Using Pan-Genomic Data Structures to Incoporate Diversity Into Genomic Analyses

The alignment of sequencing reads to the reference genome is a process subject to reference bias, a phenomenon where reads containing alternative alleles have a smaller likelihood of aligning to the reference when compared to reads that are more similar to the reference. Because the human reference genome is largely comprised of the genomic sequence of a single individual, it is apparent that either changing or modifying the representation of the reference genome in order to incorporate diversity from other individuals can reduce reference bias. We discuss methods for alleviating reference bias through the use of novel text indexing data structures and algorithms that can incorporate such diversity. First, we present data structures built on top of the Run-Length FM Index that can be used to index and query a pan-genome, ie. a representation of the genome that incorporates known variation within the species. Then, we use pan-genome indexes in a workflow for constructing a personalized genome from a set of sequencing reads. This personalized genome can be used in lieu of the reference genome during alignment in order to alleviate reference bias. We also discuss how alignments against personalized genomes can be used in downstream analyses by "lifting" these alignments back over to the reference genome

Pangenomic Genotyping with the Marker Array

We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while avoiding the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods

Computer software for generating digital cadastral databases

The most recent and major spatial information technology development in Malaysia is the establishment of the Nalional Land Information System (NaUS). It is a system which enable the exchange and sharing of la1Id related information between government bodies. private agencies and general public. Computerization and digital data are the keywords in the new venture. With this in mind. Center for Geographic Information & Analysis (CGIA) has taken a step forward in the direction of establishing a Digital Cadastral Databases (DCDB). This paper describes the development of a software package for generaling DCDB being developed by CGIA

Soil erosion analysis using prime meridian GIS package

A number of soil erosion models have been developed to predict and characterize the movement of soil. These models provide an understanding of the dynamics of soil and can be used to evaluate the effectiveness of land management practices. Nevertheless, modellers faced some major problems. They are the inability to efficiently handle, manipulate and manage large volumes of model parameters. However, recent developments in Geographic Information Systems (GIS) provide the opportunities and tools to spatially organize and effectively manage data for the modelling. Thus, this research aims to develop an interactive soil erosion modelling and prediction system within a GIS environment. Prime Meridian GIS' Spatial Database Engine by Essential Planning System Pte. Ltd. (EPS), will be the core of the designed system. This system is designed to use the universal soil loss equation and the overlay modelling technique to generate the soil erosion risk map. The goal of developing the system is to provide a spatial decision support tool in environmental impact assessment as required by the Department of Environment, Ministry of Science Technology and Environment

Quantum barriers engineering toward radiative and stable perovskite photovoltaic devices

Acknowledgements: This work was supported by the National Research Foundation of Korea (NRF) grant funded from the Government of South Korea (NRF-2022M3J1A1085279 and RS-2023-00208467), the Korea Institute of Energy Technology Evaluation and Planning (KETEP) from the Ministry of Trade, Industry & Energy (20214000000680), and the National Research Council of Science & Technology (NST) grant by the Government of South Korea (No. CAP18054-202). This research has been performed as a project NO. KS2422-10 and supported by the Korea Research Institute of Chemical Technology (KRICT). This work was also supported by the EPSRC (EP/S030638/1). S.D.S. acknowledges the Royal Society and Tata Group (UF150033), EPSRC (EP/R023980/1), and the European Research Council under the European Union’s Horizon 2020 research and innovation programme (HYPERION, grant agreement no. 756962). M.A. acknowledges funding from the Leverhulme Early Career Fellowship (grant agreement No. ECF-2019-224) funded by the Leverhulme Trust and the Isaac Newton Trust and from the Royal Academy of Engineering under the Research Fellowship programme.Funder: the Korea Institute of Energy Technology Evaluation and Planning (KETEP) from the Ministry of Trade, Industry & Energy (20214000000680)Funder: the Royal Society and Tata Group (UF150033) the European Research Council under the European Union’s Horizon 2020 research and innovation programme (HYPERION, grant agreement no. 756962)Funder: the Leverhulme Early Career Fellowship (grant agreement No. ECF-2019-224) funded by the Leverhulme Trust and the Isaac Newton Trust and from the Royal Academy of Engineering under the Research Fellowship programmeAbstractEfficient photovoltaic devices must be efficient light emitters to reach the thermodynamic efficiency limit. Here, we present a promising prospect of perovskite photovoltaics as bright emitters by harnessing the significant benefits of photon recycling, which can be practically achieved by suppressing interfacial quenching. We have achieved radiative and stable perovskite photovoltaic devices by the design of a multiple quantum well structure with long (∼3 nm) organic spacers with oleylammonium molecules at perovskite top interfaces. Our L-site exchange process (L: barrier molecule cation) enables the formation of stable interfacial structures with moderate conductivity despite the thick barriers. Compared to popular short (∼1 nm) Ls, our approach results in enhanced radiation efficiency through the recursive process of photon recycling. This leads to the realization of radiative perovskite photovoltaics with both high photovoltaic efficiency (in-lab 26.0%, certified to 25.2%) and electroluminescence quantum efficiency (19.7 % at peak, 17.8% at 1-sun equivalent condition). Furthermore, the stable crystallinity of oleylammonium-based quantum wells enables our devices to maintain high efficiencies for over 1000 h of operation and &gt;2 years of storage.</jats:p

Quantum barriers engineering toward radiative and stable perovskite photovoltaic devices.

Efficient photovoltaic devices must be efficient light emitters to reach the thermodynamic efficiency limit. Here, we present a promising prospect of perovskite photovoltaics as bright emitters by harnessing the significant benefits of photon recycling, which can be practically achieved by suppressing interfacial quenching. We have achieved radiative and stable perovskite photovoltaic devices by the design of a multiple quantum well structure with long (∼3 nm) organic spacers with oleylammonium molecules at perovskite top interfaces. Our L-site exchange process (L: barrier molecule cation) enables the formation of stable interfacial structures with moderate conductivity despite the thick barriers. Compared to popular short (∼1 nm) Ls, our approach results in enhanced radiation efficiency through the recursive process of photon recycling. This leads to the realization of radiative perovskite photovoltaics with both high photovoltaic efficiency (in-lab 26.0%, certified to 25.2%) and electroluminescence quantum efficiency (19.7 % at peak, 17.8% at 1-sun equivalent condition). Furthermore, the stable crystallinity of oleylammonium-based quantum wells enables our devices to maintain high efficiencies for over 1000 h of operation and >2 years of storage

Efficient vertical charge transport in polycrystalline halide perovskites revealed by four-dimensional tracking of charge carriers.

Fast diffusion of charge carriers is crucial for efficient charge collection in perovskite solar cells. While lateral transient photoluminescence microscopies have been popularly used to characterize charge diffusion in perovskites, there exists a discrepancy between low diffusion coefficients measured and near-unity charge collection efficiencies achieved in practical solar cells. Here, we reveal hidden microscopic dynamics in halide perovskites through four-dimensional (directions x, y and z and time t) tracking of charge carriers by characterizing out-of-plane diffusion of charge carriers. By combining this approach with confocal microscopy, we discover a strong local heterogeneity of vertical charge diffusivities in a three-dimensional perovskite film, arising from the difference between intragrain and intergrain diffusion. We visualize that most charge carriers are efficiently transported through the direct intragrain pathways or via indirect detours through nearby areas with fast diffusion. The observed anisotropy and heterogeneity of charge carrier diffusion in perovskites rationalize their high performance as shown in real devices. Our work also foresees that further control of polycrystal growth will enable solar cells with micrometres-thick perovskites to achieve both long optical path length and efficient charge collection simultaneously