Related papers: Liquid chromatography mass spectrometry-based prot…
Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a critical analytical technique for molecular identification across metabolomics, environmental chemistry, and chemical forensics. A variety of computational methods have emerged…
Electrophoretic separations of proteins are widely used in proteomic analyses, and rely heavily on SDS electrophoresis. This mode of separation is almost exclusively used when a single dimension separation is performed, and generally…
Determining the adsorption isotherms is an issue of significant importance in preparative chromatography. A modern technique for estimating adsorption isotherms is to solve an inverse problem so that the simulated batch separation coincides…
Owing to the complexity of higher eukaryotic cells, a complete proteome is likely to be very difficult to achieve. However, advantage can be taken of the cell compartmentalization to build organelle proteomes, which can moreover be viewed…
We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…
Two-dimensional mass spectrometry (2D MS) is a method for tandem mass spectrometry that enables the correlation between precursor and fragment ions without the need for ion isolation. On a Fourier transform ion cyclotron resonance mass…
A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance…
Small molecules in biological samples are studied to provide information about disease states, environmental toxins, natural product drug discovery, and many other applications. The primary window into the composition of small molecule…
Protein sequences are abundant in repeating segments, both as exact copies and as approximate segments with mutations. These repeats are important for protein structure and function, motivating decades of algorithmic work on repeat…
In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…
Optical sensors offer precision, remote read-out, and immunity to electromagnetic interference but face adoption challenges due to complex and costly readout instrumentation, mostly based on high-resolution. This article challenges the…
Proteins are arguably the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analysing biomolecules such as proteins at single-molecule level.…
Aerosols found in the atmosphere affect the climate and worsen air quality. To mitigate these adverse impacts, aerosol formation and aerosol chemistry in the atmosphere need to be better mapped out and understood. Currently, mass…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
Introduced more than fifty years ago, dynamic light scattering is routinely used to determine the size distribution of colloidal suspensions, as well as of macromolecules in solution, such as proteins, nucleic acids, and their complexes.…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
Diffusion coefficient measurements are important for many biological and material investigations, such as particle dynamics, kinetics, and size determinations. Amongst current measurement methods, single particle tracking (SPT) offers the…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…