Related papers: Predicting the orientation of adsorbed proteins st…
A theory is set up of spherical proteins interacting by screened electrostatics and constant adhesion, in which the effective adhesion parameter is optimized by a variational principle for the free energy. An analytical approach to the…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
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…
Closed-form, analytical approximations for electrostatic properties of molecules are of unique value, as these can provide computational speed, versatility, and physical insight. Here, we derive a simple, closed-form formula for the…
This work presents a fast and scalable approach for predicting surface stability and equilibrium crystal morphology in ionic materials using electrostatic analysis. The method constructs stoichiometric slab terminations and evaluates their…
We present an algorithm for accelerating the search of molecule's adsorption site based on global optimization of surface adsorbate geometries. Our approach uses a machine-learning interatomic potential (moment tensor potential) to…
The adsorption kinetics of the cationic surfactant dodecyltrimethylammonium bromide at the air-water interface has been studied by the maximum bubble pressure method at concentrations below the critical micellar concentration. At short…
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…
We analyze the effect of an external electric field on the electronic structure of molecules which have been recently studied as molecular wires or diodes. We use a self-consistent tight binding technique which provides results in good…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Using an adiabatic approximation method, which searches for Tomlinson model-like instabilities for a simple but still realistic model for two crystalline surfaces in the extremely light contact limit, with mobile molecules present at the…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Elastic netwok models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
Protein adsorption/desorption upon nanoparticle surfaces is an important process to understand for developing new nanotechnology involving biomaterials, while atomistic picture of the process and its coupling with protein conformational…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
Due to inherent complexity active transport presents a landmark hurdle for oral absorption properties prediction. We present a novel approach carrier-mediated drug absorption parameters calculation based on entirely different paradigm than…
Simulating protein-membrane interactions is an important and dynamic area of research. A proper definition of electrostatic forces on membrane surfaces is necessary for developing electromechanical models of protein-membrane interactions.…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Computational screening in heterogeneous catalysis relies increasingly on machine learning models for predicting key input parameters due to the high cost of computing these directly using first-principles methods. This becomes especially…