Abstract. In this article, we propose a model describing the transport of trapped particles in a surface potential. The potential confines particles close to the surface increasing the number of surface collisions. First, we consider the case of non charged particles. From a kinetic description, we rigorously derive a two dimensional Boltzmann equation. In the case of charged particles we intro...

The Epstein-Barr virus determinant peptide EENLLDFVRF shows high immunogenicity when presented by HLA-B*4405 allotype. This fact is accompanied by a cis-trans isomerization of the Leu5-Asp6 peptide bond upon TCR binding of the pMHC complex. Molecular dynamics simulations of pMHC/TCR structures, with the EENLLDFVRF peptide in cis and trans conformations have been employed in order to examine the...

The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes in proteins in different salt solutions. We demonstrate the existence of ion-specific attractive double-layer forces between neutral hydrophobic and hydrophilic surfaces in the presence of certain salt solutions. This is performed by solving a generalized...

SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a ...

The normal intersurface forces between nanosized probe tips functionalized with COO-- and NH3+-terminated alkanethiol self-assembling monolayers and dense polycrystalline phase pure synthetic hydroxyapatite (HA) were measured via a powerful nanomechanical technique called chemically specific high-resolution force spectroscopy. The data taken on approach of the probe tip to the HA surface was co...

This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with polarizable model, a particular boundary-element approach to problem defined by Poisson or Poisson–Boltzmann equation, but that moniker belies diversity available methods. work reviews current state-of-the art, e...

Binding of curcumin, naproxen, and ibuprofen to Aβ1-40 peptide and its fibrils is studied by docking method and all-atom molecular dynamics simulations. The Gromos96 43a1 force field and simple point charge model of water have been used for molecular dynamics simulations. It is shown that if the receptor is a monomer then naproxen and ibuprofen are bound to the same place that is different from...

The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study "multiple" conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two ...

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtai...

The coalgebra approach to the construction of classical integrable systems from Poisson coalgebras is reviewed, and the essential role played by symplectic realizations in this framework is emphasized. Many examples of Hamiltonians with either undeformed or q-deformed coalgebra symmetry are given, and their Liouville superintegrability is discussed. Among them, (quasi-maximally) superintegrable...