Related papers: Sequence Evolution, Structure and Dynamics of Tran…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
The interaction between protons and graphene is attracting a large interest due to recent experiments showing that these charged species permeate through the 2D material following a low barrier (~ 0.8 eV) activated process. A possible…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Recent advances in visual tracking showed that deep Convolutional Neural Networks (CNN) trained for image classification can be strong feature extractors for discriminative trackers. However, due to the drastic difference between image…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…
The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor. The receptor is activated by a small peptide ligand neurotensin. NTSR1 can be expressed in HEK cells by stable transfection. Previously we used the fluorescent…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…
The need of new diagnostic methods satisfying, as an early detection, a low invasive procedure and a cost-efficient value, is orienting the technological research toward the use of bio-integrated devices, in particular bio-sensors. The set…
Serotonin (5-hydroxytryptamine) is a major neurotransmitter whose release from densely distributed serotonergic varicosities shapes plasticity and network integration throughout the brain, yet its extracellular dynamics remain poorly…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
Intrinsic decomposition from a single image is a highly challenging task, due to its inherent ambiguity and the scarcity of training data. In contrast to traditional fully supervised learning approaches, in this paper we propose learning…
In this paper we will review various aspects of the biology of prions and focus on what is currently known about the mammalian PrP prion. Also we briefly describe the prions of yeast and other fungi. Prions are infectious proteins behaving…
We have investigated the influence of the substrate on the fluorescence of adsorbed organic molecules. Monolayer films of perylene-3,4,9,10-tetracarboxylic-3,4,9,10-diimide (PTCDI), a supramolecular network formed from PTCDI and melamine,…
It is commonly believed that electromagnetic spectra of atoms and molecules can be fully described by interactions of electric and magnetic multipoles. However, it has recently become clear that interactions between light and matter also…
Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a…
The interaction of proteins with small molecules is fundamental to their function in living organisms and it is widely studied in drug development. Here we compare optical trapping dynamics of streptavidin and biotinylated streptavidin…
Proline (Pro) is one kind of proteinogenic amino acid and an important signaling molecule in the process of metabolism. Hydroxyproline (Hyp) is a product on Pro oxygen sensing post-translational modification (PTM), which is efficiently…
Recent work has shown an increasing interest in understanding the structure of the endoplasmic reticulum (ER) and how ribosomes are displayed on it. Here we present a model that explains a physical reason for why the cell creates different…