Related papers: Predicting the orientation of adsorbed proteins st…
We propose a machine-learning method for evaluating the potential barrier governing atomic transport based on the preferential selection of dominant points for the atomic transport. The proposed method generates numerous random samples of…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
The electrostatic contribution to spontaneous membrane curvature is calculated within Poisson-Boltzmann theory under a variety of assumptions and emphasizing parameters in the physiological range. Asymmetric surface charges, either fixed…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
The possibility for proteins to aggregate in different superstructures, i.e. large-scale polymorphism, has been widely observed, but an understanding of the physico-chemical mechanisms behind it is still out of reach. Here we present a…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
We present a model for Desorption Induce by (Multiple) Electronic Transitions (DIET/DIMET) based on potential energy surfaces calculated with the Delta Self-Consistent Field extension of Density Functional Theory. We calculate potential…
Accurate and efficient simulation of excited state properties is an important and much aspired cornerstone in the study of adsorbate dynamics on metal surfaces. To this end, the recently proposed linear expansion \Delta Self-Consistent…
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…
The theoretical investigation of gas adsorption, storage, separation, diffusion and related transport processes in porous materials relies on a detailed knowledge of the potential energy surface of molecules in a stationary environment. In…
We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on a metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide…
The influence of the chain degree of ionization on the adsorption of weak polyelectrolytes on neutral and on oppositely and likely charged surfaces is investigated for the first time, by means of Monte Carlo simulations with the mesoscopic…
In this work, protein-surface interactions were probed in terms of adsorption and desorption of a model protein, bovine serum albumin, on a low-fouling surface with single-molecule localization microscopy. Single-molecule experiments enable…
Within the Poisson-Boltzmann (PB) approach electrolytes in contact with planar, spherical, and cylindrical electrodes are analyzed systematically. The dependences of their capacitance $C$ on the surface charge density $\sigma$ and the ionic…
Predicting the adsorption affinity of a small molecule to a target surface is of importance to a range of fields, from catalysis to drug delivery and human safety, but a complex task to perform computationally when taking into account the…
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…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…