arXiv subjects

Rasmus Nielsen

Publications and source records attributed to Rasmus Nielsen.

9 recordsLinked to original sources

arXiv2026

Hyperiax and Phylogenetic Inference from Shape Data

Phylogenetic inference on high-dimensional morphological traits requires algorithms that account for both the nonlinear geometry of the shape data and the phylogenetic tree structure. The Backward Filtering Forward Guiding (BFFG) framework provides smoothing for nonlinear stochastic processes on trees and enables inference of parameters and ancestral states. As practical adoption has been limited by a lack of efficient implementations, we present Hyperiax, an open-source library for tree traversal algorithms and message passing using JAX, designed particularly to support operations needed for BFFG. Hyperiax enables efficient execution of operations on trees with large numbers of nodes and, coupled with the BFFG-specific operations, this allows efficient inference in both discrete-time and stochastic differential equation models. Concretely, we demonstrate that Hyperiax enables parameter inference and ancestral reconstruction for butterfly wing shapes represented by landmarks in two dimensions, and analyses of avian beaks from landmarks in three dimensions. Both cases demonstrate application of BFFG on two substantially larger phylogenetic trees with 850 and 696 nodes with higher resolution shape data (118 two-dimensional landmarks and 79 three-dimensional landmarks, specifically) than previously possible.

q-bio.PE↗

arXiv2024

Increasing the Collection Efficiency in Selenium Thin-Film Solar Cells Using a Closed-Space Annealing Strategy

Elemental selenium is a promising wide-bandgap ($E_\mathrm{G}\approx$ 1.95 eV) photovoltaic material for the next generation of thin-film solar cells. To realize high-efficiency selenium solar cells, it is crucial to optimize the crystallization process of the selenium thin-film photoabsorber. However, the high vapor pressure of selenium restricts the processing conditions to a compromise between the growth of large crystal grains and the formation of pinholes. In this study, we introduce a closed-space annealing (CSA) strategy designed to suppress the sublimation of selenium, enabling thermal annealing processes at higher temperatures and for longer periods of time. As a result, we consistently improve carrier collection and the overall photovoltaic device performance in our selenium solar cells. By characterizing the carrier dynamics in our devices, we conclude that the observed improvements result from a reduction in charge transfer resistance rather than an increase in carrier diffusion length. The CSA strategy is a promising method for controlling surface morphology and roughness without reducing crystal grain sizes, which paves the way for further advancements in the efficiency and reproducibility of selenium thin-film solar cells.

cond-mat.mtrl-sci↗

arXiv2023

Monolithic Selenium/Silicon Tandem Solar Cells

Selenium is experiencing renewed interest as a promising candidate for the wide bandgap photoabsorber in tandem solar cells. However, despite the potential of selenium-based tandems to surpass the theoretical efficiency limit of single junction devices, such a device has never been demonstrated. In this study, we present the first monolithically integrated selenium/silicon tandem solar cell. Guided by device simulations, we investigate various carrier-selective contact materials and achieve encouraging results, including an open-circuit voltage of V$_\text{oc}$=1.68 V from suns-V$_\text{oc}$ measurements. The high open-circuit voltage positions selenium/silicon tandem solar cells as serious contenders to the industrially dominant single junction technologies. Furthermore, we quantify a pseudo fill factor of more than 80% using injection-level-dependent open-circuit voltage measurements, indicating that a significant fraction of the photovoltaic losses can be attributed to parasitic series resistance. This work provides valuable insights into the key challenges that need to be addressed for realizing higher efficiency selenium/silicon tandem solar cells.

cond-mat.mtrl-sci↗

arXiv2023

Laser-Annealing and Solid-Phase Epitaxy of Selenium Thin-Film Solar Cells

Selenium has resurged as a promising photovoltaic material in solar cell research due to its wide direct bandgap of 1.95 eV, making it a suitable candidate for a top cell in tandem photovoltaic devices. However, the optoelectronic quality of selenium thin-films has been identified as a key bottleneck for realizing high-efficiency selenium solar cells. In this study, we present a novel approach for crystallizing selenium thin-films using laser-annealing as an alternative to the conventionally used thermal annealing strategy. By laser-annealing through a semitransparent substrate, a buried layer of high-quality selenium crystallites is formed and used as a growth template for solid-phase epitaxy. The resulting selenium thin-films feature larger and more preferentially oriented grains with a negligible surface roughness in comparison to thermally annealed selenium thin-films. We fabricate photovoltaic devices using this strategy, and demonstrate a record ideality factor of n=1.37, a record fill factor of FF=63.7%, and a power conversion efficiency of PCE=5.0%. The presented laser-annealing strategy is universally applicable and is a promising approach for crystallizing a wide range of photovoltaic materials where high temperatures are needed while maintaining a low substrate temperature.

cond-mat.mtrl-sci↗

arXiv2020

Experimental and first-principles spectroscopy of Cu$_2$SrSnS$_4$ and Cu$_2$BaSnS$_4$ photoabsorbers

The Cu$_2$BaSnS$_4$ (CBTS) and Cu$_2$SrSnS$_4$ (CSTS) semiconductors have been recently proposed as potential wide band gap photovoltaic absorbers. Although several measurements indicate that they are less affected by band tailing than their parent compound Cu$_2$ZnSnS$_4$, their photovoltaic efficiencies are still low. To identify possible issues, we characterize CBTS and CSTS in parallel by a variety of spectroscopic methods complemented by first-principles calculations. Two main problems are identified in both materials. The first is the existence of deep defect transitions in low-temperature photoluminescence, pointing to a high density of bulk recombination centers. The second is a low electron affinity, which emphasizes the need for an alternative heterojunction partner and electron contact. We also find a tendency for downward band bending at the surface of both materials. In CBTS, this effect is sufficiently large to cause carrier type inversion, which may enhance carrier separation and mitigate interface recombination. Optical absorption at room temperature is exciton-enhanced in both CBTS and CSTS. Deconvolution of excitonic effects yields band gaps that are about 100 meV higher than previous estimates based on Tauc plots. Although the two investigated materials are remarkably similar in an idealized, defect-free picture, the present work points to CBTS as a more promising absorber than CSTS for tandem photovoltaics.

physics.app-ph↗

arXiv2015

SWEEPFINDER2: Increased sensitivity, robustness, and flexibility

SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection, as well as increased flexibility that enables the user to examine genomic regions in greater detail and to specify a fixed distance between test sites. Moreover, SweepFinder2 enables the use of invariant sites for sweep detection, increasing both its power and precision relative to SweepFinder.

q-bio.PE↗

arXiv2014

Error-prone polymerase activity causes multinucleotide mutations in humans

About 2% of human genetic polymorphisms have been hypothesized to arise via multinucleotide mutations (MNMs), complex events that generate SNPs at multiple sites in a single generation. MNMs have the potential to accelerate the pace at which single genes evolve and to confound studies of demography and selection that assume all SNPs arise independently. In this paper, we examine clustered mutations that are segregating in a set of 1,092 human genomes, demonstrating that MNMs become enriched as large numbers of individuals are sampled. We leverage the size of the dataset to deduce new information about the allelic spectrum of MNMs, estimating the percentage of linked SNP pairs that were generated by simultaneous mutation as a function of the distance between the affected sites and showing that MNMs exhibit a high percentage of transversions relative to transitions. These findings are reproducible in data from multiple sequencing platforms. Among tandem mutations that occur simultaneously at adjacent sites, we find an especially skewed distribution of ancestral and derived dinucleotides, with $\textrm{GC}\to \textrm{AA}$, $\textrm{GA}\to \textrm{TT}$ and their reverse complements making up 36% of the total. These same mutations dominate the spectrum of tandem mutations produced by the upregulation of low-fidelity Polymerase $ζ$ in mutator strains of S. cerevisiae that have impaired DNA excision repair machinery. This suggests that low-fidelity DNA replication by Pol $ζ$ is at least partly responsible for the MNMs that are segregating in the human population, and that useful information about the biochemistry of MNM can be extracted from ordinary population genomic data. We incorporate our findings into a mathematical model of the multinucleotide mutation process that can be used to correct phylogenetic and population genetic methods for the presence of MNMs.

q-bio.PE↗

arXiv2013

Natural selection reduced diversity on human Y chromosomes

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

q-bio.PE↗

arXiv2013

A model-based approach for identifying signatures of balancing selection in genetic data

While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two composite likelihood ratio tests for detecting balancing selection. Using simulations, we show that these methods outperform competing methods under a variety of assumptions and demographic models. We apply the new methods to whole-genome human data, and find a number of previously-identified loci with strong evidence of balancing selection, including several HLA genes. Additionally, we find evidence for many novel candidates, the strongest of which is FANK1, an imprinted gene that suppresses apoptosis, is expressed during meiosis in males, and displays marginal signs of segregation distortion. We hypothesize that balancing selection acts on this locus to stabilize the segregation distortion and negative fitness effects of the distorter allele. Thus, our methods are able to reproduce many previously-hypothesized signals of balancing selection, as well as discover novel interesting candidates.

q-bio.PE↗