Related papers: Poisson-Boltzmann model for protein-surface electr…
The complexity of biomolecular interactions necessitates advanced methodologies to accurately capture their behavior in solution. In this work, we focus on monoclonal antibodies and adopt a multi-scale coarse-graining strategy for their…
A partial differential equation (PDE) was developed to describe time-dependent ligand-receptor interactions for applications in biosensing using field effect transistors (FET). The model describes biochemical interactions at the sensor…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
A variational approach is used to develop a robust numerical procedure for solving the nonlinear Poisson-Boltzmann equation. Following Maggs et al., we construct an appropriate constrained free energy functional, such that its…
Protein function is executed at the molecular surface, where shape and chemistry act together to govern interaction. Yet most comparison methods treat these aspects separately, privileging either global fold or local descriptors and missing…
In this article, we develop goal-oriented error indicators to drive adaptive refinement algorithms for the Poisson-Boltzmann equation. Empirical results for the solvation free energy linear functional demonstrate that goal-oriented…
We have demonstrated a prototypical hybrid classical and quantum computational workflow for the quantification of protein-ligand interactions. The workflow combines the Density Matrix Embedding Theory (DMET) embedding procedure with the…
A half-space problem of a linear kinetic equation for gas molecules physisorbed close to a solid surface, relevant to a kinetic model of gas-surface interactions and derived by Aoki et al. [K.~Aoki et al., in: Phys. Rev. E 106:035306,…
Extensive molecular dynamics simulations reveal that the interactions between proteins and poly(ethylene glycol)(PEG) can be described in terms of the surface composition of the proteins. PEG molecules accumulate around non-polar residues…
Protein structure is central to biological function, and enabling multimodal protein models requires joint reasoning over sequence, structure, and function. A key barrier is the lack of principled protein structure tokenizers (PSTs):…
The properties of ionic solutions between charged surfaces are often studied within the Poisson-Boltzmann framework, by finding the electrostatic potential profile. For example, the osmotic pressure between two charged planar surfaces can…
Most organic and inorganic surfaces (e.g., glass, nucleic acids or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces. Stacks of like-charged…
Molecular-scale interactions between solvated macromolecules and solid surfaces govern a large number of processes, from biology to engineering. Yet, despite extensive characterization at the macroscopic level, our molecular understanding…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
The Poisson-Boltzmann (PB) theory is extensively used to gain insight on charged colloids and biological systems as well as to elucidate fundamental properties of intermolecular forces. Many works were devoted in the past to study PB…
Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking…
We investigate doping of a single-layer graphene in the presence of electrolytic top gating. The interfacial phenomena is modeled using a modified Poisson-Boltzmann equation for an aqueous solution of simple salt. We demonstrate both the…