Related papers: On morphological and functional complexity of prot…
Recent developments in deep learning-based methods demonstrated its potential to predict the 3D protein structures using inputs such as protein sequences, Cryo-Electron microscopy (Cryo-EM) images of proteins, etc. However, these methods…
The understanding of protein structure, folding, and interaction with other proteins remains one of the grand challenges of modern biology. Tremendous progress has been made thanks to X-ray- or electron-based techniques that have provided…
We perform event-driven molecular dynamics simulations of a system composed by uniaxial hard ellipsoids for different values of the aspect-ratio and packing fraction . We compare the molecular orientational-dependent structure factors…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, and dual polarization interferometry, etc are indeed very powerful tools to determine the 3D structures of proteins (including the membrane proteins), though they are…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
P-systems are abstract computational models inspired by the phospholipid bilayer membranes generated by biological cells. Illustrated here is a mechanism by which recursive liposome structures (multivesicular liposomes) may be…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
Abundant in nature, colloids also find increasingly important applications in science and technology, ranging from direct probing of kinetics in crystals and glasses to fabrication of third-generation quantum-dot solar cells. Because…
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…
The paper is devoted to the homogenization of porous piezoelectric materials saturated by electrically inert fluid. The solid part of a representative volume element consists of the piezoelectric skeleton with embedded conductors. The pore…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…
We study the self-assembly of colloidal microgel particles at a quasi-two-dimensional air-water interface of a drying droplet. Using bright-field microscopy, we demonstrate that increasing particle elasticity drives interfacial organization…
Soft particulate gels include materials we can eat, squeeze, or 3D print. From foods to bio-inks to cement hydrates, these gels are composed of a small amount of particulate matter (proteins, polymers, colloidal particles, or agglomerates…
The design of complex materials and the formation of specific patterns often arise from the properties of the individual building blocks. In this respect, colloidal systems offer a unique opportunity because nowadays they can be synthesized…
We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic…
The aggregation of protein-stabilised emulsions leads to the formation of emulsion gels. These soft solids are classically envisioned as droplet-filled matrices. Here however, it is assumed that protein-coated sub-micron droplets contribute…