Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase

The recently introduced force field (FF) QMPFF3 is thoroughly validated in gas, liquid, and solid phases. For the first time, it is demonstrated that a physically well-grounded general purpose FF fitted exclusively to a comprehensive set of high level vacuum quantum mechanical data applied as it is to simulation of condensed phase provides high transferability for a wide range of chemical compounds. QMPFF3 demonstrates accuracy comparable with that of the FFs explicitly fitted to condensed phase data, but due to high transferability it is expected to be successful in simulating large molecular complexes.     

Diffuse reflection of light from a dense random medium using fibres dipped into the medium

Diffuse reflection of a narrow collimated light beam from a slab of a dense random medium is considered theoretically and experimentally for the case of the source and the detector fibres dipped into the random medium, as is the case for an endoscopic catheter. By use of the diffusion approximation, a simple and physically clear analytical expression is derived for the distribution of the diffuse reflectance of the light beam along the surface of the random medium slab. We include the effects of reflections from the top and bottom surfaces of the slab. The analytical expression derived predicts that, in the case of small absorption, the relative reflectance is a universal function defined by the geometrical parameters and is independent of specific properties of the random medium. The theoretical prediction is found to show good agreement with the results of measurements.     

Relationship between Surface Self-Diffusion and Bubble Mobility in Solids: Theory and Atomistic Simulation

Journal of Experimental and Theoretical Physics - Diffusion processes in solids are characterized by complex mechanisms occurring at the atomistic level. The relevant theoretical concepts are...     

PLASS: Protein-ligand affinity statistical score – a knowledge-based force-field model of interaction derived from the PDB

We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.