相关论文: Poisson-Boltzmann model for protein-surface electr…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
This paper develops a computational framework with unfitted meshes to solve linear piezoelectricity and flexoelectricity electromechanical boundary value problems including strain gradient elasticity at infinitesimal strains. The high-order…
To better understand protein-solvent interaction we have analyzed a variety of physical and geometrical properties of the solvent-excluded surfaces (SESs) over a large set of soluble proteins with crystal structures. We discover that all…
In this paper we propose a computational framework for the investigation of the correlated motion between positive and negative ions exposed to the attraction of a bubble surface that mimics the (oscillating) cell membrane. The correlated…
We present an approximate method for calculating the electrostatic free energy of concentrated protein solutions. Our method uses a cell model and accounts for both the coulomb energy and the entropic cost of Donnan salt partitioning. The…
Thermodynamic properties of charge-stabilised colloidal suspensions are commonly modeled by implementing the mean-field Poisson-Boltzmann (PB) theory within a cell model. This approach models a bulk system by a single macroion, together…
Implicit shape representation, such as SDFs, is a popular approach to recover the surface of a 3D shape as the level sets of a scalar field. Several methods approximate SDFs using machine learning strategies that exploit the knowledge that…
For multispecies ions, we study boundary layer solutions of charge conserving Poisson-Boltzmann (CCPB) equations [50] (with a small parameter \k{o}) over a finite one-dimensional (1D) spatial domain, subjected to Robin type boundary…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
Egocentric interaction perception is one of the essential branches in investigating human-environment interaction, which lays the basis for developing next-generation intelligent systems. However, existing egocentric interaction…
Motivated by experimentally observed biocompatibility enhancement of nanoengineered cubic zirconia ZrO2 coatings to mesenchymal stromal cells, we have carried out computational analysis of the initial immobilization of one of known…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
Tailoring the functional properties of advanced organic/inorganic heterogeonous devices to their intended technological applications requires knowledge and control of the microscopic structure inside the device. Atomistic quantum mechanical…
Expanding the scope of graph-based, deep-learning models to noncovalent protein-ligand interactions has earned increasing attention in structure-based drug design. Modeling the protein-ligand interactions with graph neural networks (GNNs)…
We extend our previous study of surface tension of ionic solutions and apply it to the case of acids (and salts) with strong ion-surface interactions. These ion-surface interactions yield a non-linear boundary condition with an effective…
The accurate determination of electron properties is fundamental to low-temperature plasma simulations, necessitating precise solutions to the spatially inhomogeneous electron Boltzmann equation (EBE). This work explores the use of…
In this work a dynamical system approach is taken to systematically investigate the one-dimensional classical Poisson-Boltzmann (PB) equation with various boundary conditions. This framework, particularly, the phase space portrait, has a…
Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device. The importance of orientation dependent interactions…