Related papers: Protein Design is a Key Factor for Subunit-subunit…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the…
Symmetry is closely intertwined with the function, genetics, and chemical properties of multiprotein complexes. Here, we explore the relation between structural symmetry and the ability of membrane proteins to sense and induce membrane…
Molecular dimers are widely utilized as a tool to investigate the structure-property relationships behind the complex photophysical processes of condensed-phase systems, where structural tuning remains a challenge. This approach often…
We propose an experimental protocol for using cold atoms to create and probe quantum dimer models, thereby exploring the Pauling-Anderson vision of a macroscopic collection of resonating bonds. This process can allow the study of exotic…
A self-interacting polymer with one end attached to a sticky surface has been studied by means of a flat-histogram stochastic growth algorithm known as FlatPERM. We examined the four-dimensional parameter space of the number of monomers up…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
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 aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
We derive and analyze a novel approach for modeling and computing the mechanical relaxation of incommensurate 2D heterostructures. Our approach parametrizes the relaxation pattern by the compact local configuration space rather than real…
Shape Memory Alloys (SMAs) are a class of smart materials that exhibit a macroscopic contraction of up to 5% when heated via an electric current. This effect can be exploited for the development of novel unconventional actuators. Despite…
The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
In this work we develop a theory of interaction of randomly patterned surfaces as a generic prototype model of protein-protein interactions. The theory predicts that pairs of randomly superimposed identical (homodimeric) random patterns…
For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Contact unit size reduction is a widely studied mechanism as a means to improve adhesion in natural fibrillar systems, such as those observed in beetles or geckos. However, these animals also display complex structural features in the way…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…