Nonalcoholic fatty liver disease (NAFLD), a common clinical disorder, is increasing largely due to increasing consumption of diets high in fructose and fat (1–3). Indeed, NAFLD has been reported to be present in up to 30% of the U.S. population (3), closely mirroring the prevalence of obesity. Its presence carries an increased risk for type 2 diabetes, endstage liver disease, and cardiovascular...

The knowledge of the local electronic structure heterogeneous solid materials is crucial for understanding their electronic, magnetic, transport, optical, and other properties. VASP, one mostly used packages density-functional calculations, provides either by projecting wave functions on atomic spheres, or as a band-decomposed partial charge density. Here, we present simple tool which takes den...

Endothelium-derived prostacyclin and nitric oxide (NO) inhibit platelets by increasing the cytosolic concentrations of cAMP and cGMP, respectively. The increase of these second messengers leads to the activation of cAMP-dependent protein kinase (PKA) and cGMP-dependent protein kinase (PKG) and the subsequent phosphorylation of specific target proteins in platelets. One such protein is the vasod...

success of an anticoagulatory therapy, as during clopidogrel therapy, and reflects the success of platelet activation during an anticoagulatory therapy. Therefore we were wondering whether the authors think that VASP phosphorylation could be a useful monitor in their experimental system, and whether the monitoring the extent of VASP phosphorylation could be a valuable tool to monitor the clinic...

Cells sustain high rates of actin filament elongation by maintaining a large pool of actin monomers above the critical concentration for polymerization. Profilin-actin complexes constitute the largest fraction of polymerization-competent actin monomers. Filament elongation factors such as Ena/VASP and formin catalyze the transition of profilin-actin from the cellular pool onto the barbed end of...

We present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to is...

Strengthening of cell-matrix adhesions in response to applied force has been well documented. However, while implied by various lines of evidence, the force-mediated strengthening of cell-cell adhesions has not been directly demonstrated. In the current study, we present results consistent with force strengthening in adherens junctions, obtained by application of different force profiles to VE-...

Filopodia have important sensory and mechanical roles in motile cells. The recruitment of actin regulators, such as ENA/VASP proteins, to sites of protrusion underlies diverse molecular mechanisms of filopodia formation and extension. We developed Filopodyan (filopodia dynamics analysis) in Fiji and R to measure fluorescence in filopodia and at their tips and bases concurrently with their morph...

With the recent installation of Cori, a Cray XC40 system with Intel Xeon Phi Knights Landing (KNL) many integrated core (MIC) architecture, NERSC is transitioning from the multi-core to the more energy-efficient many-core era. The developers of VASP, a widely used materials science code, have adopted MPI/OpenMP parallelism to better exploit the increased on-node parallelism, wider vector units,...