Grégory F. Schneider

Bio: Grégory F. Schneider is an academic researcher from Leiden University. The author has contributed to research in topics: Graphene & Nanopore. The author has an hindex of 28, co-authored 78 publications receiving 6693 citations. Previous affiliations of Grégory F. Schneider include Harvard University & Kavli Institute of Nanoscience.

Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems

Abstract: We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project. We provide an overview of the key aspects of graphene and related materials (GRMs), ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries. We also define an extensive list of acronyms in an effort to standardize the nomenclature in this emerging field.

DNA Translocation through Graphene Nanopores

Abstract: Nanopores—nanosized holes that can transport ions and molecules—are very promising devices for genomic screening, in particular DNA sequencing. Solid-state nanopores currently suffer from the drawback, however, that the channel constituting the pore is long, ∼100 times the distance between two bases in a DNA molecule (0.5 nm for single-stranded DNA). This paper provides proof of concept that it is possible to realize and use ultrathin nanopores fabricated in graphene monolayers for single-molecule DNA translocation. The pores are obtained by placing a graphene flake over a microsize hole in a silicon nitride membrane and drilling a nanosize hole in the graphene using an electron beam. As individual DNA molecules translocate through the pore, characteristic temporary conductance changes are observed in the ionic current through the nanopore, setting the stage for future single-molecule genomic screening devices.

Distance-Dependent Fluorescence Quenching on Gold Nanoparticles Ensheathed with Layer-by-Layer Assembled Polyelectrolytes

Abstract: We report on the preparation, characterization, and photophysical study of new fluorescent core/shell nanoparticles fabricated by electrostatic layer-by-layer assembly. On the basis of gold cores with a diameter of 13 nm, these nanocolloids possess different fluorescently labeled polymer corona layers at various distances from the surface of the core metal using nonfluorescent polyelectrolytes as spacer layers. UV-visible spectroscopy and transmission electron microscopy confirm that the particle suspensions of fluorescently labeled core/shell nanoparticles are stable at all stages of their construction. Photophysical investigations reveal strongly distance-dependent fluorescence quenching in these particle systems. The contribution of the metal core to this quenching can be assesed precisely after the gentle dissolution of the gold cores by potassium cyanide. The photophysical measurements reveal clearly that the gold nanoparticles decrease the transition probability for radiative transitions.

DNA sequencing with nanopores.

Abstract: Major hurdles in the quest to sequence DNA with biological nanopores have now been overcome.

Atomic-scale electron-beam sculpting of near-defect-free graphene nanostructures.

Abstract: In order to harvest the many promising properties of graphene in (electronic) applications, a technique is required to cut, shape, or sculpt the material on the nanoscale without inducing damage to its atomic structure, as this drastically influences the electronic properties of the nanostructure. Here, we reveal a temperature-dependent self-repair mechanism that allows near-damage-free atomic-scale sculpting of graphene using a focused electron beam. We demonstrate that by sculpting at temperatures above 600 °C, an intrinsic self-repair mechanism keeps the graphene in a single-crystalline state during cutting, even though the electron beam induces considerable damage. Self-repair is mediated by mobile carbon ad-atoms that constantly repair the defects caused by the electron beam. Our technique allows reproducible fabrication and simultaneous imaging of single-crystalline free-standing nanoribbons, nanotubes, nanopores, and single carbon chains.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Abstract: Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8.2. These advances result from new overlapping and assembly algorithms, including an adaptive overlapping strategy based on tf-idf weighted MinHash and a sparse assembly graph construction that avoids collapsing diverged repeats and haplotypes. We demonstrate that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either Pacific Biosciences (PacBio) or Oxford Nanopore technologies and achieves a contig NG50 of >21 Mbp on both human and Drosophila melanogaster PacBio data sets. For assembly structures that cannot be linearly represented, Canu provides graph-based assembly outputs in graphical fragment assembly (GFA) format for analysis or integration with complementary phasing and scaffolding techniques. The combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex genomes.

Recent Advances in Ultrathin Two-Dimensional Nanomaterials

Abstract: Since the discovery of mechanically exfoliated graphene in 2004, research on ultrathin two-dimensional (2D) nanomaterials has grown exponentially in the fields of condensed matter physics, material science, chemistry, and nanotechnology. Highlighting their compelling physical, chemical, electronic, and optical properties, as well as their various potential applications, in this Review, we summarize the state-of-art progress on the ultrathin 2D nanomaterials with a particular emphasis on their recent advances. First, we introduce the unique advances on ultrathin 2D nanomaterials, followed by the description of their composition and crystal structures. The assortments of their synthetic methods are then summarized, including insights on their advantages and limitations, alongside some recommendations on suitable characterization techniques. We also discuss in detail the utilization of these ultrathin 2D nanomaterials for wide ranges of potential applications among the electronics/optoelectronics, electrocat...

Photodetectors based on graphene, other two-dimensional materials and hybrid systems

Abstract: Graphene and other two-dimensional materials, such as transition metal dichalcogenides, have rapidly established themselves as intriguing building blocks for optoelectronic applications, with a strong focus on various photodetection platforms The versatility of these material systems enables their application in areas including ultrafast and ultrasensitive detection of light in the ultraviolet, visible, infrared and terahertz frequency ranges These detectors can be integrated with other photonic components based on the same material, as well as with silicon photonic and electronic technologies Here, we provide an overview and evaluation of state-of-the-art photodetectors based on graphene, other two-dimensional materials, and hybrid systems based on the combination of different two-dimensional crystals or of two-dimensional crystals and other (nano)materials, such as plasmonic nanoparticles, semiconductors, quantum dots, or their integration with (silicon) waveguides