Related papers: Sampling the proteome by emerging single-molecule …
Leukemia, the cancer of blood cells, originates in the blood-forming cells of the bone marrow. In Chronic Myeloid Leukemia (CML) conditions, the cells partially become mature that look like normal white blood cells but do not resist…
We extend the generating function technique for calculation of single molecule photon emission statistics [Y. Zheng and F. L. H. Brown, Phys. Rev. Lett., 90,238305 (2003)] to systems governed by multi-level quantum dynamics. This opens up…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
One strategy to scale up ML-driven science is to increase wet lab experiments' information density. We present a method based on a neural extension of compressed sensing to function space. We measure the activity of multiple different…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Sequence coverage in MS analysis of protein digestion-derived peptides is a key issue for detailed characterization of proteins or identification at low quantities. In gel-based proteomics studies, the sequence coverage greatly depends on…
When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…
Imaging mass spectrometry (IMS) has transformed proteomics by providing an avenue for collecting spatially distributed molecular data. Mass spectrometry data acquired with matrix assisted laser desorption ionization (MALDI) IMS consist of…
Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for…
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.…
Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed…
Large language models (LLMs) have shown promise in various natural language processing tasks, including their application to proteomics data to classify protein fragments. In this study, we curated a limited mass spectrometry dataset with…
Single-molecule tracking (SMT) methods are under considerable expansion in many fields of cell biology, as the dynamics of cellular components in biological mechanisms becomes increasingly relevant. Despite the development of SMT…
Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. Hence, there is an imperative to…
Mitochondria are complex organelles, and their proteomics analysis requires a combination of techniques. The emphasis in this chapter is made first on mitochondria preparation from cultured mammalian cells, then on the separation of the…