A mechanism for Frenkel defect creation in amorphous SiO2 facilitated by electron injection.

Using density functional theory (DFT) calculations we demonstrate how electron injection can facilitate the creation of Frenkel defects in amorphous (a)-SiO2. The precursor sites composed of wide O-Si-O bond angles in amorphous SiO2 act as deep electron traps and can accommodate up to two extra electrons. Trapping of two electrons at these intrinsic sites results in weakening of a Si-O bond and creates an efficient bond breaking pathway for producing neutral O vacancies and [Formula: see text] interstitial ions characterized by low transition barriers. The low barriers for the migration of [Formula: see text] ions of about 0.2 eV facilitate the separation of created defects. This mechanism may have important implications for our understanding of dielectric breakdown and resistance switching in a-SiO2 based electronic and memory devices.

Efficient parametrization of complex molecule-surface force fields.

We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules.

A fluorogenic near-infrared imaging agent for quantifying plasma and local tissue renin activity in vivo and ex vivo.

The renin-angiotensin system (RAS) is well studied for its regulation of blood pressure and fluid homeostasis, as well as for increased activity associated with a variety of diseases and conditions, including cardiovascular disease, diabetes, and kidney disease. The enzyme renin cleaves angiotensinogen to form angiotensin I (ANG I), which is further cleaved by angiotensin-converting enzyme to produce ANG II. Although ANG II is the main effector molecule of the RAS, renin is the rate-limiting enzyme, thus playing a pivotal role in regulating RAS activity in hypertension and organ injury processes. Our objective was to develop a near-infrared fluorescent (NIRF) renin-imaging agent for noninvasive in vivo detection of renin activity as a measure of tissue RAS and in vitro plasma renin activity. We synthesized a renin-activatable agent, ReninSense 680 FAST (ReninSense), using a NIRF-quenched substrate derived from angiotensinogen that is cleaved specifically by purified mouse and rat renin enzymes to generate a fluorescent signal. This agent was assessed in vitro, in vivo, and ex vivo to detect and quantify increases in plasma and kidney renin activity in sodium-sensitive inbred C57BL/6 mice maintained on a low dietary sodium and diuretic regimen. Noninvasive in vivo fluorescence molecular tomographic imaging of the ReninSense signal in the kidney detected increased renin activity in the kidneys of hyperreninemic C57BL/6 mice. The agent also effectively detected renin activity in ex vivo kidneys, kidney tissue sections, and plasma samples. This approach could provide a new tool for assessing disorders linked to altered tissue and plasma renin activity and to monitor the efficacy of therapeutic treatments.

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality.

Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.

Micrometre-long covalent organic fibres by photoinitiated chain-growth radical polymerization on an alkali-halide surface.

On-surface polymerization is a promising technique to prepare organic functional nanomaterials that are challenging to synthesize in solution, but it is typically used on metal substrates, which play a catalytic role. Previous examples on insulating surfaces have involved intermediate self-assembled structures, which face high barriers to diffusion, or annealing to higher temperatures, which generally causes rapid dewetting and desorption of the monomers. Here we report the photoinitiated radical polymerization, initiated from a two-dimensional gas phase, of a dimaleimide monomer on an insulating KCl surface. Polymer fibres up to 1 µm long are formed through chain-like rather than step-like growth. Interactions between potassium cations and the dimaleimide's oxygen atoms facilitate the propagation of the polymer fibres along a preferred axis of the substrate over long distances. Density functional theory calculations, non-contact atomic force microscopy imaging and manipulations at room temperature were used to explore the initiation and propagation processes, as well as the structure and stability of the resulting one-dimensional polymer fibres.

Diffusion and aggregation of oxygen vacancies in amorphous silica.

Using density functional theory (DFT) calculations, we investigated oxygen vacancy diffusion and aggregation in relation to dielectric breakdown in amorphous silicon dioxide (a-SiO2). Our calculations indicate the existence of favourable sites for the formation of vacancy dimers and trimers in the amorphous network with maximum binding energies of approximately 0.13 eV and 0.18 eV, respectively. However, an average energy barrier height for neutral vacancy diffusion is found to be about 4.6 eV, rendering this process unfeasible. At Fermi level positions above 6.4 eV with respect to the top of the valence band, oxygen vacancies can trap up to two extra electrons. Average barriers for the diffusion of negative and double negatively charged vacancies are found to be 2.7 eV and 2.0 eV, respectively. These barriers are higher than or comparable to thermal ionization energies of extra electrons from oxygen vacancies into the conduction band of a-SiO2. In addition, we discuss the competing pathways for electron trapping in oxygen deficient a-SiO2 caused by the existence of intrinsic electron traps and oxygen vacancies. These results provide new insights into the role of oxygen vacancies in degradation and dielectric breakdown in amorphous silicon oxides.

Calculating free energies of organic molecules on insulating substrates.

The challenges and limitations in calculating free energies and entropies of adsorption and interaction of organic molecules on an insulating substrate are discussed. The adhesion of 1,3,5-tri(4'-cyano-[1,1'-biphenyl]-4-yl)benzene (TCB) and 1,4-bis(4-cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules to step edges on the KCl(001) surface and the formation of molecular dimers were studied using classical molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free energy profiles and entropy changes were calculated for step adhesion and dimer formation of these molecules. However, converging these calculations is nontrivial and comes at large computational cost. We illustrate the difficulties as well as the possibilities of applying these methods towards understanding dynamic processes of organic molecules on insulating substrates.