Related papers: Mean-Field HP Model, Designability and Alpha-Helic…
Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small:…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
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…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
We present a dual optimization concept of predicting optimal sequences as well as optimal folds of off-lattice protein models in the context of multi-scale modeling. We validate the utility of the recently introduced hidden-force Monte…
We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Self-assembled monolayers of polyalanine $\alpha$-helices exhibit distinct structural phases with implications for chiral-induced spin selectivity. We combine scanning tunneling microscopy and theoretical modeling to reveal how chiral…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
We study two designed and one natural zinc-finger peptide each with the Cys2His2 (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue…
We study the thermodynamical properties of a topology-based model proposed by Galzitskaya and Finkelstein for the description of protein folding. We devise and test three different mean-field approaches for the model, that simplify the…
Protein representation and potential function are essential ingredients for studying proteins folding and protein prediction. We introduce a novel geometric representation of contact interactions using the edge simplices from alpha shape of…
The major histocompatibility complex (MHC) class-I pathway supports the detection of cancer and viruses by the immune system. It presents parts of proteins (peptides) from inside a cell on its membrane surface enabling visiting immune cells…
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein…
Finite mixture models are fitted to spherical data. Kent distributions are used for the components of the mixture because they allow considerable flexibility. Previous work on such mixtures has used an approximate maximum likelihood…