Atomic diffusion in solid molecular hydrogen.
Ontology highlight
ABSTRACT:
SUBMITTER: Belonoshko AB
PROVIDER: S-EPMC3730164 | biostudies-other | 2013
REPOSITORIES: biostudies-other
Similar Datasets
Project description:We present a study of dynamic properties of liquid aluminum using density-functional theory within the local-density (LDA) and generalized gradient (GGA) approximations. We determine the temperature dependence of the self-diffusion coefficient as well the viscosity using direct methods. Comparisons with experimental data favor the LDA approximation to compute dynamic properties of liquid aluminum. We show that the GGA approximation induce more important backscattering effects due to an enhancement of the icosahedral short range order (ISRO) that impact directly dynamic properties like the self-diffusion coefficient. All these results are then used to test the Stokes-Einstein relation and the universal scaling law relating the diffusion coefficient and the excess entropy of a liquid.
| S-EPMC3817448 | biostudies-other
Project description:Bimetallic Pd1-x Pt x solid-solution nanoparticles (NPs) display charging/discharging of hydrogen gas, which has relevance for fuel cell technologies; however, the constituent elements are immiscible in the bulk phase. We examined these material systems using high-energy synchrotron X-ray diffraction, X-ray absorption fine structure and hard X-ray photoelectron spectroscopy techniques. Recent studies have demonstrated the hydrogen storage properties and catalytic activities of Pd-Pt alloys; however, comprehensive details of their structural and electronic functionality at the atomic scale have yet to be reported. Three-dimensional atomic-scale structure results obtained from the pair distribution function (PDF) and reverse Monte Carlo (RMC) methods suggest the formation of a highly disordered structure with a high cavity-volume-fraction for low-Pt content NPs. The NP conduction band features, as extracted from X-ray absorption near-edge spectra at the Pd and Pt L III -edge, suggest that the Pd conduction band is filled by Pt valence electrons. This behaviour is consistent with observations of the hydrogen storage capacity of these NPs. The broadening of the valence band width and the down-shift of the d-band centre away from the Fermi level upon Pt substitution also provided evidence for enhanced stability of the hydride (?H) features of the Pd1-x Pt x solid-solution NPs with a Pt content of 8-21 atomic percent.
| S-EPMC5668347 | biostudies-literature
Project description:Due to their excess surface free energy and structural instabilities, nanoparticles exhibit interesting physical and chemical properties. There has been an ever-growing interest in investigating these properties, driven by the desire to further miniaturize electronic devices, develop new functional materials and catalysts. Here, the intriguing question of how diffusion evolves in a single nanoparticle is investigated by measuring the spatial and temporal variations of the diffracted coherent X-ray intensity during copper diffusion into a gold nanocrystal. Dislocation loops formed from the insertion of single layer of extra atoms between neighbouring gold host lattice planes are detected. Au-Cu alloy channels are found to penetrate the nanocrystal due to the differential diffusion rate along different directions. With the advent of higher brilliance sources and free-electron-lasers, Bragg Coherent X-ray Diffraction Imaging can play an important role in unveiling atomic behaviours in three dimensions for nanomaterials during various fundamental processes.
| S-EPMC4208027 | biostudies-literature
Project description:For critical tests of whether diffusion-limited kinetics is an option for the solution-solid phase transition of molecular substances or whether they are determined exclusively by a transition state, we performed crystallization experiments with ferritin and apoferritin, a unique pair of proteins with identical shells but different molecular masses. We find that the kinetic coefficient for crystallization is identical (accuracy <or=7%) for the pair, indicating diffusion-limited kinetics of crystallization. Data on the kinetics of this phase transition in systems ranging from small-molecule ionic to protein and viri suggest that the kinetics of solution-phase transitions for broad classes of small-molecule and protein materials are diffusion-limited.
| S-EPMC298680 | biostudies-literature
Project description:Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to one strand of DNA with significant energetic bias compared with the other, or nonpreferred strand. The preferential DNA-strand binding becomes most prominent in the static process, from nonspecific to specific DNA binding, but less distinct during diffusive movements of the domain protein on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base-pair stepping cycle of the protein tracking along major groove of DNA with a homogeneous poly-adenosine sequence, as individual hydrogen bonds break and reform at the protein-DNA binding interface. Further DNA-groove tracking motions of the protein forward or backward, with occasional sliding as well as strand crossing to minor groove of DNA, were also captured. The processive diffusion of WRKY along DNA has been further sampled via coarse-grained MD simulations. The study thus provides structural dynamics details on diffusion of a small TF domain protein, suggests how the protein approaches a specific recognition site on DNA, and supports further high-precision experimental detection. The stochastic movements revealed in the TF diffusion also provide general clues about how other protein walkers step and slide along DNA.
| S-EPMC8201915 | biostudies-literature
Project description:Surface-assisted synthesis has become a powerful approach for generation of molecular nanostructures, which could not be obtained via traditional solution chemistry. Nowadays there is an intensive search for reactions that could proceed on flat surfaces in order to boost the versatility and applicability of synthesized nano-objects. Here we propose application of atomic hydrogen combined with on-surface synthesis in order to tune the reaction pathways. We demonstrate that atomic hydrogen could be widely applied: (1) as a cleaning tool, which allows removal of halogen residues from the surface after Ullmann couplings/polymerization, (2) by reaction with surface organometallics to provide stable hydrogenated species, and (3) as a reagent for debromination or desulfurization of adsorbed species.
| S-EPMC7596777 | biostudies-literature
Project description:We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.
| S-EPMC4971546 | biostudies-literature
Project description:Ion-solid surface interactions are one of the fundamental principles in liquid-interfacing devices ranging from various electrochemical systems to electrolyte-driven energy conversion devices. The interplays between these two phases, especially containing charge carriers in the solid layer, work as a pivotal role in the operation of these devices, but corresponding details of those effects remain as unrevealed issues in academic fields. Herein, an ion-charge carrier interaction at an electrolyte-semiconductor interface is interrogated with an ion-dynamics-induced (ionovoltaic) energy transducer, controlled by interfacial self-assembled molecules. An electricity generating mechanism from interfacial ionic diffusion is elucidated in terms of the ion-charge carrier interaction, originated from a dipole potential effect of the self-assembled molecular layer (SAM). In addition, this effect is found to be modulated via chemical functionalization of the interfacial molecular layer and transition metal ion complexation therein. With the aiding of surface analytic techniques and a liquid-interfacing Hall measurement, electrical behaviors of the device depending on the magnitude of the ion-ligand complexation are interrogated, thereby demonstrating the ion-charge carrier interplays spanning at electrolyte-SAM-semiconductor interface. Hence, this system can be applied to study molecular interactions, including chemical and physical influences, occurring at the solid-liquid interfacial region.
| S-EPMC8728816 | biostudies-literature
Project description:Targeted protein degradation (TPD) has emerged as a powerful approach for removing (rather than inhibiting) proteins implicated in diseases. A key step in TPD is the formation of an induced proximity complex where a degrader molecule recruits an E3 ligase to the protein of interest (POI), facilitating the transfer of ubiquitin to the POI and initiating the proteasomal degradation process. Here, we address three critical aspects of the TPD process using atomistic simulations: 1) formation of the ternary complex induced by a degrader molecule, 2) conformational heterogeneity of the ternary complex, and 3) degradation efficiency via the full Cullin Ring Ligase (CRL) macromolecular assembly. We combine experimental biophysical data---in this case hydrogen-deuterium exchange mass spectrometry (HDX-MS, which measures the solvent exposure of protein residues)---with molecular dynamics (MD) simulations aided by enhanced sampling techniques to accurately predict ternary complex structures at atomic resolution. We demonstrate improved efficiency, accuracy, and reliability in the ternary structure predictions of the bromodomain of the cancer target SMARCA2 with the E3 ligase VHL mediated by three different degrader molecules. The simulations accurately reproduce X-ray crystal structures -- including a new structure that we determined in this work (PDB ID: 7S4E) -- with root mean square deviations (RMSD) of 1.1 to 1.6 \r{A}. The simulations also reveal a structural ensemble of low-energy conformations of the ternary complex. Snapshots from these simulations are used as seeds for additional simulations, where we perform 7.1 milliseconds of aggregate simulation time using Folding@home. The detailed free energy surface captures the crystal structure conformation within a low-energy basin and is consistent with solution-phase experimental data (HDX-MS and SAXS). Finally, we graft a structural ensemble of the ternary complexes onto the full CRL and perform enhanced sampling simulations, which suggest that differences in degradation efficiency may be related to the proximity distribution of lysine residues on the POI relative to the E2-loaded ubiquitin. Several of the predicted ubiquitinated lysine residues have been validated through a ubiquitin mapping proteomics experiment. DOI 10.1038/s41467-022-33575-4
2022-10-01 | PXD033763 | Pride
Project description:Hydrogen diffusion has an important role in solute-dependent hydrogen embrittlement in metals and metallic alloys. In spite of extensive studies, the complexity of hydrogen diffusion in solids remains a phenomenon that needs to be clarified. In this paper, we investigate the anisotropy of hydrogen diffusion in pure nickel single crystals using both an experimental approach and a thermodynamic development. As a first approximation, experimental data from electrochemical permeation and thermal desorption spectroscopy are described using the classical Fick's laws and an apparent diffusion tensor. Within a thermodynamic framework, the diffusion equation can be derived from Fick's laws with an apparent diffusion coefficient which contains an added solute content dependent term β. This term is due to the elastic strain field associated with the insertion of solute atoms. For nickel crystals, the dependence of β on the crystallographic orientation arises from the elastic anisotropy. Additionally, our results elucidate the discrepancies between the thermodynamic model and experimental observations of the effect of the solute concentration on the diffusion process. Moreover, this highlights the importance of the impact of hydrogen on vacancy formation and the subsequent consequences on the anisotropy of the apparent diffusion coefficient.
| S-EPMC5361197 | biostudies-literature