Related papers: Soliton concepts and the protein structure
Scattering of solitons and dark solitons by potential walls is studied in the nonlinear Schroedinger equation under various conditions. We investigate the conditions under which solitons are split into two solitons at the potential wall. We…
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
Models such as AlphaFold2 and OpenFold have transformed protein structure prediction, yet their inner workings remain poorly understood. We present a methodology to systematically evaluate the contribution of individual OpenFold components…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…
In this paper we perform a numerical study on the interesting phenomenon of soliton reflection of solid walls. We consider the 2D nonlinear Schrodinger equation as the underlying mathematical model and we use an implicit-explicit type…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
The structure of a linear block code is pivotal in defining fundamental properties, particularly weight distribution, and code design. In this study, we characterize the Type II structure of polar codewords with weights less than twice the…
It has been observed that certain classical chains admit topologically protected zero-energy modes that are localized on the boundaries. The static features of such localized modes are captured by linearized equations of motion, but the…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
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…
Using a variational approximation we study discrete solitons of a nonlinear Schroedinger lattice with a cubic-quintic nonlinearity. Using an ansatz with six parameters we are able to approximate bifurcations of asymmetric solutions…
Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further…
Given two binary codes of length n, using Plotkin construction we obtain a code of length 2n. The construction works for linear and nonlinear codes. For the linear case, it is straightforward to see that the dimension of the final code is…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…