Electronic Friction Near Metal Surface: Incorporating Nuclear Quantum Effect with Ring Polymer Molecular Dynamics

Molecular dynamics with electronic friction (MDEF) approach can describe nonadiabatic effects accurately at metal surfaces in the weak nonadiabatic limit. That being said, MDEF treats nuclear motion classically, such that the nuclear quantum effects are missing completely in the approach. To address this limitation, we combine electronic friction with Ring Polymer Molecular Dynamics (RPMD). In particular, we apply the averaged electronic friction from the metal surface to the centroid mode of the ring polymer. We benchmark our approach against quantum dynamics to show that electronic friction with RPMD (EF-RPMD) can capture zero-point energy as well as transition dynamics accurately. In addition, we show EF-RPMD can correctly predict the electronic transfer rate near metal surfaces in the tunneling limit as well as the barrier crossing limit. We expect our approach will be very useful to study nonadiabatic dynamics near metal surface when nuclear quantum effects become essential

From Ontology to Semantic Similarity: Calculation of Ontology-Based Semantic Similarity

Advances in high-throughput experimental techniques in the past decade have enabled the explosive increase of omics data, while effective organization, interpretation, and exchange of these data require standard and controlled vocabularies in the domain of biological and biomedical studies. Ontologies, as abstract description systems for domain-specific knowledge composition, hence receive more and more attention in computational biology and bioinformatics. Particularly, many applications relying on domain ontologies require quantitative measures of relationships between terms in the ontologies, making it indispensable to develop computational methods for the derivation of ontology-based semantic similarity between terms. Nevertheless, with a variety of methods available, how to choose a suitable method for a specific application becomes a problem. With this understanding, we review a majority of existing methods that rely on ontologies to calculate semantic similarity between terms. We classify existing methods into five categories: methods based on semantic distance, methods based on information content, methods based on properties of terms, methods based on ontology hierarchy, and hybrid methods. We summarize characteristics of each category, with emphasis on basic notions, advantages and disadvantages of these methods. Further, we extend our review to software tools implementing these methods and applications using these methods

Single-layer behavior and slow carrier density dynamic of twisted graphene bilayer

We report scanning tunneling microscopy (STM) and spectroscopy (STS) of twisted graphene bilayer on SiC substrate. For twist angle ~ 4.5o the Dirac point ED is located about 0.40 eV below the Fermi level EF due to the electron doping at the graphene/SiC interface. We observed an unexpected result that the local Dirac point around a nanoscaled defect shifts towards the Fermi energy during the STS measurements (with a time scale about 100 seconds). This behavior was attributed to the decoupling between the twisted graphene and the substrate during the measurements, which lowers the carrier density of graphene simultaneously

Effect of a poloxamer 407-based thermosensitive gel on minimization of thermal injury to diaphragm during microwave ablation of the liver.

AIM: To assess the insulating effect of a poloxamer 407 (P407)-based gel during microwave ablation of liver adjacent to the diaphragm. METHODS: We prepared serial dilutions of P407, and 22.5% (w/w) concentration was identified as suitable for ablation procedures. Subsequently, microwave ablations were performed on the livers of 24 rabbits (gel, saline, control groups, n = 8 in each). The P407 solution and 0.9% normal saline were injected into the potential space between the diaphragm and liver in experimental groups. No barriers were applied to the controls. After microwave ablations, the frequency, size and degree of thermal injury were compared histologically among the three groups. Subsequently, another 8 rabbits were injected with the P407 solution and microwave ablation was performed. The levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), blood urea nitrogen (BUN) and creatinine (Cr) in serum were tested at 1 d before microwave ablation and 3 and 7 d after operation. RESULTS: In vivo ablation thermal injury to the adjacent diaphragm was evaluated in the control, saline and 22.5% P407 gel groups (P = 0.001-0.040). However, there was no significant difference in the volume of ablation zone among the three groups (P \u3e 0.05). Moreover, there were no statistical differences among the preoperative and postoperative gel groups according to the levels of ALT, AST, BUN and Cr in serum (all P \u3e 0.05). CONCLUSION: Twenty-two point five percent P407 gel could be a more effective choice during microwave ablation of hepatic tumors adjacent to the diaphragm. Further studies for clinical translation are warranted