Related papers: Strong Traces Model of Self-Assembly Polypeptide S…
Cooperative self-assembly can result in complex nano-networks with new hyperbolic geometry. However, the relation between the hyperbolicity and spectral and dynamical features of these structures remains unclear. Using the model of…
Traces and their extension called combined traces (comtraces) are two formal models used in the analysis and verification of concurrent systems. Both models are based on concepts originating in the theory of formal languages, and they are…
A graph H is strongly immersed in G if H is obtained from G by a sequence of vertex splittings (i.e., lifting some pairs of incident edges and removing the vertex) and edge removals. Equivalently, vertices of H are mapped to distinct…
The strain induced pseudo-magnetic field in supported graphene deposited on top of a nanostructured substrate is investigated by using atomistic simulations. Step, elongated trench, one dimensional barrier, spherical bubbles, Gaussian bump…
Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibit excellent stability and affinity. Although deep generative…
The thriving area of synthetic carbon allotropes witnesses theoretic proposals and experimental syntheses of many new two-dimensional ultrathin structures, which are often achieved by careful arrangement of non-hexagon $\mathrm{sp^2}$…
Many physical systems can be best understood as sets of discrete data with associated relationships. Where previously these sets of data have been formulated as series or image data to match the available machine learning architectures,…
We propose a novel probabilistic dimensionality reduction framework that can naturally integrate the generative model and the locality information of data. Based on this framework, we present a new model, which is able to learn a smooth…
Porous graphene (PG) is a graphene derivative endowed of nanoporous architectures. This material possesses a particular structure with interconnected networks of high pore volume, producing membranes with a large surface area. Experiments…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
Computational and machine learning approaches to model the conformational landscape of macrocyclic peptides have the potential to enable rational design and optimization. However, accurate, fast, and scalable methods for modeling macrocycle…
Readily synthesizable nano-graphene and poly ethylene glycol based stable gels have been synthesized employing an easy refluxing method and exhaustive rheological and viscoelastic characterizations have been performed to understand the…
Deep learning has received much attention lately due to the impressive empirical performance achieved by training algorithms. Consequently, a need for a better theoretical understanding of these problems has become more evident in recent…
In social networks the {\sc Strong Triadic Closure} is an assignment of the edges with strong or weak labels such that any two vertices that have a common neighbor with a strong edge are adjacent. The problem of maximizing the number of…
Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…
Weighted digraphs are used to model a variety of natural systems and can exhibit interesting structure across a range of scales. In order to understand and compare these systems, we require stable, interpretable, multiscale descriptors. To…
We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters we…
Persistent homology (PH) has been widely applied to graph data to extract topological features. However, little attention has been paid to how different distance functions on a graph affect the resulting persistence barcodes and their…
Peptides offer great biomedical potential and serve as promising drug candidates. Currently, the majority of approved peptide drugs are directly derived from well-explored natural human peptides. It is quite necessary to utilize advanced…
Graph pattern matching is often defined in terms of subgraph isomorphism, an NP-complete problem. To lower its complexity, various extensions of graph simulation have been considered instead. These extensions allow pattern matching to be…