Accelerating molecular dynamic simulation on graphics processing units

We describe a complete implementation of all‐atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Down-regulation of Bcl-2 and Akt induced by combination of photoactivated hypericin and genistein in human breast cancer cells

Presented experiment considers combination of genistein and photodynamic therapy with hypericin with a view to achieve higher therapeutic outcome in human breast adenocarcinoma cell lines MCF-7 and MDA-MB-231, both identified in our conditions as photodynamic therapy resistant. Since genistein is known to suppress Bcl-2 expression, we predicted that photodynamic therapy with hypericin might benefit from mutual therapeutic combination. In line with our expectations, combined treatment led to down-regulation of Bcl-2 and up-regulation of Bax in both cell lines as well as to suppression of Akt and Erk1/2 phosphorylation induced by photoactivated hypericin in MCF-7 cells. Although Akt and Erk1/2 phosphorylation was not stimulated by photodynamic therapy with hypericin in MDA-MB-231 cells, it was effectively suppressed in combination. Variations in cell death signaling favoring apoptosis were indeed accompanied by cell cycle arrest in G₂/M-phase, activation of caspase-7, PARP cleavage and increased occurrence of cells with apoptotic morphology of nucleus. All these events corresponded with suppression of proliferation and significantly lowered clonogenic ability of treated cells. In conclusion, our results indicate that pre-treatment with tyrosine kinase inhibitor genistein may significantly improve the effectiveness of photodynamic therapy with hypericin in MCF-7 and MDA-MB-231 breast cancer cells.     

Structure elucidation of highly polar basic degradants by on-line hydrogen/deuterium exchange hydrophilic interaction chromatography coupled to tandem mass spectrometry

A hydrophilic interaction liquid chromatography (HILIC) method was used to separate a commonly used pharmaceutical starting material, 4-aminomethylpyridine (4-AMP), and its degradants. The structures of the major degradants were characterized and elucidated without prior isolation by accurate mass measurement, MS/MS analysis and on-line hydrogen/deuterium (H/D) exchange experiments. The mass spectra obtained from H/D exchange experiments are particularly useful to differentiate structural isomers, to elucidate the fragmentation pathways, and to aid in structure elucidation in the absence of MS/MS fragmentation information. The impact of deuterium oxide and temperature on HILIC separation has also been explored here. The integration of H/D exchange with HILIC has been described here for the first time and has been demonstrated to be a powerful structure elucidation tool via the study of degradants in 4-AMP.     

Controlling ghost traps in holographic optical tweezers

Computer-generated holograms displayed by phase-modulating spatial light modulators have become a well-established tool for beam shaping purposes in holographic optical tweezers. Still, the generation of light intensity patterns with high spatial symmetry and simultaneously without interfering ghost traps is a challenge. We have implemented an iterative Fourier transform algorithm that is capable of controlling these ghost traps and demonstrate the benefit of this approach in the experiment.     

How to predict viscous fingering in three component flow

In a WAG process (Water Alternate Gas), water and a miscible solvent (gas) are injected into a reservoir containing water and oil. The solvent will finger through the oil, leading to early breakthrough and poor recovery. Compared with a miscible flood, when only solvent is injected, fingering is supressed by the simultaneous injection of water, since this reduces the apparent mobility contrast between the injected and displaced fluids. The fingering in a miscible flood, with only hydrocarbon flowing, can be modelled successfully using a Todd and Longstaff fractional flow. In this paper, we demonstrate how to modify the effective Todd and Longstaff mobility ratio self-consistently to account for fingering in three component systems. The resultant empirical equations of flow are solved exactly in one dimension and are in excellent agreement with the averaged saturation and concentration profiles computed using two dimensional high resolution simulation, for a variety of injected water saturations, in both secondary and tertiary displacements.     

Boron trifluoride–etherate mediated synthesis of 3-desoxyanthocyanidins including a total synthesis of tricetanidin from black tea

The synthesis of a series of 3-desoxyanthocyanidins via a BF₃·Et₂O-mediated aldol condensation between a substituted acetophenone and salicylaldehyde derivatives is described. Using this new synthetic methodology the synthesis of tricetanidin, a natural pigment isolated from black tea, was accomplished.     

The effect of polyethylene addition on the morphology of polystyrene/polyamide blends

The effect of a small admixture of high‐density polyethylene (HDPE) with a high or low viscosity to polystyrene/polyamide (PS/PA) blends of various compositions was studied. PS/PA blends with composition near 50/50 form sheet‐like or fiber‐like morphology at mixing that passes to the cocontinuous structure during compression molding. Ternary PS/PA/HDPE blends with PS/PA ratio about 50/50 show similar behavior. Generally, neither continuity nor shape of PS and PA phases was changed qualitatively by the addition of a small amount of HDPE. In agreement with existing rules for ternary blends, HDPE particles prefer a contact with PS phase to PA phase. On the other hand, none of these rules explains why a number of small HDPE subinclusions were dispersed into PS particles instead of HDPE‐PS core‐shell structure with a lower Gibbs free energy. Quantitative evaluation of the size of PA particles in blends with PS matrix showed that the previously proposed rule stating, that the addition of a small amount of a third immiscible component leads to a strong decrease in the size of dispersed particles, was not valid for the blends studied in this work. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 2158–2170, 2009