Charging of electron beam irradiated amorphous carbon thin films at liquid nitrogen temperature.

We studied the charging behavior of an amorphous carbon thin film kept at liquid-nitrogen temperature under focused electron-beam irradiation. Negative charging of the thin film is observed. The charging is attributed to a local change in the work function of the thin film induced by electron-stimulated desorption similar to the working principle of the hole free phase plate in its Volta potential implementation at elevated temperature. The negative bias of the irradiated film arises from the electron beam induced desorption of water molecules from the carbon film surface. The lack of positive charging, which is expected for non-conductive materials, is explained by a sufficient electrical conductivity of the carbon thin film even at liquid-nitrogen temperature as proven by multi-probe scanning tunneling microscopy and spectroscopy measurements

Consistent probe spacing in multi-probe STM experiments

Multi-probe scanning tunneling microscopy can play a role in various electrical measurements and characterization of nanoscale objects. The consistent close placement of multiple probes relies on very sharp apexes with no other interfering materials along the shank of the tip. Electrochemically etched tips can prepare very sharp apex tips; however, other asperities on the shank can cause interference and limit the close positioning of multiple tips to beyond the measured radii. Gallium focused ion beam (FIB) milling is used to remove any interfering material and allow closely spaced tips with a consistent yield. The tip apex radius is evaluated with field ion microscopy, and the probe spacing is evaluated with STM on hydrogen terminated silicon surfaces. FIB prepared tips can consistently achieve the measured probe to probe spacing distances of 25 nm–50 nm

Pt atoms adsorbed on TiO2(110)-(1 × 1) studied with noncontact atomic force microscopy and first-principles simulations

We have studied the local properties of single Pt atoms adsorbed on hydroxylated TiO2(110)-(1 × 1) by combining noncontact atomic force microscopy (nc-AFM) and first-principles calculations. Room-temperature high-resolution nc-AFM images for the most frequently observed contrast modes reveal bright and elongated protrusions that can be traced back to the Pt atoms, and that are centered on the fivefold coordinated titanium rows, confined between two bridging oxygen rows. These observations are in line with the theoretical results, as the lowest energy sites for the Pt atom on the TiO2(110) surface are in the neighborhood of the titanium rows, and high energy barriers have to be overcome to displace the Pt atom over the bridging oxygen rows. Single Pt atoms can be distinguished from H adsorbates (OH defects) due to their characteristic shape and binding site and, because they appear as the brightest surface features in all of the contrast modes. Force spectroscopy data over the protrusion and hole imaging modes and the corresponding tip-sample forces, simulated with O and OH terminated TiO2 nanoclusters, provide an explanation for this puzzling result in terms of the intrinsic strength of the interaction with the Pt adatom and the adatom and tip apex relaxations induced by the tip-sample interaction. These imaging mechanisms can be extended to other electropositive metal dopants and support the use of nc-AFM not only to characterize their adsorption structure but also to directly probe their chemical reactivityThis work was supported by Grants-in-Aid for Scientific Research (No. 22221006, No. 25106002, No. 24360016, No. 26600099, No. 2600015, No. 26110516, and No. 20760024) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan, Funding Program for Next Generation World-Leading Researchers and by the Ministerio de Economia y Competitividad (MINECO, Spain) uder Projects No. MAT2011-23627, No. CSD2010-00024, and No. PLE2009-006

Relativistic quantum effects of Dirac particles simulated by ultracold atoms

Quantum simulation is a powerful tool to study a variety of problems in physics, ranging from high-energy physics to condensed-matter physics. In this article, we review the recent theoretical and experimental progress in quantum simulation of Dirac equation with tunable parameters by using ultracold neutral atoms trapped in optical lattices or subject to light-induced synthetic gauge fields. The effective theories for the quasiparticles become relativistic under certain conditions in these systems, making them ideal platforms for studying the exotic relativistic effects. We focus on the realization of one, two, and three dimensional Dirac equations as well as the detection of some relativistic effects, including particularly the well-known Zitterbewegung effect and Klein tunneling. The realization of quantum anomalous Hall effects is also briefly discussed.Comment: 22 pages, review article in Frontiers of Physics: Proceedings on Quantum Dynamics of Ultracold Atom

Challenges in measuring individual differences in functional connectivity using fMRI: The case of healthy aging.

Many studies report individual differences in functional connectivity, such as those related to age. However, estimates of connectivity from fMRI are confounded by other factors, such as vascular health, head motion and changes in the location of functional regions. Here, we investigate the impact of these confounds, and pre-processing strategies that can mitigate them, using data from the Cambridge Centre for Ageing & Neuroscience (www.cam-can.com). This dataset contained two sessions of resting-state fMRI from 214 adults aged 18-88. Functional connectivity between all regions was strongly related to vascular health, most likely reflecting respiratory and cardiac signals. These variations in mean connectivity limit the validity of between-participant comparisons of connectivity estimates, and were best mitigated by regression of mean connectivity over participants. We also showed that high-pass filtering, instead of band-pass filtering, produced stronger and more reliable age-effects. Head motion was correlated with gray-matter volume in selected brain regions, and with various cognitive measures, suggesting that it has a biological (trait) component, and warning against regressing out motion over participants. Finally, we showed that the location of functional regions was more variable in older adults, which was alleviated by smoothing the data, or using a multivariate measure of connectivity. These results demonstrate that analysis choices have a dramatic impact on connectivity differences between individuals, ultimately affecting the associations found between connectivity and cognition. It is important that fMRI connectivity studies address these issues, and we suggest a number of ways to optimize analysis choices. Hum Brain Mapp 38:4125-4156, 2017. © 2017 Wiley Periodicals, Inc

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing—aliasbioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead