相关论文: Poisson-Boltzmann model for protein-surface electr…
The Poisson Boltzmann equation is known for its success in describing the Debye layer that arises from the charge separation phenomenon at the silica/water interface. However, by treating only the mobile ionic charges in the liquid, the…
The possibility to control electrokinetic transport through carbon and hexagonal boron nitride (hBN) nanotubes has recently opened new avenues for nanofluidic approaches to face outstanding challenges such as energy production and…
Electrostatic interactions fundamentally govern the structure, stability, and dynamics of charged (bio)matter, yet the impact of heterogeneous and anisotropic charge distributions on the behavior of protein solutions remains elusive. Here,…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…
Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models…
We present a fast and accurate method to calculate the electrostatic energy and forces of interacting particles with the boundary conditions appropriate to surfaces, i.e periodic in the two directions parallel to the surface and free in the…
In this thesis, the electrostatic interaction between two chemically identical colloids, both carrying constant surface potential is studied in the limit of short inter-particle separation at the interface of two immiscible fluids. Using an…
The Boltzmann transport equation (BTE) with electron-phonon (e-ph) interactions computed from first principles is widely used to study electronic transport and nonequilibrium dynamics in materials. Calculating the e-ph collision integral is…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
The Poisson-Boltzmann equation is widely used to model molecular electrostatics; however, it is usually solved in linearised form because the sinh nonlinearity is challenging, limiting its applicability in highly charged systems such as…
The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
Molecular surface representations have been advertised as a great tool to study protein structure and functions, including protein-ligand binding affinity modeling. However, the conventional surface-area-based methods fail to deliver a…
We present an accurate and efficient algorithm to calculate the electrostatic interaction of charged point particles with partially periodic boundary conditions that are confined along the nonperiodic direction by two metallic parallel…
We present an explicit solver of the three-dimensional screened and unscreened Poisson's equation which combines accuracy, computational efficiency and versatility. The solver, based on a mixed plane-wave / interpolating scaling function…
When solid surfaces are immersed in aqueous solutions, some of their charges can dissociate and leave behind charge patches on the surface. Although the charges are distributed heterogeneously on the surface, most of the theoretical models…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…