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Rigidity, arising in discrete geometry, is the property of a structure that does not flex. Laman provides a combinatorial characterization of rigid graphs in the Euclidean plane, and thus rigid graphs in the Euclidean plane have…
Nonlinear contraction theory is a comparatively recent dynamic control system design tool based on an exact differential analysis of convergence, in essence converting a nonlinear stability problem into a linear time-varying stability…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
Cycle packing is a fundamental problem in optimization, graph theory, and algorithms. Motivated by recent advancements in finding vertex-disjoint paths between a specified set of vertices that either minimize the total length of the paths…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
In this paper, we design and analyze a Hybrid-High Order (HHO) approximation for a class of quasilinear elliptic problems of nonmonotone type. The proposed method has several advantages, for instance, it supports arbitrary order of…
Packing problems, which ask how to arrange a collection of objects in space to meet certain criteria, are important in a great many physical and biological systems, where geometrical arrangements at small scales control behaviour at larger…
Lattice protein folding models are a cornerstone of computational biophysics. Although these models are a coarse grained representation, they provide useful insight into the energy landscape of natural proteins. Finding low-energy…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
Theoretical quest of flat-band tight-binding models usually relies on lattice structures on which electrons reside. Typical examples of candidate lattice structures include the Lieb-type lattices and the line graphs. Meanwhile, there can be…
We study Clustered Planarity with Linear Saturators, which is the problem of augmenting an $n$-vertex planar graph whose vertices are partitioned into independent sets (called clusters) with paths - one for each cluster - that connect all…
We establish recursions counting various classes of chains in the noncrossing partition lattice of a finite Coxeter group. The recursions specialize a general relation which is proven uniformly (i.e. without appealing to the classification…
We study the topological structure of random geometric forests $G$ in the Euclidean plane under mild assumptions: non-crossing edges, stationarity, and finite edge intensity. The framework covers a broad range of constructions, including…
We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost…
Indentation is a common experimental technique to study the mechanics of polymeric materials. The main advantage of using indentation is because this provides a direct correlation between the microstructure and the small-scale mechanical…
In this paper, we investigate rigid-ruling folding motions of crease-rule patterns, that is, conjugacy-preserving isometries of developable semi-discrete conjugate nets. We derive two conditions for the rigid-ruling foldability of pairs of…