相关论文: Poisson-Boltzmann model for protein-surface electr…
Protein-protein interactions (PPIs) are fundamental for deciphering cellular functions,disease pathways,and drug discovery.Although existing neural networks and machine learning methods have achieved high accuracy in PPI prediction,their…
We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but…
Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a…
In biomimetic and biological systems, interactions between surfaces are often mediated by adhesive molecules, nanoparticles, or colloids dispersed in the surrounding solution. We present here a general, statistical-mechanical model for two…
We implemented a nanoelectronic interface between graphene field effect transistors (FETs) and soluble proteins. This enables production of bioelectronic devices that combine functionalities of the biomolecular and inorganic components. The…
Colloid models have frequently been used to successfully describe the influence of protein-protein interactions on antibody solution properties, but they suffer from inherent problems due to the anisotropic shape of the particles. The net…
Generative models offer a direct way of modeling complex data. Energy-based models attempt to encode the statistical correlations observed in the data at the level of the Boltzmann weight associated with an energy function in the form of a…
The electric double layer structure in an electrolyte close to a solid substrate near the three-phase contact line is approximated by considering the linearized Poisson-Boltzmann equation in a wedge geometry. The mathematical approach…
A nonlinear Poisson--Boltzmann equation with transmission boundary conditions at the interface between two materials is investigated. The model describes the electrostatic potential generated by a vector of ion concentrations in a periodic…
Ionic microgels are soft colloidal particles, composed of crosslinked polymer networks, that ionize and swell when dispersed in a good solvent. Swelling of these permeable, compressible particles involves a balance of electrostatic,…
Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
Accurate prediction of protein active-site structures remains a central challenge in structural biology, particularly for short and flexible peptide fragments where conventional and simulation-based methods often fail. Here, we present a…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
We study the ionic distribution near a charged surface. A new method for performing Monte Carlo simulations in this geometry is discussed. A theory is then presented that allows us to accurately reproduce the density profiles obtained in…
The electrostatic interaction between two non-identical, moderately charged colloids situated in close proximity of each other at a fluid interface is studied. By resorting to a well-justified model system, this problem is analytically…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
Kinetic theories constitute one of the most promising tools to decipher the characteristic spatio-temporal dynamics in systems of actively propelled particles. In this context, the Boltzmann equation plays a pivotal role, since it provides…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…