Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development.

Molecular simulations begin with an underlying energy model or force field and from this can predict diverse physical properties. However, force fields were often developed with relatively limited data sets, yet accuracy for diverse properties across a broad chemical space is desirable; therefore, tests of such accuracy are particularly important. Here, to this end, we calculated 237 infinite dilution activity coefficients (IDACs), comparing with experimental values from NIST's ThermoML database.

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

To compare ordered water positions from experiment with those from molecular dynamics (MD) simulations, a number of MD models of water structure in crystalline endoglucanase were calculated. The starting MD model was derived from a joint X-ray and neutron diffraction crystal structure, enabling the use of experimentally assigned protonation states. Simulations were performed in the crystalline state, using a periodic 2 × 2 × 2 supercell with explicit solvent.

Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

Partition coefficients describe how a solute is distributed between two immiscible solvents. They are used in drug design as a measure of a solute's hydrophobicity and a proxy for its membrane permeability. We calculate partition coefficients from transfer free energies using molecular dynamics simulations in explicit solvent.

Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study.

Accurate predictions of free energies of binding of ligands to proteins are challenging partly because of the nonadditivity of protein-ligand interactions; i.e., the free energy of binding is the sum of numerous enthalpic and entropic contributions that cannot be separated into functional group contributions.

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes.

Protein-carbohydrate recognition is crucial in many vital biological processes including host-pathogen recognition, cell-signaling, and catalysis. Accordingly, computational prediction of protein-carbohydrate binding free energies is of enormous interest for drug design. However, the accuracy of current force fields (FFs) for predicting binding free energies of protein-carbohydrate complexes is not well understood owing to technical challenges such as the highly polar nature of the complexes, anomerization, and conformational flexibility of carbohydrates.

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data.

Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory.

An efficient methodology has been developed to quantify water energetics by analysis of explicit solvent molecular simulations of organic and biomolecular systems. The approach, grid cell theory (GCT), relies on a discretization of the cell theory methodology on a three-dimensional grid to spatially resolve the density, enthalpy, and entropy of water molecules in the vicinity of solute(s) of interest. Entropies of hydration are found to converge more efficiently than enthalpies of hydration.

[Substernal goiter: pre-, intra- and postoperative problems].

The Authors report their experience with problems in treating substernal goiter. They then explain at length the complex haemodynamic or respiratory situations encountered and the therapeutic management of the condition. Also discussed are technical surgical problems, and the prevention and therapy of possible complications.

Warthin's tumour of the parotid gland.

The authors, after examining two recent cases, explain a number of basic concepts regarding the diagnosis and therapy of Warthin's tumour of the parotid gland. Despite their low frequency, such tumours are very important because of their aetiopathogenesis, which is still controversial, and the recent increase in their incidence in females. Today, the diagnostic protocol, undertaken after the necessary clinical examination, relies mainly on ultrasonography and CT, but only a postoperative histological examination is capable of yielding a sure diagnosis and establishing the main histomorphological characteristics of the tumour.