Related papers: Comparative analysis of rigidity across protein fa…
Generative machine learning models are increasingly being used to design novel proteins for therapeutic and biotechnological applications. However, the current methods mostly focus on the design of proteins with a fixed backbone structure,…
The rigorous convergence analysis of adaptive finite element methods for regularized variational models of quasi-static brittle fracture in strain-limiting elastic solids is presented. This work introduces two novel adaptive mesh refinement…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
Recent interest for the development of high-temperature gas reactors has increased the need for more advanced understanding of flow characteristics in randomly packed pebble beds. A proper understanding of these flow characteristics can…
Accurately determining a change in protein binding affinity upon mutations is important for the discovery and design of novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations…
Using a recently developed algorithm for generic rigidity of two-dimensional graphs, we analyze rigidity and connectivity percolation transitions in two dimensions on lattices of linear size up to L=4096. We compare three different…
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…
The paper presents a new stiffness modelling method for multi-chain parallel robotic manipulators with flexible links and compliant actuating joints. In contrast to other works, the method involves a FEA-based link stiffness evaluation and…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…
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…
Soft-granular media, such as dense emulsions, foams or tissues, exhibit either fluid- or solid-like properties depending on the applied external stresses. Whereas bulk rheology of such materials has been thoroughly investigated, the…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…
The influence of structural constraints on the relaxation dynamics of three polyurea networks with varying degree of crosslinking, has been studied by means of a thorough analysis of broadband dielectric spectroscopy measurements. Two…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
We study the elastic response of rigid, wire frame particles in concentrated, glassy suspensions to a step strain by applying the simple, geometric methods developed in part I. The wire frame particles are comprised of thin, rigid rods of…
Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…
Hydrogen bonds and other non-covalent interactions play a crucial role in maintaining the structural integrity and functionality of biological macromolecules such as proteins and nucleic acids. Accurate identification and analysis of these…