Related papers: Simultaneous identification of multiple binding si…
Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the…
Protein adsorption at the solid-liquid interface is an important phenomenon that often can be observed as a first step in biological processes. Despite its inherent importance, still relatively little is known about the underlying…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…
An original spectral study of the compressible hybrid lattice Boltzmann method (HLBM) on standard lattice is proposed. In this framework, the mass and momentum equations are addressed using the lattice Boltzmann method (LBM), while finite…
To accurately model the electron density and polarization, a polarizable multipole (PM) model using the AMOEBA force field has been introduced \cite{Ren:2003, Shi:2013} recently. In the AMOEBA force field, the traditional point atomic…
We review the standard lock and key (LK) model for binding small ligands to larger adsorbent molecule. We discuss three levels of the traditional LK model for binding. Within this model the binding constant or the Gibbs energy of the…
Ionic liquids (ILs) feature a tailorable and wide range of structural, chemical and electronic properties that make this class of materials suitable to a broad variety of forefront applications in next-generation electronics. Yet, their…
Understanding intrusion and extrusion in nanoporous materials is a challenging multiscale problem of utmost importance for applications ranging from energy storage and dissipation to water desalination and hydrophobic gating in ion…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
We investigate the coupled dynamics of charge and energy in interacting lattice models with dipole conservation. We formulate a generic hydrodynamic theory for this combination of fractonic constraints and numerically verify its…
We address protein structure prediction in the 3D Hydrophobic-Polar lattice model through two novel deep learning architectures. For proteins under 36 residues, our hybrid reservoir-based model combines fixed random projections with…
Strongly interacting dipolar bosons in optical lattices exhibit diverse quantum phases that are rich in physics. As the strength of the long-range boson-boson interaction increases, the system transitions across different phases: from a…
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
We develop a phenomenological vector model of polar liquids capable to describe aqueous interactions of macroscopic bodies. It is shown that a strong, long-range and orientationally dependent interaction between macroscopic objects appears…
Biological membranes are self-assembled complex fluid interfaces that host proteins, molecular motors and other macromolecules essential for cellular function. These membranes have a distinct in-plane fluid response with a surface viscosity…
When a highly charged globular macromolecule, such as a dendritic polyelectrolyte or charged nanogel, is immersed into a physiological electrolyte solution, monovalent and divalent counterions from the solution bind to the macromolecule in…
A novel statistical model for the cooperative binding of monomeric ligands to a linear lattice is developed to study the interaction of ionic surfactant molecules with flexible polyion chain in dilute solution. Electrostatic binding of a…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…