Showing papers by "Lixin Zhang published in 2004"

Superconductivity Modulated by Quantum Size Effects

Abstract: We have fabricated ultrathin lead films on silicon substrates with atomic-scale control of the thickness over a macroscopic area. We observed oscillatory behavior of the superconducting transition temperature when the film thickness was increased by one atomic layer at a time. This oscillating behavior was shown to be a manifestation of the Fabry-Perot interference modes of electron de Broglie waves (quantum well states) in the films, which modulate the electron density of states near the Fermi level and the electron-phonon coupling, which are the two factors that control superconductivity transitions. This result suggests the possibility of modifying superconductivity and other physical properties of a thin film by exploiting well-controlled and thickness-dependent quantum size effects.

Nitric Oxide Functions as a Signal in Salt Resistance in the Calluses from Two Ecotypes of Reed

Abstract: Calluses from two ecotypes of reed (Phragmites communis Trin.) plant (dune reed [DR] and swamp reed [SR]), which show different sensitivity to salinity, were used to study plant adaptations to salt stress. Under 200 mm NaCl treatment, the sodium (Na) percentage decreased, but the calcium percentage and the potassium (K) to Na ratio increased in the DR callus, whereas an opposite changing pattern was observed in the SR callus. Application of sodium nitroprusside (SNP), as a nitric oxide (NO) donor, revealed that NO affected element ratios in both DR and SR calluses in a concentration-dependent manner. Nω-nitro-l-arginine (an NO synthase inhibitor) and 2-phenyl-4,4,5,5-tetramethyl-imidazoline-1-oxyl-3-oxyde (a specific NO scavenger) counteracted NO effect by increasing the Na percentage, decreasing the calcium percentage and the K to Na ratio. The increased activity of plasma membrane (PM) H+-ATPase caused by NaCl treatment in the DR callus was reversed by treatment with Nω-nitro-l-arginine and 2-phenyl-4,4,5,5-tetramethyl-imidazoline-1-oxyl-3-oxyde. Western-blot analysis demonstrated that NO stimulated the expression of PM H+-ATPase in both DR and SR calluses. These results indicate that NO serves as a signal in inducing salt resistance by increasing the K to Na ratio, which is dependent on the increased PM H+-ATPase activity.

Mambo: a full system simulator for the PowerPC architecture

Abstract: Mambo is a full-system simulator for modeling PowerPC-based systems. It provides building blocks for creating simulators that range from purely functional to timing-accurate. Functional versions support fast emulation of individual PowerPC instructions and the devices necessary for executing operating systems. Timing-accurate versions add the ability to account for device timing delays, and support the modeling of the PowerPC processor microarchitecture. We describe our experience in implementing the simulator and its uses within IBM to model future systems, support early software development, and design new system software.

Negative control of apoptosis signal-regulating kinase 1 through phosphorylation of Ser-1034.

Abstract: Apoptosis signal-regulating kinase 1 (ASK1) is a serine/threonine kinase that mediates cell stress signaling initiated by diverse stimuli, such as H2O2 and TNFα. Owing to its critical role in promoting apoptosis, ASK1 activity is highly controlled in cells. Phosphorylation of ASK1 at Thr-845 has been correlated with its activation, while phosphorylation at Ser-967 negatively controls its death promoting activity. Here, we report the identification of a novel phosphorylation site at Ser-1034 in the C-terminal regulatory domain of ASK1. Mutating Ser-1034 to an unphosphorylatable Ala led to increased catalytic activity of ASK1 and enhanced proapoptotic function of ASK1. Thus, the proapoptotic function of ASK1 is suppressed in part by phosphorylation at its C-terminal regulatory domain, which may couple upstream survival kinases to the death regulatory machinery.

Comparison of d 13C values and gas exchange of assimilating shoots of desert plants Haloxylon ammodendron and Calligonum mongolicum with other plants

Abstract: The photosynthetic characters and water use efficiency of the desert plants Haloxylon ammodendron and Calligonum mongolicum, which grow in conditions of extreme stress, were studied. The mechanisms of their acclimation to harsh desert conditions and their potential capacity for sand stabilizing are revealed. The stable carbon isotope ratios (d 13C or 13C/12C) of leaves or assimilating shoots of desert plants growing at the southern edge of the Badain Jaran Desert were analyzed by mass spectrometry and compared. The diurnal course of net photosynthesis rate (Pn), Pn/light and Pn/CO2 curves, and water use efficiency (WUE, Pn/E) were measured by using the LI-6400 Portable Photosynthesis System. The results showed that: (1) Assimilating shoots of H. ammodendron and C. mongolicum have Kranz anatomy; (2) The d 13C values of H. ammodendron and C. mongolicum were -14.3‰ and -14.8‰, respectively, whereas the corresponding values of Caragana korshinskii, Nitraria sphaerocarpa, Hedysarum scoparium, and Reaumuria soo...

Affinity capillary electrophoresis analyses of protein-protein interactions in target-directed drug discovery.

Abstract: Protein-protein interactions are instrumental in virtually all biological processes and their understanding will shed light on designing novel and effective drugs for therapeutic interventions targeting the pathways in which they function. Protein-protein interactions have been studied using many genetic and biochemical methods, most recently, affinity capillary electrophoresis (ACE). We used ACE as a high-throughput screening assay to establish and define binding interactions between a therapeutic target protein and chemical entities from natural product or synthetic chemical libraries. Furthermore, ACE has demonstrated its value in the measurement of binding constants, the estimation of kinetic rate constants, and the determination of the stoichiometry of protein-protein interactions. Herein, we will describe qualitatively several assay formats using ACE for detecting protein-protein interactions, and discuss their advantages and limitations.

Highly efficient synchronization based on active memory operations

Abstract: Summary form only given. Synchronization is a crucial operation in many parallel applications. As network latency approaches thousands of processor cycles for large scale multiprocessors, conventional synchronization techniques are failing to keep up with the increasing demand for scalable and efficient synchronization operations. We present a mechanism that allows atomic synchronization operations to be executed on the home memory controller of the synchronization variable. By performing atomic operations near where the data resides, our proposed mechanism can significantly reduce the number of network messages required by synchronization operations. Our proposed design also enhances performance by using fine-grained updates to selectively "push " the results of offloaded synchronization operations back to processors when they complete (e.g., when a barrier count reaches the desired value). We use the proposed mechanism to optimize two of the most widely used synchronization operations, barriers and spin locks. Our simulation results show that the proposed mechanism outperforms conventional implementations based on load-linked/store-conditional, processor-centric atomic instructions, conventional memory-side atomic instructions, or active messages. It speeds up conventional barriers by up to 2.1 (4 processors) to 61.9 (256 processors) and spin locks by a factor of up to 2.0 (4 processors) to 10.4 (256 processors).

Spin driving reconstructions on the GaAs(001):Mn surface

Abstract: The scanning tunneling microscopy (STM) experiment reveals a $2\ifmmode\times\else\texttimes\fi{}2$ surface reconstruction on GaAs(001):Mn. A comprehensive theory for spin-driven reconstructions is developed by the first-principles methods: Mn incorporation results in two structural motifs to accommodate the spin degree of freedom. Low-energy reconstructions are generally antiferromagnetic to preserve the semiconducting band gaps. The gaps, however, decrease with increasing Mn coverage, leading to metallic surfaces. At one-monolayer coverage, the transition is complete. The calculated STM images agree with experiment.

The survival mechanism of dune reed (Phragmites communis) cultures under high sodium chloride concentration

Abstract: Adaptations to salt stress were studied in embryogenic cultures from two ecotypes of reed (Phragmites communisT.). In the 600 mM NaCl treatment, relative cell viability of dune reed embryogenic cultures from a desert region was 56% greater than the control, 198% greater than swamp reed embryogenic cultures. After treatment with different NaCl concentrations, their relative growth rates (RGRs), pyridine nucleotides, activities of antioxidant enzymes and plasma membrane H+-ATPase (EC 3.6.1.35) were determined. The results showed that NADPH content, NADPH/NADP+ ratio and the activity of plasma membrane H+-ATPase in dune reed embryogenic cultures were higher than those of the control in the present of 600 mM NaCl. The activities of peroxidase (POD, EC 1.11.1.7) and catalase (CAT, EC 1.11.1.6) increased more in dune reed embryogenic cultures than in swamp reed embryogenic cultures. Dune reed embryogenic cultures tolerated higher concentration of NaCl than swamp reed embryogenic cultures. Under high concentration of NaCl, the survival of dune reed embryogenic cultures might be due to reductive status maintenance and ions absorption regulation in the plant cells. This phenomenon would be a result of cross-adaptation in nature.

Screening for synergistic compounds

Abstract: This invention provides a powerful systematic approach to discovering next generation of chemical compounds or formulation that acts synergistically with the low dosage of known drugs. Existing drug or dropped drug candidate is selected. Then a library of either natural products or synthetic chemicals (pure or combinatorial) including macromolecules like nucleic acids and proteins is created. A functional assay including biochemical, cell based assays, animal models or clinical treatments are established, and a sub-optimal dose (10 % - 40 % of the maximum activity) of the selected drug is determined. Under this condition, the library at different titration would be screened in a high throughput manner that should give a 0.1 % to 1 % hit rate. The synergistic co-drug hit should generate 70 % - 100 % of the maximum activity by combination with the sub-optimal concentration of existing drug. Finally, the co-drug hits would be purified and identified. The co-drug could be a pure synthetic molecule, a compound from a combinatorial synthetic library or a mixture from nature or synthetic resources.

System and method for performing address translation in a computer system

Abstract: An address translation unit generates a physical address for access to a memory from a virtual address using either a translation lookaside buffer or a segmentation buffer. If the virtual address falls within a predetermined range, the address translation unit will use the segmentation buffer to generate the physical address. Upon generation of the physical address, the memory will either receive data from or provide data to a processor in accordance with the instructions being processed by the processor.

Preliminary Investigation of Active Memory Operations

Abstract: We are rapidly approaching a time when large-scale shared memory supercomputers will have remote memory latencies measured in the thousands of cycles and cross-section bandwidth will be a limiting performance factor. For these machines to scale, mechanisms that minimize interprocessor communication will be essential. We propose one such mechanism, active memory, which allows operations to be sent to and executed on the home memory controller of particular data items. Performing the operations near where the data resides, rather than moving it across the network, operating on it, and moving it back, eliminates significant network traffic, introduces opportunities for additional parallelism, and hides high remote memory latencies. Active memory provides many of the benefits of PIMs without the need for non-standard DRAMs, and enables significantly better application scaling than conventional shared memory synchronization and range operations. In this paper we investigate an active memory design that supports three classes of memorycentric operations that benefit common parallel constructs: atomic scalar, range, and reduction operations. We present architectural and programming models for active memory and compare its performance against a baseline conventional shared memory system implementation and a variety of optimized memory architectures. We find that active memory easily outperforms the conventional shared memory and other architectures by factors of over 10x on a collection of parallel constructs.

Scalable barrier synchronisation for large-scale shared-memory multiprocessors

Abstract: Barrier synchronisation is very important in scalable multiprocessors. As network latency rapidly approaches thousands of processor cycles and multiprocessors systems become larger and larger, conventional barrier techniques are failing to keep up with the increasing demand for efficient synchronisation. In this paper, we present a memory controller-based operation that optimises the barrier function of an OpenMP library. The proposed mechanism allows atomic operations on the barrier variable to be executed on the home memory controller and the home memory controller to send fine-grained updates to waiting processors when a barrier variable reaches certain values. On a cycle-accurate execution-driven simulator, experiment results show that the proposed barrier implementation outperforms a conventional LL/SC (Load-Linked/ Store-Conditional) version by 20.8X, a conventional processor-side atomic instruction version by 15.5X, and an active messages version by 13.4X. To the best of our knowledge, the proposed barrier achieves better performance than all other existing non-hardwired implementations, and with an improved programming interface.