General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium Green's function

Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce an atomistic approach based on density functional theory and non-equilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-V bias curves simulations. We apply this method to characterize an Ag/Si interface relevant for photovoltaic applications and study the rectifying-to-Ohmic transition as function of the semiconductor doping.We also demonstrate that the standard "Activation Energy" method for the analysis of I-V bias data might be inaccurate for non-ideal interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping, due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid alternative to conventional procedures for the accurate characterization of metal-semiconductor interfaces

Computational dosimetry in MRI in presence of hip, knee or shoulder implants: do we need accurate surgery models?

Objective. To quantify the effects of different levels of realism in the description of the anatomy around hip, knee or shoulder implants when simulating, numerically, radiofrequency and gradient-induced heating in magnetic resonance imaging. This quantification is needed to define how precise the digital human model modified with the implant should be to get realistic dosimetric assessments. Approach. The analysis is based on a large number of numerical simulations where four 'levels of realism' have been adopted in modelling human bodies carrying orthopaedic implants. Main results. Results show that the quantification of the heating due to switched gradient fields does not strictly require a detailed local anatomical description when preparing the digital human model carrying an implant. In this case, a simple overlapping of the implant CAD with the body anatomy is sufficient to provide a quite good and conservative estimation of the heating. On the contrary, the evaluation of the electromagnetic field distribution and heating caused by the radiofrequency field requires an accurate description of the tissues around the prosthesis. Significance. The results of this paper provide hints for selecting the 'level of realism' in the definition of the anatomical models with embedded passive implants when performing simulations that should reproduce, as closely as possible, the in vivo scenarios of patients carrying orthopaedic implants

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

Bacterial Expression of Mouse Argonaute 2 for Functional and Mutational Studies

RNA interference (RNAi) is a post-transcriptional gene-silencing process that occurs in many eukaryotic organisms upon intracellular exposure to double-stranded RNA. Argonaute 2 (Ago2) protein is the catalytic engine of mammalian RNAi. It contains a PIWI domain that is structurally related to RNases H and possibly shares with them a two-metal-ion catalysis mechanism. Here we describe the expression in E. coli of mouse Ago2 and testing of its enzymatic activity in a RISC assay, i.e., for the ability to cleave a target RNA in a single position specified by a complementary small interfering RNA (siRNA). The results show that the enzyme can load the siRNA and cleave the complementary RNA in absence of other cellular factors, as described for human Ago2. It was also found that mutation of Arg669, a residue previously proposed to be involved in substrate and/or B metal ion binding, doesn’t affect the enzymatic activity, suggesting that this residue doesn’t belong to the active site

Clinical research on COVID-19: perceptions and barriers to participation in The Gambia.

INTRODUCTION: The need to rapidly identify safe and efficacious drug therapies for COVID-19 has resulted in the implementation of multiple clinical trials investigating potential treatment options. These are being undertaken in an unprecedented research environment and at a higher speed than ever before. It is unclear how West African communities perceive such activities and how such perceptions influence participation in COVID-19 clinical trials. This qualitative study was conducted to assess the level of acceptability of a clinical trial on the prevention and treatment of COVID-19 in The Gambia and identify strategies to better engage communities in participating in such a trial. METHODS: Data were collected using digitally recorded semistructured interviews (SSIs) and focus group discussions (FGDs) in Brikama and Kanifing local government areas. These are two of the most densely populated administrative subdivisions in The Gambia, where the clinical trial was to be implemented by the MRC Unit The Gambia. 26 men and 22 women aged between 19 and 70 years, with diverse socioeconomic profiles, participated in 8 FGDs (n=36) and 12 SSIs (n=12). Thematic analysis was used to analyse the data. RESULTS: Fear of stigmatisation of patients with COVID-19 was a recurring theme in most FGDs and SSIs, with detrimental effects on willingness to accept COVID-19 testing and home visits to follow up patients with COVID-19 and their household contacts. Preserving the privacy of individuals enrolled in the study was key to potentially increase trial participation. Trust in the implementing institution and its acknowledged expertise were facilitators to accepting the administration of investigational products to sick individuals and their close contacts. CONCLUSION: COVID-19 is a stigmatising disease. Developing a research-participant collaboration through an ongoing engagement with community members is crucial to a successful enrolment in COVID-19 clinical trials. Trust and acknowledged expertise of the implementing institution are key facilitators to foster such collaboration