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The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…
We consider braids with repeating patterns inside arbitrary knots which provides a multi-parametric family of knots, depending on the "evolution" parameter, which controls the number of repetitions. The dependence of knot (super)polynomials…
We discuss the possibility of measuring generalized parton distributions in exclusive electroproduction of mesons off the nucleon and estimate the uncertainty from perturbatively induced higher-twist corrections. We find that, while the…
We present a systematic study of the evolution of the band structure in the Fe-based superconductor family BaFe$_{2-x}$M$_x$As$_2$ (M = Cr, Co, Cu, Ru and Mn) using polarization-dependent angle-resolved photoemission spectroscopy (ARPES).…
Collective plasmon excitations in solids that result from the process of photoemission are an important area of fundamental research. In this study, we identify a significant number ($n$) of multiple bulk plasmons ($n\omega_p$) in the hard…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
The full-potential linear augmented plane-wave calculations have been applied to investigate the systematic change of electronic structures in CaAlSi due to different stacking sequences of AlSi layers. The present ab-initio calculations…
We report new measurements and calculations of the non-resonant inelastic x-ray scattering (NRIXS) from Mg and Al for a wide range of momentum transfers, q. Extended oscillations in the dynamic structure factor S(q,w) due to scattering from…
Animal mitochondrial genomes usually have two transfer RNAs for Leucine: one, with anticodon UAG, translates the four-codon family CUN, whilst the other, with anticodon UAA, translates the two-codon family UUR. These two genes must differ…
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through Position…
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which…
Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events…
Accurate prediction of materials phase diagrams from first principles remains a central challenge in computational materials science. Machine-learning interatomic potentials can provide near-DFT accuracy at a fraction of the cost, but their…
Altermagnetism, as a new branch of magnetism independent of traditional ferromagnetism and antiferromagnetism, has attracted extensive attention recently. At present, researchers have proved several kinds of three-dimensional altermagnets,…
Skull-induced aberrations remain a major drawback of transcranial ultrasound localization microscopy (ULM), degrading sensitivity and spatial accuracy through microbubble mislocalization, false detections, and imaging artifacts, such as…
The development of X-Ray microscopy (XRM) technology has enabled non-destructive inspection of semiconductor structures for defect identification. Deep learning is widely used as the state-of-the-art approach to perform visual analysis…
Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made…
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct…
We consider two-photon exchange (TPE) in the elastic electron-proton scattering and study the contribution arising from the production of Delta(1232) resonance in the intermediate state. We calculate all three TPE amplitudes (generalized…