Related papers: Poisson-Boltzmann model for protein-surface electr…
The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…
Atomic diffusion affects the properties of various engineering materials, which predominantly occur in the polycrystalline state. A rigorous description of polycrystalline diffusion must therefore account for crystallographic defects,…
The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor…
We discuss recent investigations of the interaction of polyelectrolytes with proteins. In particular, we review our recent studies on the interaction of simple proteins such as human serum albumin (HSA) or lysozyme with linear…
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…
Elliptic partial differential equations are important both from application and analysis points of views. In this paper we apply the Closest Point Method to solving elliptic equations on general curved surfaces. Based on the closest point…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
Surface sensitive synchrotron x-ray scattering studies were performed to obtain the distribution of monovalent ions next to a highly charged interface. A lipid phosphate (dihexadecyl hydrogen-phosphate) was spread as a monolayer at the…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
This paper presents an efficient high-order sharp-interface method for solving the three-dimensional (3D) Poisson equation with Dirichlet boundary conditions on a nonuniform Cartesian grid with irregular domain boundaries. The new approach…
Predicting favorable protein-peptide binding events remains a central challenge in biophysics, with continued uncertainty surrounding how nonlocal effects shape the global energy landscape. Here, we introduce peripheral surface information…
In this paper we revisit the derivation of boundary conditions for the Boltzmann Equation. The interaction between the wall atoms and the gas molecules within a thin surface layer is described by a kinetic equation introduced in [9] and…
A quantitative understanding of the electromagnetic response of materials is essential for the precise engineering of maximal, versatile, and controllable light--matter interactions. Material surfaces, in particular, are prominent platforms…
The Poisson-Boltzmann mean-field description of ionic solutions has been successfully used in predicting charge distributions and interactions between charged macromolecules. While the electrostatic model of charged fluids, on which the…
We present a simple model for the underlying structure of protein-protein pairwise interaction graphs that is based on the way in which proteins attach to each other in experiments such as yeast two-hybrid assays. We show that data on the…
Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta \Delta G$ data,…
We develop an immersed boundary (IB) method for modeling flows around fixed or moving rigid bodies that is suitable for a broad range of Reynolds numbers, including steady Stokes flow. The spatio-temporal discretization of the fluid…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
Detecting specific target analytes and differentiating them from interfering background effects is a crucial but challenging task in complex multi-component solutions commonly encountered in environmental, chemical, biological, and medical…
This paper tests a dielectric model for variation of hydration free energy with geometry of complex solutes in water. It works out some basic aspects of the theory of boundary integral methods for these problems. One aspect of the…