Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Since any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our distribution predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.Comment: 20 pages, including Appendi

Antilocalization of Coulomb Blockade in a Ge-Si Nanowire

The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length ($l_{so}$ < 20 nm), consistent with values extracted in the Coulomb blockade regime ($l_{so}$ < 25 nm).Comment: Supplementary Information available at http://bit.ly/19pMpd

Hole Spin Coherence in a Ge/Si Heterostructure Nanowire

Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time $T_2^* \sim 0.18~\mathrm{\mu s}$ exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.Comment: 15 pages, 4 figure

Gate Coupling to Nanoscale Electronics

The realization of single-molecule electronic devices, in which a nanometer-scale molecule is connected to macroscopic leads, requires the reproducible production of highly ordered nanoscale gaps in which a molecule of interest is electrostatically coupled to nearby gate electrodes. Understanding how the molecule-gate coupling depends on key parameters is crucial for the development of high-performance devices. Here we directly address this, presenting two- and three-dimensional finite-element electrostatic simulations of the electrode geometries formed using emerging fabrication techniques. We quantify the gate coupling intrinsic to these devices, exploring the roles of parameters believed to be relevant to such devices. These include the thickness and nature of the dielectric used, and the gate screening due to different device geometries. On the single-molecule (~1nm) scale, we find that device geometry plays a greater role in the gate coupling than the dielectric constant or the thickness of the insulator. Compared to the typical uniform nanogap electrode geometry envisioned, we find that non-uniform tapered electrodes yield a significant three orders of magnitude improvement in gate coupling. We also find that in the tapered geometry the polarizability of a molecular channel works to enhance the gate coupling

Influence of Different Strain Rates on the Flow Curve and the Formability of Thin Aluminium and Tinplate Sheets

Due to this high number of produced units and the very thin sheet metals used for beverage cans, precise production processes with high production volumes are necessary. To save expenses, while optimising these processes, numerical simulation methods are exploited. Considering this, it is indispensable to identify the material behaviour as exactly as possible. In practise, often results of quasi static tensile tests are used, although these are insufficient for the precise modelling of the material behaviour during can production, since strain rates of up to 10³ s-1 can occur, here. Therefore, quasi static and high speed tensile test have been done on specimens featuring the typical materials and thicknesses of semi-finished parts used for beverage can production. The results were compared with similar materials at higher sheet metal thicknesses and authenticated by numerical simulation. It was shown that there is an influence of the strain rate on the material behaviour and it is necessary to determine material characteristics at strain rates, which are close to the process speed. Furthermore, the results were classified in their signification for beverage can production and forming technologies in general

Covalently Functionalized Nanotubes as Nanometer-Sized Probes in Chemistry and Biology

Carbon nanotubes combine a range of properties that make them well suited for use as probe tips in applications such as atomic force microscopy (AFM)1, 2, 3. Their high aspect ratio, for example, opens up the possibility of probing the deep crevices4 that occur in microelectronic circuits, and the small effective radius of nanotube tips significantly improves the lateral resolution beyond what can be achieved using commercial silicon tips5. Another characteristic feature of nanotubes is their ability to buckle elastically4, 6, which makes them very robust while limiting the maximum force that is applied to delicate organic and biological samples. Earlier investigations into the performance of nanotubes as scanning probe microscopy tips have focused on topographical imaging, but a potentially more significant issue is the question of whether nanotubes can be modified to create probes that can sense and manipulate matter at the molecular level7. Here we demonstrate that nanotube tips with the capability of chemical and biological discrimination can be created with acidic functionality and by coupling basic or hydrophobic functionalities or biomolecular probes to the carboxyl groups that are present at the open tip ends. We have used these modified nanotubes as AFM tips to titrate the acid and base groups, to image patterned samples based on molecular interactions, and to measure the binding force between single protein ligand pairs. As carboxyl groups are readily derivatized by a variety of reactions8, the preparation of a wide range of functionalized nanotube tips should be possible, thus creating molecular probes with potential applications in many areas of chemistry and biology.Chemistry and Chemical Biolog

Atomic layer deposition of ZnS nanotubes

We report on growth of high-aspect-ratio ($\gtrsim300$) zinc sulfide nanotubes with variable, precisely tunable, wall thicknesses and tube diameters into highly ordered pores of anodic alumina templates by atomic layer deposition (ALD) at temperatures as low as 75 $^{\circ}$C. Various characterization techniques are employed to gain information on the composition, morphology, and crystal structure of the synthesized samples. Besides practical applications, the ALD-grown tubes could be envisaged as model systems for the study of a certain class of size-dependent quantum and classical phenomena.Comment: 1 LaTeX source file, 8 eps figures, and the manuscript in PDF forma

Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency

The nonhomologous DNA end-joining (NHEJ) pathway is a key mechanism for repairing dsDNA breaks that occur often in eukaryotic cells. In the simplest model, these breaks are first recognized by Ku, which then interacts with other NHEJ proteins to improve their affinity at DNA ends. These include DNA-PK$_{cs}$ and Artemis for trimming the DNA ends; DNA polymerase μ and λ to add nucleotides; and the DNA ligase IV complex to ligate the ends with the additional factors, XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor/Cernunos), and PAXX (paralog of XRCC4 and XLF). $\textit{In vivo}$ studies have demonstrated the degrees of importance of these NHEJ proteins in the mechanism of repair of dsDNA breaks, but interpretations can be confounded by other cellular processes. $\textit{In vitro}$ studies with NHEJ proteins have been performed to evaluate the nucleolytic resection, polymerization, and ligation steps, but a complete system has been elusive. Here we have developed a NHEJ reconstitution system that includes the nuclease, polymerase, and ligase components to evaluate relative NHEJ efficiency and analyze ligated junctional sequences for various types of DNA ends, including blunt, 5' overhangs, and 3' overhangs. We find that different dsDNA end structures have differential dependence on these enzymatic components. The dependence of some end joining on only Ku and XRCC4·DNA ligase IV allows us to formulate a physical model that incorporates nuclease and polymerase components as needed.National Institutes of Health, Cancer Research UK Program Grant IDs: C6/A11224, C6946/A14492), Wellcome Trust (Grant IDs: WT092096, WT093167

Imaging a 1-electron InAs quantum dot in an InAs/InP nanowire

Nanowire heterostructures define high-quality few-electron quantum dots for nanoelectronics, spintronics and quantum information processing. We use a cooled scanning probe microscope (SPM) to image and control an InAs quantum dot in an InAs/InP nanowire, using the tip as a movable gate. Images of dot conductance vs. tip position at T = 4.2 K show concentric rings as electrons are added, starting with the first electron. The SPM can locate a dot along a nanowire and individually tune its charge, abilities that will be very useful for the control of coupled nanowire dots

InAs nanowire hot-electron Josephson transistor

At a superconductor (S)-normal metal (N) junction pairing correlations can "leak-out" into the N region. This proximity effect [1, 2] modifies the system transport properties and can lead to supercurrent flow in SNS junctions [3]. Recent experimental works showed the potential of semiconductor nanowires (NWs) as building blocks for nanometre-scale devices [4-7], also in combination with superconducting elements [8-12]. Here, we demonstrate an InAs NW Josephson transistor where supercurrent is controlled by hot-quasiparticle injection from normal-metal electrodes. Operational principle is based on the modification of NW electron-energy distribution [13-20] that can yield reduced dissipation and high-switching speed. We shall argue that exploitation of this principle with heterostructured semiconductor NWs opens the way to a host of out-of-equilibrium hybrid-nanodevice concepts [7, 21].Comment: 6 pages, 6 color figure