Related papers: Protein Design is a Key Factor for Subunit-subunit…
We investigate contact angle hysteresis on chemically patterned and superhydrophobic surfaces, as the drop volume is quasi-statically increased and decreased. We consider both two, and three, dimensions using analytical and numerical…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
Membrane proteins often form dimers and higher-order oligomers whose stability and spatial organization depend sensitively on their lipid environment. To investigate the physical principles underlying this coupling, we employ a lattice…
We design toy protein mimicking a machine-like function of an enzyme. Using an insight gained by the study of conformation space of compact lattice polymers, we demonstrate the possibility of a large scale conformational rearrangement which…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
The dimer model is the study of random dimer covers (perfect matchings) of a graph. A double-dimer configuration on a graph $G$ is a union of two dimer covers of $G$. We introduce quaternion weights in the dimer model and show how they can…
Achieving long-range ferrimagnetic order in purely organic systems remains a major challenge in molecular magnetism. Here we report the synthesis and characterization of heterospin-coupling motifs, formed by covalently linking spin-1/2 and…
High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pairs, impairing generative model performance. We leverage…
The rates or formation and concentration distributions of a dimer reaction showing hysteresis behavior are examined in an ab initio chemical reaction designed as elementary and where the hysteresis structure precludes the formation of…
We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
We construct lattice gauge theories in which the elements of the link matrices are represented by non-commuting operators acting in a Hilbert space. These quantum link models are related to ordinary lattice gauge theories in the same way as…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
A dynamic wetting problem is studied for a moving thin fiber inserted in fluid and with a chemically inhomogeneous surface. A reduced model is derived for contact angle hysteresis by using the Onsager principle as an approximation tool. The…
Symmetries impose structure on the Hilbert space of a quantum mechanical model. The mathematical units of this structure are the irreducible representations of symmetry groups and I consider how they function as conceptual units of…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…