A simple local expression for the prefactor in transition state theory.

We present a simple and accurate computational technique to determine the frequency prefactor in harmonic transition state theory without necessitating full phonon density of states (DOS) calculations. The atoms in the system are partitioned into an "active region," where the kinetic process takes place, and an "environment" surrounding the active region. It is shown that the prefactor can be obtained by a partial phonon DOS calculation of the active region with a simple correction term accounting for the environment, under reasonable assumptions regarding atomic interactions. Convergence with respect to the size of the active region is investigated for different systems, as well as the reduction in computational costs when compared to full phonon DOS calculation. Additionally, we provide an open source implementation of the algorithm that can be added as an extension to Large-scale Atomic/Molecular Massively Parallel Simulator software.

The free energy of mechanically unstable phases.

Phase diagrams provide 'roadmaps' to the possible states of matter. Their determination traditionally rests on the assumption that all phases, even unstable ones, have well-defined free energies under all conditions. However, this assumption is commonly violated in condensed phases due to mechanical instabilities. This long-standing problem impedes thermodynamic database development, as pragmatic attempts at solving this problem involve delicate extrapolations that are highly nonunique and that lack an underlying theoretical justification. Here we propose an efficient computational solution to this problem that has a simple interpretation, both as a topological partitioning of atomic configuration space and as a minimally constrained physical system. Our natural scheme smoothly extends the free energy of stable phases, without relying on extrapolation, thus enabling a formal assessment of widely used extrapolation schemes.

Frequency of Polyomavirus BK Infection in Kidney Transplant Patients Suspected to Nephropathy.

BACKGROUND: Polyomavirus BK is a major cause of nephropathy in immunosuppressed transplanted patients. Non-invasive diagnostic protocols such as molecular detection of polyomavirus BK replication are a useful strategy to predict BK virus-associated nephropathy (BKVAN). OBJECTIVE: To determine the prevalence of polyomavirus BK infection among kidney transplant patients suspected to have BKVAN. METHODS: In a cross-sectional study 108 kidney transplanted patients whose laboratory and clinical presentation were in favor of nephropathy between 2010 and 2012, were enrolled for analysis. Polyomavirus BK replication was evaluated in plasma and tissue samples of studied patients using a quantitative real-time PCR. Active cytomegalovirus infection was analyzed in studied patients using antigenemia method. A possible association between polyomavirus BK infection with clinical and laboratory risk factors of BKVAN were evaluated. RESULTS: The polyomavirus BK replication was found in 17 (15.7%) of 108 of plasma and 9 (11%) of 82 tissue samples in kidney transplanted patients. Cytomegalovirus co-infection was found in 3 of 17 and 3 of 9 plasma and tissue samples in polyomavirus BK infected patients, respectively. Significant associations were found between polyomavirus BK infection with tubulointerstitial nephritis and acute cellular rejection, as important pathologic findings of BKVAN. CONCLUSION: Diagnosis of single and co-infection of polyomavirus BK infection in plasma samples is a useful assay to evaluate the risk of BKVAN in kidney transplant patients. Established threshold values for studied viral infections have beneficial use in screening of kidney transplant patients at risk of BKVAN, need to confirm and standardized in completed further studies.