Related papers: Simultaneous identification of multiple binding si…

Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the…

We present a progress report on our work on lattice Boltzmann methods for colloidal suspensions. We focus on the treatment of colloidal particles in binary solvents and on the inclusion of thermal noise. For a benchmark problem of colloids…

We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA…

We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…

Efficient and high capacity storage materials are indispensable for a hydrogen-based economy. In silico tools can accelerate the process of discovery of new adsorbent materials with optimal hydrogen adsorption enthalpies. Density functional…

We present a recently developed one-dimensional dipole lattice model that accurately captures the key properties of water in narrow nanopores. For this model, we derive three equivalent representations of the Hamiltonian that together yield…

We derive the partial differential equation (PDE) to which the pseudo-potential lattice Boltzmann method (P-LBM) converges under diffusive scaling, providing a rigorous basis for its consistency analysis. By establishing a direct link…

The equilibrium states of one-dimensional proton conductors in the systems with hydrogen bonds are investigated. Our extended hard-core boson lattice model includes short-range interactions between hydrogen ions, their transfer along the…

On a basis of a two-length scale description of hydrophobic interactions we develop a continuous self-consistent theory of solute-water interactions which allows to determine a hydrophobic layer of a solute molecules of any geometry with…

Simple coarse-grained hydrophobic-polar models for heteropolymers as the lattice HP and the off-lattice AB model allow a general classification of characteristic behaviors for hydrophobic-core based tertiary folding. The strongly reduced…

We develop theory and computational methods to investigate particle inclusions embedded within curved lipid bilayer membranes. We consider the case of spherical lipid vesicles where inclusion particles are coupled through (i) intramembrane…

We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…

We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly…

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…

A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy…

The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealised coarse-grained lattice models.…

We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs…

The OH-terminated self-assembled monolayers, as protein-resistant surfaces, have significant potential in biocompatible implant devices, which can avoid or reduce adverse reactions caused by protein adhesion to biomaterial surfaces, such as…

Anion exchange membranes are used in alkaline fuel cells and offer a promising alternative to the more expensive proton exchange membrane fuel cells. However, hydroxide ion conductivity in anion exchange membranes is low, and the quest for…