相关论文: Probing protein orientation near charged nanosurfa…
Direct observation of single-molecule interactions and dynamic configurations in situ is a demanding challenge but crucial for both chemical and biological systems. However, optical microscopy that relies on bulk measurements cannot meet…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Researchers are currently exploring nanoporous two-dimensional materials, such as hexagonal boron nitride (hBN), as potential desalination membranes. Here, we study the effect of grain boundaries (GBs) and interfacial electrostatic…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
The contribution of electrostatic interactions to the free energy of binding between model protein and a ceramic implant surface in the aqueous solvent, considered in the framework of the non-local electrostatic model, is calculated as a…
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…
Polarized neutron diffraction allows to determine the local susceptibility tensor on the magnetic site both in single crystals and powders. It is widely used in the studies of single crystals, but it is still hardly applicable to a number…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete…
Nanopore sensing is a key technology for single-molecule detection and analysis. Solid-state nanopores have emerged as a versatile platform, since their fabrication allows to engineer their properties by controlling size, shape, and…
We demonstrated a biosensing approach which, for the first time, combines the high-sensitivity of whispering gallery modes (WGM) with a metallic nanoparticle based assay. We provided a computational model based on generalized Mie theory to…
Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
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…
One key task in virtual screening is to accurately predict the binding affinity ($\triangle$$G$) of protein-ligand complexes. Recently, deep learning (DL) has significantly increased the predicting accuracy of scoring functions due to the…
An exact, analytic solution for a simple electrostatic model applicable to biomolecular recognition is presented. In the model, a layer of high dielectric constant material (representative of the solvent, water) whose thickness may vary…
The solvation of charged, nanometer-sized spherical solutes in water, and the effective, solvent-induced force between two such solutes are investigated by constant temperature and pressure Molecular Dynamics simulations of model solutes…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…