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A large experimental program is being mounted to search for neutrinoless double-beta decay over the next decade. Multiple experiments using different target isotopes are being prepared to explore the whole parameter space allowed for…
Nonlinear light-matter interactions and their applications are constrained by properties of available materials. The use of metamaterials opens the way to achieve precise control over electromagnetic properties at a microscopic level,…
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
One-dimensional NMR spectroscopy is one of the most widely used techniques for the characterization of organic compounds and natural products. For molecules with up to 36 non-hydrogen atoms, the number of possible structures has been…
Nuclear matrix elements (NMEs) for two-neutrino double-beta decay ($2\nu\beta\beta$) are studied in the framework of relativistic nuclear energy density functional (REDF). The properties of nuclei involved in the decay are obtained using…
Model-driven analysis of biophysical phenomena is gaining increased attention and utility for medical imaging applications. In magnetic resonance imaging (MRI), the availability of well-established models for describing the relations…
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
X-ray microspectroscopic techniques are essential for studying morphological and chemical changes in materials, providing high-resolution structural and spectroscopic information. However, its practical data analysis for reliably retrieving…
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a…
An amino acid insertion or deletion, or InDel, can have profound and varying functional impacts on a protein's structure. InDel mutations in the transmembrane conductor regulator protein for example give rise to cystic fibrosis.…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…