Related papers: Kinematic Flexibility Analysis: Hydrogen Bonding P…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
We develop a graph-based model of the hydrogen bond network in water, with a view towards quantitatively modeling the molecular-level correlational structure of the network. The networks are formed are studied by the constructing the model…
Soft biological tissues often have complex mechanical properties due to variation in structural components. In this paper, we develop a novel UNet-based neural network model for inversion in elasticity (El-UNet) to infer the spatial…
Mixtures of linear dynamical systems (MoLDS) provide a path to model time-series data that exhibit diverse temporal dynamics across trajectories. However, its application remains challenging in complex and noisy settings, limiting its…
Entangled networks are ubiquitous in tissues, polymers, and fabrics. However, their mechanics remain insufficiently understood due to the complexity of the topological constraints at the network level. Here, we develop a mathematical…
Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and functions. Recently theoretical models have…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Gaussian network model(GNM) and anisotropic network model(ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM(gGNM) and ANM methods and show that the…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
The paper deals with relationships between the individual transmembrane fluxes of binary electrolyte solution components and the experimentally measurable quantities describing rates of transfer processes, namely, the electric current, the…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
This study proposes a novel topology optimization method for unsteady fluid flows induced by actively moving rigid bodies. The key idea of the proposed method is to decouple the design and analysis domains by using separate grids. The…
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…
Over the years, plenty of classical interaction potentials for water have been developed and tested against structural, dynamical and thermodynamic properties. On the other hands, it has been recently observed (F. Martelli et. al,…
The thermodynamics and dynamics of supercooled liquids correlate with their elasticity. In particular for covalent networks, the jump of specific heat is small and the liquid is {\it strong} near the threshold valence where the network…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…