Search

COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes almost 6 million coding mutations across 1.4 million tumour samples, curated from over 26 000 publications. In addition to coding mutations, COSMIC covers all the genetic mechanisms by which somatic mutations promote cancer, including non-coding mutations, gene fusions, copy-number variants and drug-resistance mutations. COSMIC is primarily hand-curated, ensuring quality, accuracy and descriptive data capture. Building on our manual curation processes, we are introducing new initiatives that allow us to prioritize key genes and diseases, and to react more quickly and comprehensively to new findings in the literature. Alongside improvements to the public website and data-download systems, new functionality in COSMIC-3D allows exploration of mutations within three-dimensional protein structures, their protein structural and functional impacts, and implications for druggability. In parallel with COSMIC’s deep and broad variant coverage, the Cancer Gene Census (CGC) describes a curated catalogue of genes driving every form of human cancer. Currently describing 719 genes, the CGC has recently introduced functional descriptions of how each gene drives disease, summarized into the 10 cancer Hallmarks.

The process of photosynthesis, the main source of energy in the living world, converts sunlight into chemical energy. The high efficiency of this process is believed to be enabled by an interplay between the quantum nature of molecular structures in photosynthetic complexes and their interaction with the environment. Investigating these effects in biological samples is challenging due to their complex and disordered structure. Here we experimentally demonstrate a technique for studying photosynthetic models based on superconducting quantum circuits, which complements existing experimental, theoretical, and computational approaches. We demonstrate a high degree of freedom in design and experimental control of our approach based on a simplified three-site model of a pigment protein complex with realistic parameters scaled down in energy by a factor of 105. We show that the excitation transport between quantum-coherent sites disordered in energy can be enabled through the interaction with environmental noise. We also show that the efficiency of the process is maximized for structured noise resembling intramolecular phononic environments found in photosynthetic complexes., Nature Communications, 9 (1), ISSN:2041-1723

A system for approximate number discrimination has been shown to arise in at least two types of hierarchical neural network models—a generative Deep Belief Network (DBN) and a Hierarchical Convolutional Neural Network (HCNN) trained to classify natural objects. Here, we investigate whether the same two network architectures can learn to recognise exact numerosity. A clear difference in performance could be traced to the specificity of the unit responses that emerged in the last hidden layer of each network. In the DBN, the emergence of a layer of monotonic ‘summation units’ was sufficient to produce classification behaviour consistent with the behavioural signature of the approximate number system. In the HCNN, a layer of units uniquely tuned to the transition between particular numerosities effectively encoded a thermometer-like ‘numerosity code’ that ensured near-perfect classification accuracy. The results support the notion that parallel pattern-recognition mechanisms may give rise to exact and approximate number concepts, both of which may contribute to the learning of symbolic numbers and arithmetic.

COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk/cosmic) is a continual effort to integrate all available information on somatic mutations and other molecular alterations causing every form of human cancer. Being the world’s largest and most comprehensive database of somatic mutations in human cancer, it also provides web-based tools for exploration and interpretation of collected data. The content of the database is primarily obtained from the scientific literature by the team of experienced post-doctoral curators and combined with information from online sources, including the TCGA and ICGC. During thorough & exhaustive manual curation, all the available information about mutations and tumor samples (e.g. disease type, demographic data, treatments) are collected, standardized and integrated to allow for both creation of wide virtual cohorts and large-scale studies, as well as precise analysis at the level of a single sample, gene or mutation. The 87th release of COSMIC (Nov 2018) encompasses 5,992,260 coding mutations and 19,574 gene fusions, curated from 1,403,267 cancer samples, including 35,490 whole cancer exomes/genomes, primarily hand-curated data from 26,494 scientific publications. Additionally, COSMIC describes 1,179,545 Copy Number Variants, 9,147,833 gene expression variants, and 7,879,142 differentially methylated CPGs. In addition to this broad database, COSMIC includes a range of specialized projects highlighting specific aspects of cancer in order to emphasize events with a higher impact in disease etiology. This includes the Cancer Gene Census (http://cancer.sanger.ac.uk/census), which defines and describes genes (currently 719) and their dysfunctions driving oncogenesis, and characterizes their impact on hallmarks of cancer. COSMIC3D (http://cancer.sanger.ac.uk/cosmic3d) provides an interactive view of cancer mutations in the context of 3D protein structures, and predicts potential drug-binding sites. Significantly updated 4 times a year, COSMIC is available free-of-charge for academic and non-profit users via COSMIC webpage (http://cancer.sanger.ac.uk/cosmic) or to download through COSMIC downloads (http://cancer.sanger.ac.uk/cosmic/download). Citation Format: Simon Andrew Forbes, david beare, charalampos boutselakis, sally bamford, kate noble, claire rye, john tate, chai yin kok, charlie hathaway, laura ponting, christopher ramshaw, raymund stefancsik, samantha thompson, bhavana harsha, nidhi bindal, shicai wang, steven jupe, helen speedy, celestino creatore, peter fish, sari ward, charlotte cole, elisabeth dawson, zbyslaw sondka. COSMIC: Describing the world’s knowledge of somatic mutations in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 906.

Trapped charges at oxide interfaces in field effect transistors are well known sources of noise and generally degrade the device performance. At low temperatures, operating in the sub-threshold regime, conduction electrons can be confined to percolation pathways [1]. The scattering potential produced by trapped charge can then have a dramatic effect on the conductance, normally observed as random telegraph noise [2]. Here we show that it is possible to coherently excite the trapped electrons with microwave fields, which induce polarization fields that interact with the percolating electrons, measured as high-quality resonances (Q ∼ 104 – 105) in the transistor current. Implementing single-shot measurements gives the possibility to study the dynamics of the trapped electrons, and using a standard Ramsey protocol, coherent control is achieved. Given the long coherence times observed (T 2 ∼ 10 µs) and since each resonance can be addressed independently in frequency space, the possibility to use such systems as quantum memories or quantum bits is discussed.

The remarkable performance and quantum efficiency of biological light-harvesting complexes has prompted a multidisciplinary interest in engineering biologically inspired antenna systems as a possible route to novel solar cell technologies. Key to the effectiveness of biological “nanomachines” in light capture and energy transport is their highly ordered nanoscale architecture of photoactive molecules. Recently, DNA origami has emerged as a powerful tool for organizing multiple chromophores with base-pair accuracy and full geometric freedom. Here, we present a programmable antenna array on a DNA origami platform that enables the implementation of rationally designed antenna structures. We systematically analyze the light-harvesting efficiency with respect to number of donors and interdye distances of a ring-like antenna using ensemble and single-molecule fluorescence spectroscopy and detailed Förster modeling. This comprehensive study demonstrates exquisite and reliable structural control over multichromophoric geometries and points to DNA origami as highly versatile platform for testing design concepts in artificial light-harvesting networks.

The electrical control and readout of single two-level state defects in a defective oxide film grown directly on the channel of a thin-film FET allow for the extraction of individual long relaxation times. Electronic defect states at material interfaces provide highly deleterious sources of noise in solid-state nanostructures, and even a single trapped charge can qualitatively alter the properties of short one-dimensional nanowire field-effect transistors (FET) and quantum bit (qubit) devices1,2,3,4,5. Understanding the dynamics of trapped charge is thus essential for future nanotechnologies, but their direct detection and manipulation is rather challenging2,4,5. Here, a transistor-based set-up is used to create and probe individual electronic defect states that can be coherently driven with microwave (MW) pulses. Strikingly, we resolve a large number of very high quality (Q ∼ 1 × 105) resonances in the transistor current as a function of MW frequency and demonstrate both long decoherence times (∼1 μs—40 μs) and coherent control of the defect-induced dynamics. Efficiently characterizing over 800 individually addressable resonances across two separate defect-hosting materials, we propose that their properties are consistent with weakly driven two-level systems.

The process of photosynthesis, the main source of energy in the living world, converts sunlight into chemical energy. The high efficiency of this process is believed to be enabled by an interplay between the quantum nature of molecular structures in photosynthetic complexes and their interaction with the environment. Investigating these effects in biological samples is challenging due to their complex and disordered structure. Here we experimentally demonstrate a technique for studying photosynthetic models based on superconducting quantum circuits, which complements existing experimental, theoretical, and computational approaches. We demonstrate a high degree of freedom in design and experimental control of our approach based on a simplified three-site model of a pigment protein complex with realistic parameters scaled down in energy by a factor of 105. We show that the excitation transport between quantum-coherent sites disordered in energy can be enabled through the interaction with environmental noise. We also show that the efficiency of the process is maximized for structured noise resembling intramolecular phononic environments found in photosynthetic complexes., Investigating photosynthesis processes in biological samples is challenging due to their complex and disordered structure. Based on analog quantum simulations with superconducting quantum circuits, the authors show how the interplay of quantum coherence and environmental interactions affects energy transport.

INTRODUCTION AND BACKGROUND Photovoltaic (PV) solar energy conversion is one of the most promising emerging renewable energy technologies and is likely to play an ever-increasing role in the future of electricity generation. The potential of photovoltaics is considered to be much larger than the current energy demand, which is equivalent to ≈13,000 millions tons of oil (BP, 2014). Together with other renewable energy sources, photovoltaics could thus considerably aid the decarbonization of the energy sector in the near future, an objective, which is (should be) seriously sought after to meet the IPCC 2°C target1. Indeed, PV energy conversion is an ever-increasing research field having an impact on other sectors: technological (e.g., dealing with energy storage and distribution issues) and economical (e.g., evaluating the costs of PV devices compared to conventional energy technologies). The typical working principle of a photovoltaic cell is quite simple, and well understood in terms of doped inorganic semiconductors (Wurfel, 2009). Photovoltaic technology has significantly moved forward since the first silicon (Si) solar cell having an efficiency of ≈4% was invented in 1950s in Bell Laboratories, following the breakthrough of the p–n junction developed by Shockley, Brattain, and Bardeen (Chapin et al., 1954). Since then, research on PV has led to singlejunction and multi-junction solar cells with record efficiencies in controlled (laboratory) environments of ≈29% (Green et al., 2014) and 46% (Fraunhofer-ISE, 2014), respectively. However, the efficiency of the most popular technologies in the commercial market – which belong to the so called first generation of solar cells, mainly based on crystalline Si – is in the 10–18% range and around 25% in laboratory. A second generation of cells, mainly aimed at reducing the fabrication costs, is based on thin film architectures, where light is absorbed and charge generated in a solid thin layer of semiconductor (e.g., CdTe, CIGS), with efficiencies restrained to around 22%. Beyond these technologies, a variety of other PV designs has emerged, mainly driven by the progress on materials research and the need of low-cost manufacture devices, organic photovoltaic (OPV) being one of the most interesting solutions. The latest scientific developments in this field have taken various directions (using different concepts, materials, and geometries), all having the potential to result in high-efficiency PV devices. Most current approaches, which have been termed third generation PV [see e.g., Green (2003)], explore schemes beyond the guidelines given by Shockley and Queisser (1961), which are based on the assumption that each photon absorbed above the band gap of the semiconductor photovoltaic material generates a single electron-hole pair. These methods include solar cells exploiting multiple-exciton generation in both inorganic and organic materials, hot carriers collection, upand down-conversions. Reviewing the extensive literature about the past and present PV schemes is beyond the scope of this Opinion, many excellent reviews having already succeeded in this (challenging) task. Here, we will illustrate and highlight our point of view on an emergent strategy for PV and artificial light-harvesting in general. This strategy holds onto an interdisciplinary framework encompassing biology and quantum mechanics. Ideas, which have been developed within this nascent trend, are inspired by the recent discovery of quantum effects in biological systems (Mohseni et al., 2014), and aim to model and reproduce the highly efficient reactions often exhibited by these systems using the tools of quantum mechanics and nanotechnology platforms. Novel theoretical proposals, for instance (Scully, 2010; Blankenship et al., 2011; Scully et al., 2011; Creatore et al., 2013; Zhang et al., 2015), have underlined the relevance of effects of quantum coherence to enhance the performance of photocells whose working principle is inspired by the architecture of biological light-harvesting complexes (LHCs).

The strong and weak coupling regimes are analyzed for quantum well excitons interacting with the light field. The strong-weak coupling transition point is described and quantified in terms of a discrete topological change (from an intersection to an anticrossing) of the quantum well polariton dispersion curves, which occurs at a critical damping rate of excitons

Nature Materials 16, 208–213 (2017); published online 19 September 2016; corrected after print 30 June 2017 In this work we reported the development of a rigorous mathematical and physical framework in order to model the detailed time-resolved behaviour of over 800 resonances that we studied, through continuous-wave and single-pulse microwave spectroscopy measurements in a field-effect transistor.

We investigate the mean-field dynamics of a system of interacting photons in an array of coupled cavities in presence of dissipation and disorder. We follow the evolution of on an initially prepared Fock state, and show how the interplay between dissipation and disorder affects the coherence properties of the cavity emission and that these properties can be used as signatures of the many-body phase of the whole array., 8 pages, 10 figures, new reference added

Artificially implementing the biological light reactions responsible for the remarkably efficient photon-to-charge conversion in photosynthetic complexes represents a new direction for the future development of photovoltaic devices. Here, we develop such a paradigm and present a model photocell based on the nanoscale architecture and molecular elements of photosynthetic reaction centers. Quantum interference of photon absorption and emission induced by the dipole-dipole interaction between molecular excited states guarantees an enhanced light-to-current conversion and power generation for a wide range of electronic, thermal, and optical parameters for optimized dipolar geometries. This result opens a promising new route for designing artificial light-harvesting devices inspired by biological photosynthesis and quantum technologies.

We consider performing adiabatic rapid passage (ARP) using frequency-swept driving pulses to excite a collection of interacting two-level systems. Such a model arises in a wide range of many-body quantum systems, such as cavity QED or quantum dots, where a nonlinear component couples to light. We analyze the one-dimensional case using the Jordan-Wigner transformation, as well as the mean-field limit where the system is described by a Lipkin-Meshkov-Glick Hamiltonian. These limits provide complementary insights into the behavior of many-body systems under ARP, suggesting our results are generally applicable. We demonstrate that ARP can be used for state preparation in the presence of interactions, and identify the dependence of the required pulse shapes on the interaction strength. In general, interactions increase the pulse bandwidth required for successful state transfer, introducing new restrictions on the pulse forms required.

Quantum state preparation through external control is fundamental to established methods in quantum information processing and in studies of dynamics. In this respect, excitons in semiconductor quantum dots (QDs) are of particular interest since their coupling to light allows them to be driven into a specified state using the coherent interaction with a tuned optical field such as an external laser pulse. We propose a protocol, based on adiabatic rapid passage, for the creation of entangled states in an ensemble of pairwise coupled two-level systems, such as an ensemble of QD molecules. We show by quantitative analysis using realistic parameters for semiconductor QDs that this method is feasible where other approaches are unavailable. Furthermore, this scheme can be generically transferred to some other physical systems including circuit QED, nuclear and electron spins in solid-state environments, and photonic coupled cavities., 10 pages, 2 figures. Added reference, minor changes. Discussion, results and conclusions unchanged

We present a quantum-electrodynamical formalism to study the spontaneous emission from dipoles embedded in a non-absorbing and lossless multilayer dielectric structure. In this model the electromagnetic field is quantized by a proper choice of a complete and orthonormal set of classical modes and the analytical expressions for the emission rates are obtained within the framework of perturbation theory. We apply our model to investigate the 1.54??m transition of Er3+-doped SiO2 thin layers acting as active material in planar slot waveguides in polycrystalline silicon. The theoretical results show that a strong reduction of the radiative lifetime does occur in the slot waveguide. Furthermore, by using the theoretical analysis together with photoluminescence measurements, we estimate also the radiative efficiency which is found to be only slightly reduced with respect to the value for Er3+ in a bulk of SiO2. These results are important for future realization of silicon-compatible active optical devices and show the relevance of our model to study the spontaneous emission processes in multilayer structures.

Periodic structures resonantly coupled to excitonic media allow the existence of extra intragap modes ('Braggoritons'), due to the coupling between Bragg photon modes and 3D bulk excitons. This induces unique and unexplored dispersive features, which can be tailored by properly designing the photonic bandgap around the exciton resonance. We report that one-dimensional Braggoritons realized with semiconductor gratings have the ability to mimic the dispersion of quantum-well microcavity polaritons. This will allow the observation of new nonlinear phenomena, such as slow-light-enhanced nonlinear propagation and an efficient parametric scattering at two 'magic frequencies'.

A transition between the strong (coherent) and weak (incoherent) coupling limits of resonant interaction between quantum well (QW) excitons and bulk photons is analyzed and quantified as a function of the incoherent damping rate caused by exciton-phonon and exciton-exciton scattering. For confined QW polaritons, a second, anomalous, damping-induced dispersion branch arises and develops with increasing damping. In this case, the strong-weak coupling transition is attributed to a critical damping rate, when the intersection of the normal and damping-induced dispersion branches occurs. For the radiative states of QW excitons, i.e., for radiative QW polaritons, the transition is described as a qualitative change of the photoluminescence spectrum at grazing angles along the QW structure. Furthermore, we show that the radiative corrections to the QW exciton states with in-plane wavevector approaching the photon cone are universally scaled by an energy parameter rather than diverge. The strong-weak coupling transition rates are also proportional to the same energy parameter. The numerical evaluations are given for a GaAs single quantum well with realistic parameters., Published in Physical Review B. 29 pages, 12 figures

We present a fully quantum-electrodynamical formalism suitable to evaluate the spontaneous emission rate and pattern from a dipole embedded in a non-absorbing and lossless multilayer dielectric structure. In the model here developed the electromagnetic field is quantized by a proper choice of a complete and orthonormal set of classical spatial modes, which consists of guided and radiative (partially and fully) states. In particular, by choosing a set of radiative states characterized by a single outgoing component, we get rid of the problem related to the quantum interference between different outgoing modes, which arises when the standard radiative basis is used to calculate spontaneous emission patterns. After the derivation of the local density of states, the analytical expressions for the emission rates are obtained within the framework of perturbation theory. First we apply our model to realistic Silicon-based structures such as a single Silicon/air interface and a Silicon waveguide in both the symmetric and asymmetric configurations. Then, we focus on the analysis of the spontaneous emission process in a silicon-on-insulator (SOI) Slot waveguide (a 6 layers model structure) doped with erbium ions (emitting at the telecom wavelength). In this latter case we find a very good agreement with the experimental evidence [M. Galli et al., Appl. Phys. Lett. 89, 241114 (2006)] of an enhanced TM/TE photoluminescence signal. Hence, this model is relevant to study the spontaneous emission in Silicon-based multilayer structures which nowadays play a fundamental role for the development of highly integrated multifunctional devices., Comment: 36 pages, 13 figures

We study the strong coupling between photons and bulk excitons in a one-dimensional Bragg grating. The dispersion of the resulting Bragg-polariton states resembles the dispersion of quantum-well microcavity polaritons. We report on a parametric scattering process at two "magic frequencies" occurring due to the strong excitonic nonlinearity.

The authors report a systematic study of the lifetime of the 1.54 μm transition of Er3+-doped SiO2 thin film as active material in planar slot waveguides in polycrystalline silicon. The lifetime shows a strong reduction when compared with values measured in three other configurations. The experimental results, combined with a rigorous quantum-electrodynamical formalism, are consistent with a sizable increase in both the radiative and nonradiative decay rates of Er3+ transition in slot waveguide. The radiative efficiency is only slightly reduced with respect to Er3+ in the bulk oxide, this result being important for future realization of Si-compatible active optical devices.

A simple model based on the 1D nonlinear Schrödinger equation is studied, which contains both spatially and temporally dispersive terms. Parametric instabilities for plane waves are analyzed in detail, and solitary waves (both bright and dark) are found. The model presented here is able to describe the non-trivial unstable dynamics of intense, nonlinear light propagation near a material resonance in presence of negative spatial dispersion. We provide as a practical example the light propagation near the tail of an exciton-polariton resonance in a specially designed semiconductor superlattice.

The work described in this thesis is a theoretical investigation of the properties of exciton-polaritons in quantum wells (QWs). The polariton effect is first studied in the case of a completely coherent interaction between QW excitons and bulk photons, i.e. in the so called strong coupling limit. Then, an incoherent damping rate for the exciton states is included and the resulting modifications in the polariton dispersion are analyzed. A microscopic model which accounts for the scattering of QW excitons by random impurities is also proposed. In the strong coupling limit, a definitive and correct description of the QW polariton dispersion, for both confined and radiative modes, is obtained when the exciton- photon coupling is treated non perturbatively. A self-consistent perturbation theory which qualitatively agrees with the obtained results is also formulated. With increasing the incoherent damping, the orthogonality between radiative and confined polariton states is not affected, but a phase transition from the strong coupling regime to a weak coupling one occurs for both modes. The crossover between the two regimes is attributed to a topological change of the polariton dispersion curves when the damping rate reaches a critical value. A microscopic approach dealing with scattering of excitons by random impurities is formulated in terms of a quadratic Hamiltonian for QW excitons, bulk photons and localised impurities. By analyzing the preliminary results based on the calculation of the relevant eigenstates, the mixing between radiative and confined modes is observed.