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Polymerization and formation of crosslinked polymer networks are important processes in manufacturing, materials fabrication, and in the case of hydrated polymer networks, synthesis of biomedical materials, drug delivery, and tissue…
Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico…
The spring network model constitutes the backbone in the representations of a host of physical systems. In this work, we report the disturbance-driven microscopic dynamics of an isolated, closed spring network of spherical topology in…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
We present a clear and rigorous derivation of the Ewald-like method for calculation of the electrostatic energy of the systems infinitely periodic in two-dimensions and of finite size in the third dimension (slabs) which is significantly…
In the context of mathematical modeling, it is sometimes convenient to integrate models of different nature. These types of combinations, however, might entail difficulties even when individual models are well-understood, particularly in…
Solvation of ions is ubiquitous on our planet. Solvated ions have a profound effect on the behavior of ionic solutions, which is crucial in nature and technology. Experimentally, ions have been classified into "structure makers" or…
Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…
The neural network method of solving differential equations is used to approximate the electric potential and corresponding electric field in the slit-well microfluidic device. The device's geometry is non-convex, making this a challenging…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
The intermolecular interactions in the title compound are investigated using self-consistent charge density functional based tight binding molecular dynamics. Emphasis is put on the analysis of correlated motions of ion pairs using ideas of…
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…
A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
We present an edge-based framework for the study of geometric elastic network models to model mechanical interactions in physical systems. We use a formulation in the edge space, instead of the usual node-centric approach, to characterise…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
In the present work, a hyperelastic constitutive model based on neural networks is proposed which fulfills all common constitutive conditions by construction, and in particular, is applicable to compressible material behavior. Using…
The dynamics of soft mechanical metamaterials provides opportunities for many exciting engineering applications. Previous studies often use discrete systems, composed of rigid elements and nonlinear springs, to model the nonlinear dynamic…
We consider an elastic/viscoelastic transmission problem for the Bresse system with fully Dirichlet or Dirichlet-Neumann-Neumann boundary conditions. The physical model consists of three wave equations coupled in certain pattern. The system…
We present a theory of the dielectric response of a solution containing large solutes, of a nanometer size, in a molecular solvent. It combines the molecular dipole moment of the solute with the polarization of a large subensemble of…