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     

Results on Biorthogonal Filter Banks

For a maximally decimated nonuniform filter bank, the perfect reconstruction (PR) property is equivalent to biorthogonality. We start from this result and derive a number of properties of PR filter banks. For example, no two integer decimators in a biorthogonal system can be coprime; moreover, if all analysis and synthesis filters have unit energy, then perfect reconstruction is equivalent to orthonormality. We also generalize the Nyquist and power complementary properties of orthonormal filter banks, for the biorthogonal case. We then show that whenever the decimation ratios are such that biorthogonality is possible with rational filters, it is, in particular, possible to obtain orthonormality with rational filters. This is done by developing an orthonormalization procedure. While reminiscent of the Gram–Schmidt approach, the procedure converges in a finite number of steps and furthermore preserves the filter-bank-like form of the basis functions. We also show how this technique can be applied for the decorrelation of subband signals. We will consider the problem of alias cancellation and obtain a generalization of a previously known necessary condition called compatibility.     

Induction and Purification by Three-Phase Partitioning of Aryl Alcohol Oxidase (AAO) from <Emphasis Type="Italic">Pleurotus ostreatus</Emphasis>

Aryl alcohol oxidase (AAO) is an extracellular flavoenzyme involved in lignin degradation by white rot fungi. Screening of lignolytic and AAO activity from twenty different fungal species were carried out. Among them, seven species showed lignolytic activity and three of them (Pleurotus ostreatus, Pleurotus eous, and Pleurotus platypus) were found to be AAO positive. Maximal AAO activity was observed in batch cultures of P. ostreatus and was found to be induced by aromatic amino acids and aryl alcohols up to a level of 289 U/l. Purification of AAO was carried out by three-phase partitioning (TPP). The 67 kDa enzyme was purified up to 10.19-fold by TPP with an overall recovery of 10.95%. Optimum pH and temperature for P. ostreatus AAO activity was found to be around 6 and 40 °C, respectively. From the LB plot, K _m value of AAO for oxidizing veratryl alcohol was determined to be 0.6 mM. Results of the study indicate that P. ostreatus is the best producers of AAO, and they could be employed as promising fungal species for biotechnological applications.     

Micellar catalysed chlorination of acetophenone by chloramine-T

The chlorination of acetophenone by chloramine-T cat has been catalysed by anionic micelle, sodium lauryl sulphate (NaLS). Though the order in cat is one, the order in acetophenone is fractional at lower concentration and becomes zero at higher concentration in the presence and absence of NaLS. This is probably due to the change in rate-determining step. At lower acetophenone concentration, the decomposition of enol-chlorinating species complex is rate-determining whereas at higher concentration, the formation of chlorinating species is rate determining. The graph ofk ₂ versus detergent concentration is sigmoidal and the positive co-operativityversus log[D] graph is 1.11, indicating possible interaction between micelle and substrate.     

Coulometric determination of uranium in perchloric acid medium and its applications

Amorphous samples of a new inorganic ion exchanger, cerium(IV) selenite have been prepared under varying conditions. The material prepared by mixing 0.025M ceric sulfate and 0.025M sodium selenite in the ratio of 11 was studied in detail for its ion-exchange capacity, chemical stability, IR, thermogravimetry and K_d values. Separations of metal ions have been performed on columns of this ion exchanger.     

Control of defect concentrations within a semiconductor through adsorption

The technologically useful properties of a crystalline solid depend upon the concentration of defects it contains. Here we show that defect concentrations as deep as 0.5 microm within a semiconductor can be profoundly influenced by gas adsorption. Self-diffusion rates within silicon show that nitrogen atoms adsorbed at less than 1% of a monolayer lead to defect concentrations that vary controllably over several orders of magnitude. The results show that previous measurements of diffusion and defect thermodynamics in semiconductors may have suffered from neglect of adsorption effects.     

TOF-SIMS investigation of Streptomyces coelicolor, a mycelial bacterium

Streptomyces coelicolor is a mycelial microorganism that produces several secondary metabolites, including antibiotics. The physiology of the organism has largely been investigated in liquid cultures due to ease of monitoring different physiological parameters and more homogeneous culture conditions. However, solid cultures reflect the natural physiology of the microorganism better, given that in its natural state it grows in the soil. Imaging mass spectrometry with TOF-SIMS and C₆₀⁺ primary ion beams offers a potential route to studying chemical changes at the molecular level, both intracellular and extracellular that can help in understanding the natural physiology of the microorganism. Here, we report the application of the technique for studying the lateral distribution of the chemical species detected in a population, grown in both liquid and solid cultures. The capability of the technique for studying biological systems with minimal system intervention is demonstrated.     

Depurinating acylfulvene-DNA adducts: characterizing cellular chemical reactions of a selective antitumor agent

Acylfulvenes (AFs) are a class of semisynthetic agents with high toxicity toward certain tumor cells, and for one analogue, hydroxymethylacylfulvene (HMAF), clinical trials are in progress. DNA alkylation by AFs, mediated by bioreductive activation, is believed to contribute to cytotoxicity, but the structures and chemical properties of corresponding DNA adducts are unknown. This study provides the first structural characterization of AF-specific DNA adducts. In the presence of a reductive enzyme, alkenal/one oxidoreductase (AOR), AF selectively alkylates dAdo and dGuo in reactions with a monomeric nucleoside, as well as in reactions with naked or cellular DNA, with 3-alkyl-dAdo as the apparently most abundant AF-DNA adduct. Characterization of this adduct was facilitated by independent chemical synthesis of the corresponding 3-alkyl-Ade adduct. In addition, in naked or cellular DNA, evidence was obtained for the formation of an additional type of adduct resulting from direct conjugate addition of Ade to AF followed by hydrolytic cyclopropane ring-opening, indicating the potential for a competing reaction pathway involving direct DNA alkylation. The major AF-dAdo and AF-dGuo adducts are unstable under physiologically relevant conditions and depurinate to release an alkylated nucleobase in a process that has a half-life of 8.5 h for 3-alkyladenine and less than approximately 2 h for dGuo adducts. DNA alkylation further leads to single-stranded DNA cleavage, occurring exclusively at dGuo and dAdo sites, in a nonsequence-specific manner. In AF-treated cells that were transfected with either AOR or control vectors, the DNA adducts identified match those from in vitro studies. Moreover, a positive correlation was observed between DNA adduct levels and cell sensitivity to AF. The potential contributing roles of AOR-mediated bioactivation and adduct stability to the cytotoxicity of AF are discussed.     

Accelerating molecular dynamic simulation on the cell processor and Playstation 3

Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors.     

Analysis,synchronization and circuit design of a novel butterfly attractor

This research paper introduces a novel three-dimensional autonomous system, whose dynamics support periodic and chaotic butterfly attractors as certain parameters vary. A special case of this system, exhibiting reflectional symmetry, is amenable to analytical and numerical analysis. Qualitative properties of the new chaotic system are discussed in detail. Adaptive control laws are derived to achieve global chaotic synchronization of the new chaotic system with unknown parameters. Furthermore, a novel electronic circuit realization of the new chaotic system is presented, examined and realized using Orcad-PSpice program and physical components. The proposed novel butterfly chaotic attractor is very useful for the deliberate generation of chaos in applications.