Related papers: Towards proteinoid computers
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Photonic molecules, named by analogy with chemical molecules, are clusters of closely located electromagnetically interacting microcavities or "photonic atoms". As two or several microcavities are brought close together, their optical modes…
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…
It is well known that lipid membranes respond to a threshold transmembrane electric field through a reversible mechanism called electroporation, where hydrophilic water pores form across the membrane, an effect widely used in biological…
The use of biomaterials - with techniques such as DNA-directed assembly or bio-directed synthesis - can surpass top-down fabrication techniques in creating plasmonic superstructures, in terms of spatial resolution, range of functionality…
We consider nucleation of amyloid fibrils in the case when the process occurs by the mechanism of direct polymerization of practically fully extended protein segments, i.e. beta-strands, into beta-sheets. Applying the classical nucleation…
We introduce a simplified protein model where the water degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover both the warm and the cold protein denaturation within a…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly.…
Proteinaceous aggregation occurs through self-assembly-- a process not entirely understood. In a recent article [1], an analytical theory for amyloid fibril growth via secondary rather than primary nucleation was presented. Remarkably, with…
The canonical thermodynamic model has been used frequently to describe the disassembly of hot nuclear matter consisting of neutrons and protons. Such matter is formed in intermediate energy heavy ion collisions. Here we extend the method to…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion…
The revolution in artificial intelligence (AI) brings up an enormous storage and data processing requirement. Large power consumption and hardware overhead have become the main challenges for building next-generation AI hardware. To…
A predictive model for the evolution of porous Ge layer upon thermal treatment is reported. We represent an idealized etched dislocation core as an axially symmetric elongated hole and computed its dynamics during annealing. Numerical…
We examine changes in the molecular abundances resulting from increased heating due to a self-luminous planetary companion embedded within a narrow circumstellar disk gap. Using 3D models that include stellar and planetary irradiation, we…
Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose…
Using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins.…
A cold electron beam propagating through a background plasma is subject to filamentation process due to theWeibel instability. If the initial beam radius is large compared with the electron skin depth and the beam density is much smaller…