Securing a semiconducting bandgap is essential for applying graphene layers in switching devices. Theoretical studies have suggested a created bulk bandgap in a graphene layer by introducing an asymmetry between the A and B sub-lattice sites. A recent transport measurement demonstrated the presence of a bandgap in a graphene layer where the asymmetry was introduced by placing a graphene layer on a hexagonal boron nitride (h-BN) substrate. Similar bandgap has been observed in graphene layers on metal substrates by local probe measurements; however, this phenomenon has not been observed in graphene layers on a near-insulating substrate. Here, we present bulk bandgap-like features in a graphene layer epitaxially grown on an h-BN substrate using scanning tunneling spectroscopy. We observed edge states at zigzag edges, edge resonances at armchair edges, and bandgap-like features in the bulk.
Amyloid deposits of Aβ protein in neuronal cells are known to be a major symptom of Alzheimer’s disease. In particular, Aβ42 shows relatively high toxicity among the different Aβ isoforms, and its toxicity is thought to be because of its structural features. Recent ssNMR and cryo-EM experiments identified that Aβ42 shows an S-shaped triple-β structure, in contrast to the previously suggested U-shaped β-arch structure. In order to associate the high toxicity of Aβ42 with its structural features, it is essential to explain the conformational stability and aggregation mechanisms of this triple-β motif. We utilized several different simulation methods, including extensive straight molecular dynamics simulation, steered molecular dynamics simulation, and replica-exchange molecular dynamics simulation. The S-shaped triple-β motif showed remarkable structural stability because of its complex residual interactions that form stable hydrophobic cores. The triple-β structure of Aβ42 is primarily made up of three β-sheet regions and two hydrophobic cores formed between β-sheet regions. Our analysis of β-sheet rupture patterns between adjacent chains showed that its two hydrophobic cores have different degrees of stability, indicating a lock phase mechanism. Our analysis of the docking pathway of monomeric Aβ42 to the fibril motif using REMD simulations showed that each of the three β-sheet sequences plays a distinct role in the docking process by changing their conformational features. Our results provide an understanding for the stability and consequent high toxicity of the triple-β structure Aβ42.
Although the replica exchange methods (REMs) were developed as efficient conformational sampling methods for bio-molecular simulations, their application to very large bio-systems is somewhat limited. We propose a new replica exchange scheme (Tq-REM) created by combining the conventional temperature-REM (T-REM) and one of the Hamiltonian-REMs, q-REM, using the effective potential with reduced barriers. In the proposed Tq-REM scheme, high temperature replicas in T-REM are substituted with q-replicas. This combined scheme is expected to exploit advantages of the T-REM and q-REM resulting in improved sampling efficiency while minimizing the drawbacks of both approaches. We investigated the performance of Tq-REM compared with T-REM by performing all-atom MD simulations on Met-enkephalin, (AAQAA), and Trpzip2. It was found that convergence of the free energy surfaces was improved by Tq-REM over the conventional T-REM. In particular, the trajectories of Tq-REM were able to sample the relevant conformations for all of the metastable folding intermediates, while some of the local minimum structures are poorly represented by T-REM. The results of the present study suggest that Tq-REM can provide useful tools to investigate systems where metastable states play important roles.
The detection efficiency of a newly built photon detection system was measured using photons emitted from a scanning tunneling microscope junction. The efficiency was estimated from the instrumental yield and the geometry of the system on a clean Ag(111) surface using a measured photon map and a simultaneously measured topography image. The photon generation rates of gold three-dimensional (3D) islands and two-dimensional flat layers grown on a Si(111) surface were compared, and an enhanced photon generation rate was observed for the 3D island nanostructures.
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