Increasing the active surface of titanium islands on graphene by nitrogen sputtering

Titanium-island formation on graphene as a function of defect density is investigated. When depositing titanium on pristine graphene, titanium atoms cluster and form islands with an average diameter of about 10nm and an average height of a few atomic layers. We show that if defects are introduced in the graphene by ion bombardment, the mobility of the deposited titanium atoms is reduced and the average diameter of the islands decreases to 5nm with monoatomic height. This results in an optimized coverage for hydrogen storage applications since the actual titanium surface available per unit graphene area is significantly increased

Carbon budget of an agroforestry system after being converted from a poplar short rotation coppice

Poplar (Populus L. spp.) Short Rotation Coppice systems (SRCs) for bioenergy production are being converted back to arable land. Transitioning to Alley Cropping Systems (ACSs) could be a suitable strategy for integrating former tree rows and arable crops. A field trial (Pisa, Central Italy) was set up with the aim of assessing the C storage of an ACS system based on hybrid poplar and sorghum (Sorghum bicolor L. Moench) and comparing it with that of an SRC cultivation system. The carbon budget at the agroecosystem scale was assessed in the first year of the transition using the net biome production (NBP) approach with a simplified method. The overall NBP for the SRC was positive (96 ± 40 g C m−2 year−1), highlighting that the system was a net carbon sink (i.e., NBP > 0). However, the ACS registered a net C loss (i.e., NBP < 0), since the NBP was −93 ± 56 g C m−2 year−1. In the first year of the transition, converting the SRC into an ACS counteracted the potential beneficial effect of C storage in tree belowground biomass due to the high heterotrophic respiration rate recorded in the ACS, which was fostered by the incorporation of residues and tillage disturbance in the alley. Additional years of heterotrophic respiration measurements could allow for an estimate of the speed and extent of C losses

Gated Diffusion-controlled Reactions

The binding and active sites of proteins are often dynamically occluded by motion of the nearby polypeptide. A variety of theoretical and computational methods have been developed to predict rates of ligand binding and reactivity in such cases. Two general approaches exist, "protein centric" approaches that explicitly treat only the protein target, and more detailed dynamical simulation approaches in which target and ligand are both treated explicitly. This mini-review describes recent work in this area and some of the biological implications

Spontaneous formation and stability of small GaP fullerenes

We report the spontaneous formation of a GaP fullerene cage in ab-initio Molecular Dynamics simulations starting from a bulk fragment. A systematic study of the geometric and electronic properties of neutral and ionized GaP clusters suggests the stability of hetero-fullerenes formed by a compound with zincblend bulk structure. We find that GaP fullerenes up to 28 atoms have high symmetry, closed electronic shells, large HOMO-LUMO energy gaps and do not dissociate when ionized. We compare our results for GaP with those obtained by other groups for the corresponding BN clusters.Comment: To appear on PRL, 4 pages, 1 figure, Late

Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots

A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist of no more than 250 amino acids. Our previous studies have dealt with 7510 proteins of no more than 150 amino acids. The proteins are ranked according to the strength of the resistance. Most of the predicted top-strength proteins have not yet been studied experimentally. Architectures and folds which are likely to yield large forces are identified. New types of potent force clamps are discovered. They involve disulphide bridges and, in particular, cysteine slipknots. An effective energy parameter of the model is estimated by comparing the theoretical data on characteristic forces to the corresponding experimental values combined with an extrapolation of the theoretical data to the experimental pulling speeds. These studies provide guidance for future experiments on single molecule manipulation and should lead to selection of proteins for applications. A new class of proteins, involving cystein slipknots, is identified as one that is expected to lead to the strongest force clamps known. This class is characterized through molecular dynamics simulations.Comment: 40 pages, 13 PostScript figure

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation

Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse the self- assembly of peptides into fibrillar structures. The simulation of a system of hundreds of peptides over the millisecond timescale enables us to show that the mechanism of aggregation involves a first phase in which small structurally disordered oligomers assemble onto the nanoparticle and a second phase in which they evolve into highly ordered beta-sheets as their size increases

The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase

The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS). TRPS uses a set of α/β–dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand–bound conformations. Our simulations also revealed that the α/β–dimeric unit stabilizes the substrate–protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function

Local field factors in a polarized two-dimensional electron gas

We derive approximate expressions for the static local field factors of a spin polarized two-dimensional electron gas which smoothly interpolate between their small- and large-wavevector asymptotic limits. For the unpolarized electron gas, the proposed analytical expressions reproduce recent diffusion Monte Carlo data. We find that the degree of spin polarization produces important modifications to the local factors of the minority spins, while the local field functions of the majority spins are less affected.Comment: 8 pages, 10 figure