Analytic many-body potential for GaAs(001) homoepitaxy: Bulk and surface properties

We employ atomic-scale simulation methods to investigate bulk and surface properties of an analytic Tersoff- Abell type potential for describing interatomic interactions in GaAs. The potential is a modified form of that proposed by Albe and colleagues [Phys. Rev. B 66, 035205 (2002)] in which the cut-off parameters for the As-As interaction have been shortened.With this modification, many bulk properties predicted by the potential for solid GaAs are the same as those in the original potential, but properties of the GaAs(001) surface better match results from first-principles calculations with density-functional theory (DFT). We tested the ability of the potential to reproduce the phonon dispersion and heat capacity of bulk solid GaAs by comparing it to experiment and the overall agreement is good. In the modified potential, the GaAs(001) β2(2 × 4) reconstruction is favored under As-rich growth conditions in agreement with DFT calculations. Additionally, the binding energies and diffusion barriers for a Ga adatom on the β2(2 × 4) reconstruction generally match results from DFT calculations. These studies indicate that the potential is suitable for investigating aspects of GaAs(001) homoepitaxy

Directing Anisotropic Assembly of Metallic Nanoclusters by Exploiting Linear Trio Interactions and Quantum Size Effects: Au Chains on Ag(100) Thin Films

Discovery and understanding of mechanisms for kinetically controlled growth of metal nanoclusters can be enabled by realistic atomistic-level modeling with ab initio kinetics. KMC simulation of such a model for Au deposition on Ag(100) films reveals the formation of single-atom-wide Au chains below 275 K, even though 2D islands are thermodynamically preferred. Chain formation is shown to reflect a combination of strong linear trio attractions guiding assembly and a weak driving force and slow rate of transformation of 1D chains to 2D islands (or sometimes irreversible rounding of adatoms from chain sides to ends). Behavior can also be tuned by quantum size effects: chain formation predominates on 2-monolayer Ag(100) films supported on NiAl(100) at 250 K for low coverages but not on 1- or 3-monolayer films, and longer chains form than on bulk Ag(100). Our predictive kinetic modeling shows the potential for simulation-guided discovery and analysis of novel self-assembly processes

Poboljšanje fizičko-mehaničkih svojstava karbamazepina prekristalizacijom pri različitim pH

The morphology of crystals has an appreciable impact on the physicochemical properties of drugs. Drug properties such as flowability, dissolution, hardness and bioavailability may be affected by crystallinity behaviors of drugs. The objective of this study was to achieve improved physicomechanical properties of carbamazepine powder through recrystallization from aqueous solutions at different pH values. For this purpose, carbamazapine was recrystallized from aqueous solutions at different pH values (1, 7, 11). The morphology of crystals was investigated using scanning electron microscopy; X-ray powder diffraction (XRPD) was used to identify polymorphism; thermodynamic properties were analyzed using differential scanning calorimetery (DSC). Dissolution was determined using USP dissolution apparatus. Mechanical behavior of recrystallized carbamazepine powders was investigated by making tablets under different compaction pressures and measuring their hardness. SEM studies showed that carbamazepine crystallization in different media affected the morphology and size of carbamazepine crystals. The shape of carbamazepine crystals changed from flaky or thin plate-like to needle-shaped. XRPD and DSC results ruled out any crystallinity changes occurring due to the temperature or pH of crystallization media. The crushing strength of tablets indicated that all the recrystallized carbamazepine samples had better compactibility than the original carbamazepine powder. In vitro dissolution studies of carbamazepine samples showed a higher dissolution rate of carbamazepine crystals obtained from media with pH 11 and 1. Carbamazepine particles recrystallized from aqueous solutions of different pH values (all media) appeared to have superior mechanical properties to those of the original carbamazepine sample.Morfologija kristala ima značajan utjecaj na fizičko-mehanička svojstva lijekova. Kristaliničnost može utjecati na tečnost, oslobađanje, tvrdoću i bioraspoloživost lijekova. Cilj ovog rada bio je poboljšati fizičko-mehanička svojstva praha karbamazepina prekristalizacijom iz vodenih otopina pri različitim pH vrijednostima (1, 7 i 11). Fizičko-mehanička svojstva prekristaliziranog karbamazepina određivana su na sljedeći način: morfologija kristala ispitivana je pretražnom elektronskom mikroskopijom, polimorfi su identificirani rendgenskom difrakcijom praha (XRPD), a termodinamička svojstva analizirana su diferencijalnom pretražnom kalorimetrijom (DSC). Topljivost je određena pomoću aparata prema USP. Mehanička svojstva prekristaliziranog karbamazepina ispitivana su tijekom tabletiranja pri različitim tlakovima i mjerenjem tvrdoće nastalih tableta. SEM ispitivanja pokazala su da kristalizacija karbamazepina iz različitih medija utječe na morfologiju i veličinu kristala. Oblik kristala mijenjao se od pahuljastog ili pločastog do igličastog. Rezultati dobiveni XRPD i DSC metodama isključili su promjene kristaliničnosti zbog temperature ili pH medija. Mjerenjem lomljivosti tableta utvrđeno je da su svi prekristalizirani uzorci karbamazepina bili kompaktniji od polaznog praškastog uzorka. Ispitivanja topljivosti in vitro pokazala su da su kristali dobiveni iz otopine s pH 11 i 1 topljiviji. Uzorci karbamazepina dobiveni prekristalizacijom iz vodenih otopina različite pH vrijednosti imali su bolja mehanička svojstva od originalnog uzorka karbamazepina

The impact of point mutations in the human androgen receptor : classification of mutations on the basis of transcriptional activity

Peer reviewedPublisher PD

The PRIDE database and related tools and resources in 2019: improving support for quantification data

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas

From covalent bonding to coalescence of metallic nanorods

Growth of metallic nanorods by physical vapor deposition is a common practice, and the origin of their dimensions is a characteristic length scale that depends on the three-dimensional Ehrlich-Schwoebel (3D ES) barrier. For most metals, the 3D ES barrier is large so the characteristic length scale is on the order of 200 nm. Using density functional theory-based ab initio calculations, this paper reports that the 3D ES barrier of Al is small, making it infeasible to grow Al nanorods. By analyzing electron density distributions, this paper shows that the small barrier is the result of covalent bonding in Al. Beyond the infeasibility of growing Al nanorods by physical vapor deposition, the results of this paper suggest a new mechanism of controlling the 3D ES barrier and thereby nanorod growth. The modification of local degree of covalent bonding, for example, via the introduction of surfactants, can increase the 3D ES barrier and promote nanorod growth, or decrease the 3D ES barrier and promote thin film growth

Using metadynamics to explore complex free-energy landscapes

Metadynamics is an atomistic simulation technique that allows, within the same framework, acceleration of rare events and estimation of the free energy of complex molecular systems. It is based on iteratively \u2018filling\u2019 the potential energy of the system by a sum of Gaussians centred along the trajectory followed by a suitably chosen set of collective variables (CVs), thereby forcing the system to migrate from one minimum to the next. The power of metadynamics is demonstrated by the large number of extensions and variants that have been developed. The first scope of this Technical Review is to present a critical comparison of these variants, discussing their advantages and disadvantages. The effectiveness of metadynamics, and that of the numerous alternative methods, is strongly influenced by the choice of the CVs. If an important variable is neglected, the resulting estimate of the free energy is unreliable, and predicted transition mechanisms may be qualitatively wrong. The second scope of this Technical Review is to discuss how the CVs should be selected, how to verify whether the chosen CVs are sufficient or redundant, and how to iteratively improve the CVs using machine learning approaches