first discuss the asymptotic limit of the system as the viscosity coefficient of the order parameter equation tends to 0: the convergence of solutions to the corresponding solutions for the limit problem is proven. Then, we study the long-time behavior of the system for both problems, with positive or zero viscosity coefficient, and characterize the omega-limit set in both cases