Related papers: Protein Design is a Key Factor for Subunit-subunit…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
Recent advancements in machine learning techniques for protein folding motivate better results in its inverse problem -- protein design. In this work we introduce a new graph mimetic neural network, MimNet, and show that it is possible to…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
Deep generative models show promise for $\textit{de novo}$ protein design, yet reliably producing designs that are geometrically plausible, evolutionarily consistent, functionally relevant, and dynamically stable remains challenging. We…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
We report a surprising hysteretic behavior in the dynamics of a simple one-dimensional nonlinear model inspired by the tribological problem of two sliding surfaces with a thin solid lubricant layer in between. In particular, we consider the…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
Structural damping is known to be approximately rate-independent in many cases. Popular models for rate-independent dissipation are hysteresis models; and a highly popular hysteresis model is the Bouc-Wen model. If such hysteretic…
We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Some general dynamical properties of models for compaction of granular media based on master equations are analyzed. In particular, a one-dimensional lattice model with short-ranged dynamical constraints is considered. The stationary state…