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Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently…
Systems biology of plants offers myriad opportunities and many challenges in modeling. A number of technical challenges stem from paucity of computational methods for discovery of the most fundamental properties of complex dynamical…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex…
Main path analysis has long been used to trace knowledge trajectories in citation networks, yet it lacks solid theoretical foundations. To understand when and why this approach succeeds, we analyse directed acyclic graphs created from two…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
While deep learning has revolutionized the prediction of rigid protein structures, modelling the conformational ensembles of Intrinsically Disordered Proteins (IDPs) remains a key frontier. Current AI paradigms present a trade-off: Protein…
Modularity is a popular metric for quantifying the degree of community structure within a network. The distribution of the largest eigenvalue of a network's edge weight or adjacency matrix is well studied and is frequently used as a…
This paper introduces some tools from graph theory and distributed consensus algorithms to construct an optimal, yet robust, hierarchical information sharing structure for large-scale decision making and control problems. The proposed…
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
We interpret the subgraph centrality as the partition function of a network. The entropy, the internal energy and the Helmholtz free energy are defined for networks and molecular graphs on the basis of graph spectral theory. Various…
We consider a broad class of walk-based, parameterized node centrality measures for network analysis. These measures are expressed in terms of functions of the adjacency matrix and generalize various well-known centrality indices, including…
It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…
The theoretical investigation of gas adsorption, storage, separation, diffusion and related transport processes in porous materials relies on a detailed knowledge of the potential energy surface of molecules in a stationary environment. In…
A stabilized version of the fundamental solution method to catch ill-conditioning effects is investigated with focus on the computation of complex-valued elastic interior transmission eigenvalues in two dimensions for homogeneous and…
Background and Objectives: The mechanics of the nucleus depends on cellular structures and architecture, and impact a number of diseases. Nuclear mechanics is yet rather complex due to heterogeneous distribution of dense heterochromatin and…
One of the most promising technologies for next-generation wireless networks is integrated communication and sensing (ISAC). It is considered a key enabler for applications that require both enhanced communication and accurate sensing…