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     

Some sufficient conditions for the E- and MV-optimality of block designs having blocks of unequal size

Summary In this paper we consider experimental situations in which ν treatments are to be tested inb blocks whereb _i blocks containk _i experimental units,i=1,...,p, k ₁<k ₂<...<k _p . The idea of a group divisible (GD) design is extended to that of a group divisible design with unequal block sizes (GDUB design) and then a number of results concerning the E- and MV-optimality of GD designs are generalized to the case of GDUB designs.     

Über die Kristallisation von Jod und Jodiden in Gelen

Zusammenfassung Aus einer Reihe von Untersuchungen über Bildung, Niederschlagung, scheinbaren Bewegung und Austausch von kristallinem Jod und unl?slichen kristallinen Jodiden in verschiedenen Gelen und anderen Mitteln wurde gefolgert, da? die Prozesse der Niederschlagung des Reaktionsproduktes und der Diffusion dieses Produktes nicht voneinander getrennt werden k?nnen. Es wurde darauf hingewiesen, da? die offensichtliche Wanderung von kristallinem Jod und unl?slichen kristallinen Jodiden in Gelstrukturen sich als eine Folge der Wiederaufl?sung in einem Teil der Kristallmasse und der Wiederablagerung an einem andern Teile zu ergeben scheint. Untersuchungen über den Austausch von kristallinem Jod durch unl?sliche Jodide und umgekehrt haben gezeigt, da? unter gewissen passenden Diffusionsbedingungen, wie z. B. im Kiesels?uregel, sich pseudomorphe Kristalle bilden k?nnen. Pseudomorphe Kristalle wurden in kapillaren R?umen zwischen Glasplatten nicht erhalten, obzwar sich eine ausgesprochene Neigung hierzu zeigte. Material wurde dargelegt, um zu zeigen, da? sich verschiedene Arten von Jodablagerungen als eine Folge der Wirkung des Mittels ergeben k?nnen. Diese Ablagerungen k?nnen sich von kolloiden bis zu makroskopischen Dimensionen und von sehr verzerrten bis zu fast vollkommenen kristallinen Formen erstrecken. Unter gewissen Bedingungen scheinen sich Somatoide zu bilden. Umgebungen, in denen diese Reaktionen ausgeführt wurden, waren a) verschiedene Gele, b) Schichten zwischen Glasplatten, c) Poren absorbierenden Papiers und d) Membranoberfl?chen.     

Synthesis and Structures of Gallium‐β‐Diketiminate Complexes: Isolation of a Dinuclear Gallium(II) Complex

The sterically demanding β‐diketiminate ligand L^dmp [L^dmp = HC{(CMe)N(dmp)}₂, dmp = C₆H₃‐2,6‐Me₂] was used to stabilize various gallium complexes in the formal oxidation states +II and +III. The reaction of in situ generated [L^dmpLi] with gallium chloride affords [L^dmpGaCl₂] ( 1 ), which was used as starting complex to synthesize a variety of gallium(III) compounds [L^dmpGaX₂] [X = F ( 2 ), I ( 3 ), H ( 4 ), and Me ( 5 )]. Synthesis of the dinuclear complex [L^dmpGaI]₂ ( 6 ), with gallium in the formal oxidation state +II was accomplished by converting “GaI” with in situ generated [L^dmpLi] in toluene. All compounds were characterized by elemental analyses, NMR spectroscopy, LIFDI‐TOF‐MS, and single‐crystal X‐ray diffraction. Additionally DFT calculations were performed for analysis of the bonding in 6 .     

System Maps for Retention of Small Neutral Compounds on a Superficially Porous Ethyl-Bridged,Octadecylsiloxane-Bonded Silica Stationary Phase in Reversed-Phase Liquid Chromatography

The system constants of the solvation parameter model are used to prepare system maps for the retention of small neutral compounds on an ethyl-bridged, ocatadecylsiloxane-bonded superficially porous silica stationary phase (Kinetex EVO C18) for aqueous mobile phases containing 10–70% (v/v) methanol or acetonitrile. Electrostatic interactions (cation-exchange) are important for the retention of weak bases with acetonitrile–water but not methanol–water mobile phase compositions. Compared with a superficially porous octadecylsiloxane-bonded silica stationary phase (Kinetex C18) with a similar morphology but different topology statistically significant differences in selectivity at the 95% confidence level are observed for neutral compounds that vary by size and hydrogen-bond basicity with other intermolecular interactions roughly similar. These selectivity differences are dampened with acetonitrile–water mobile phases, but are significant for methanol–water mobile phase compositions containing <30% (v/v) methanol. A comparison of a totally porous ethyl-bridged, octadecylsiloxane-bonded silica stationary phase (XBridge C18) with Kinetex EVO C18 indicated that they are effectively selectivity equivalent.     

Solvent- and metal-free selective oxidation of thiols to disulfides using I2/DMSO catalytic system

We describe herein a simple, fast and inexpensive protocol for the oxidative coupling of thiols employing a stoichiometric amount of DMSO and iodine as the catalyst. Various aromatic disulfides were obtained in good to excellent yields in short reaction times at room temperature, while aliphatic disulfides were achieved in good yields when the reactions were conducted under microwave irradiation.     

Modeling study of non-line-narrowed hole-burned spectra in weakly coupled dimers and multi-chromophoric molecular assemblies

Several different models have been proposed to explain the origin of the complex anti-hole features observed in hole-burned (HB) spectra of excitonically coupled systems such as photosynthetic complexes. This lack of consensus presents a serious constraint on the interpretation of HB spectra and the underlying electronic structures of these systems. To resolve this problem we present results of modeling studies of non-resonant HB spectra taking uncorrelated excitation energy transfer and excitonic interactions into account. Simplified analytical results are compared with Monte Carlo simulations in which excitonic interactions are explicitly taken into account in order to disentangle a number of distinct effects. It is shown that these effects can accurately account for both hole shapes and the broad anti-hole structure observed in excitonically coupled systems. We argue that these models will provide a necessary framework for probing the electronic structure of these systems via HB spectroscopy.     

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.