272 research outputs found
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
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