Related papers: Improvements of the REDCRAFT Software Package
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
Nonnegative Tucker decomposition (NTD) is a powerful tool for the extraction of nonnegative parts-based and physically meaningful latent components from high-dimensional tensor data while preserving the natural multilinear structure of…
The development of systematic effective field theories (EFTs) for nuclear forces and advances in solving the nuclear many-body problem have greatly improved our understanding of dense nuclear matter and the structure of finite nuclei. For…
In nuclear reaction experiments, the measured decay energy spectra can give insights into the shell structure of decaying systems. However, extracting the underlying physics from the measurements is challenging due to detector resolution…
Effective properties of composite materials are defined as the ensemble average of property-specific PDE solutions over the underlying microstructure distributions. Traditionally, predicting such properties can be done by solving PDEs…
The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…
Software systems nowadays are complex and difficult to maintain due to continuous changes and bad design choices. To handle the complexity of systems, software products are, in general, decomposed in terms of packages/modules containing…
LDPC (Low Density Parity Check) codes are among the most powerful and widely adopted modern error correcting codes. The iterative decoding algorithms required for these codes involve high computational complexity and high processing…
Widely employed Near-Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopy probes a system by excitation of core electrons to unoccupied states. A variety of different methodologies are available to simulate corresponding spectra from…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Native shortcut networks (SCN0) are sub-graphs of native protein residue networks (PRN0). In this paper, we propose the Network Dynamics (ND) model, which reconstructs a PRN0 by adding back its edges according to some recipe, while its…
Understanding the fracture mechanisms in composite materials across scales, from nano- to micro-scales, is essential for an in-depth understanding of the reinforcement mechanisms and designing the next generation of lightweight,…
High frame-corruption is widely observed in Long Range Wide Area Networks (LoRaWAN) due to the coexistence with other networks in ISM bands and an Aloha-like MAC layer. LoRa's Forward Error Correction (FEC) mechanism is often insufficient…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
In NMR spectroscopy, undersampling in the indirect dimensions causes reconstruction artifacts whose size can be bounded using the so-called {\it coherence}. In experiments with multiple indirect dimensions, new undersampling approaches were…
Coherent imaging systems, such as medical ultrasound and synthetic aperture radar (SAR), are subject to corruption from speckle due to sub-resolution scatterers. Since speckle is multiplicative in nature, the constituent image regions…
Many images and videos are primarily processed by computer vision algorithms, involving only occasional human inspection. When this content requires compression before processing, e.g., in distributed applications, coding methods must…
Spectroscopy requires high-precision wavelength discrimination but typically requires bulky, alignment-sensitive instrumentation. To address this, we present a compact computational spectrometer built from a single germanium PN photodiode.…