Stimulation by DIF causes an increase of intracellular Ca2+ in Dictyostelium discoideum

Using fluorescence- activated cell sorting (FAGS), we have studied the effect of the differentiation-inducing factor (DIF) on cellular Ca2+ in Dictyostelium discoideum. We have shown previously that freshly starved or postaggregation amoebae are heterogenous with respect to the amounts of cellular Ca2+ that they contain; the L or ''low Ca2+'' class exhibits a prespore tendency and the H or ''high Ca2+'' class exhibits a prestalk tendency. Upon adding DIF, within 2 min there is an approximately twofold increase in the relative fraction of amoebae falling in the H class. A major part of the increase is caused by Ca2+ influx from the extracellular medium. Therefore a rise in the level of cellular Ca2+ is an early step in the signal transduction pathway following stimulation by DIF. Also, in parallel with the cellular heterogeneity in respect of Ca2+ content, there is a heterogeneity in the response to DIF, which appears to be restricted to L cells. (C) 1997 Academic Press.

Parallel Computation of 2D Morse-Smale Complexes

The Morse-Smale complex is a useful topological data structure for the analysis and visualization of scalar data. This paper describes an algorithm that processes all mesh elements of the domain in parallel to compute the Morse-Smale complex of large two-dimensional data sets at interactive speeds. We employ a reformulation of the Morse-Smale complex using Forman's Discrete Morse Theory and achieve scalability by computing the discrete gradient using local accesses only. We also introduce a novel approach to merge gradient paths that ensures accurate geometry of the computed complex. We demonstrate that our algorithm performs well on both multicore environments and on massively parallel architectures such as the GPU.

Mutual inhibition and capacity sharing during parallel preparation of serial eye movements

Many common activities, like reading, scanning scenes, or searching for an inconspicuous item in a cluttered environment, entail serial movements of the eyes that shift the gaze from one object to another. Previous studies have shown that the primate brain is capable of programming sequential saccadic eye movements in parallel. Given that the onset of saccades directed to a target are unpredictable in individual trials, what prevents a saccade during parallel programming from being executed in the direction of the second target before execution of another saccade in the direction of the first target remains unclear. Using a computational model, here we demonstrate that sequential saccades inhibit each other and share the brain's limited processing resources (capacity) so that the planning of a saccade in the direction of the first target always finishes first. In this framework, the latency of a saccade increases linearly with the fraction of capacity allocated to the other saccade in the sequence, and exponentially with the duration of capacity sharing. Our study establishes a link between the dual-task paradigm and the ramp-to-threshold model of response time to identify a physiologically viable mechanism that preserves the serial order of saccades without compromising the speed of performance.

Parallel Computation of 3D Morse-Smale Complexes

The Morse-Smale complex is a topological structure that captures the behavior of the gradient of a scalar function on a manifold. This paper discusses scalable techniques to compute the Morse-Smale complex of scalar functions defined on large three-dimensional structured grids. Computing the Morse-Smale complex of three-dimensional domains is challenging as compared to two-dimensional domains because of the non-trivial structure introduced by the two types of saddle criticalities. We present a parallel shared-memory algorithm to compute the Morse-Smale complex based on Forman's discrete Morse theory. The algorithm achieves scalability via synergistic use of the CPU and the GPU. We first prove that the discrete gradient on the domain can be computed independently for each cell and hence can be implemented on the GPU. Second, we describe a two-step graph traversal algorithm to compute the 1-saddle-2-saddle connections efficiently and in parallel on the CPU. Simultaneously, the extremasaddle connections are computed using a tree traversal algorithm on the GPU.

Boundary perturbations and the Helmholtz equation in three dimensions

We propose an analytic perturbative scheme in the spirit of Lord Rayleigh's work for determining the eigenvalues of the Helmholtz equation in three dimensions inside an arbitrary boundary where the eigenfunction satisfies either the Dirichlet boundary condition or the Neumann boundary condition. Although numerous works are available in the literature for arbitrary boundaries in two dimensions, to the best of our knowledge the formulation in three dimensions is proposed for the first time. In this novel prescription, we have expanded the arbitrary boundary in terms of spherical harmonics about an equivalent sphere and obtained perturbative closed-form solutions at each order for the problem in terms of corrections to the equivalent spherical boundary for both the boundary conditions. This formulation is in parallel with the standard time-independent Rayleigh-Schrodinger perturbation theory. The efficacy of the method is tested by comparing the perturbative values against the numerically calculated eigenvalues for spheroidal, superegg and superquadric shaped boundaries. It is shown that this perturbation works quite well even for wide departure from spherical shape and for higher excited states too. We believe this formulation would find applications in the field of quantum dots and acoustical cavities.

Halogen Bonds in Crystal Engineering: Like Hydrogen Bonds yet Different

CONSPECTUS: The halogen bond is an attractive interaction in which an electrophilic halogen atom approaches a negatively polarized species. Short halogen atom contacts in crystals have been known for around 50 years. Such contacts are found in two varieties: type I, which is symmetrical, and type II, which is bent. Both are influenced by geometric and chemical considerations. Our research group has been using halogen atom interactions as design elements in crystal engineering, for nearly 30 years. These interactions include halogen center dot center dot center dot halogen interactions (X center dot center dot center dot X) and halogen center dot center dot center dot heteroatom interactions (X center dot center dot center dot B). Many X center dot center dot center dot X and almost all X center dot center dot center dot B contacts can be classified as halogen bonds. In this Account, we illustrate examples of crystal engineering where one can build up from previous knowledge with a focus that is provided by the modern definition of the halogen bond. We also comment on the similarities and differences between halogen bonds and hydrogen bonds. These interactions are similar because the protagonist atoms halogen and hydrogen are both electrophilic in nature. The interactions are distinctive because the size of a halogen atom is of consequence when compared with the atomic sizes of, for example, C, N, and O, unlike that of a hydrogen atom. Conclusions may be drawn pertaining to the nature of X center dot center dot center dot X interactions from the Cambridge Structural Database (CSD). There is a clear geometric and chemical distinction between type I and type II, with only type II being halogen bonds. Cl/Br isostructurality is explained based on a geometric model. In parallel, experimental studies on 3,4-dichlorophenol and its congeners shed light on the nature of halogen center dot center dot center dot halogen interactions and reveal the chemical difference between Cl and Br. Variable temperature studies also show differences between type I and type II contacts. In terms of crystal design, halogen bonds offer a unique opportunity in the strength, atom size and interaction gradation; this may be used in the design of ternary cocrystals. Structural modularity in which an entire crystal structure is defined as a combination of modules is rationalized on the basis of the intermediate strength of a halogen bond. The specific directionality of the halogen bond makes it a good tool to achieve orthogonality in molecular crystals. Mechanical properties can be tuned systematically by varying these orthogonally oriented halogen center dot center dot center dot halogen interactions. In a further development, halogen bonds are shown to play a systematic role in organization of LSAMs (long range synthon aufbau module), which are bigger structural units containing multiple synthons. With a formal definition in place, this may be the right time to look at differences between halogen bonds and hydrogen bonds and exploit them in more subtle ways in crystal engineering.

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of beta-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer. (C) 2014 AIP Publishing LLC.

Experimental Study on Switching Characteristics of an Inverter Leg Consisting of IGBTs of Dissimilar Makes

Usually the top and bottom IGBT devices in an inverter leg are of the same make (i.e. from same manufacturer). At low power level, these two devices even may be contained in the same module. However at high power levels the top and bottom devices are in separate modules. Sometimes, in the event of device failure, device of particular make may be replaced by one of another make, but of same ratings (on account of non-availability of the original make). This paper investigates the effect of such intermixing of two different makes of high power IGBTs in an inverter leg on the switching characteristics. The switching transitions between IGBT and diode of similar make and those of IGBT and diode of dissimilar make are compared experimentally at various DC link voltages and currents. The comparisons are made in terms of, IGBT peak turn-on di/dt, IGBT peak turn-off di/dt, peak diode reverse recovery current (I-rr), peak IGBT voltage overshoot and switching energy losses.

Genetic diversity and proviral DNA load in different neural compartments of HIV-1 subtype C infection

In India, the low prevalence of HIV-associated dementia (HAD) in the Human immunodeficiency virus type 1 (HIV-1) subtype C infection is quite paradoxical given the high-rate of macrophage infiltration into the brain. Whether the direct viral burden in individual brain compartments could be associated with the variability of the neurologic manifestations is controversial. To understand this paradox, we examined the proviral DNA load in nine different brain regions and three different peripheral tissues derived from ten human subjects at autopsy. Using a highly sensitive TaqMan probe-based real-time PCR, we determined the proviral load in multiple samples processed in parallel from each site. Unlike previously published reports, the present analysis identified uniform proviral distribution among the brain compartments examined without preferential accumulation of the DNA in any one of them. The overall viral DNA burden in the brain tissues was very low, approximately 1 viral integration per 1000 cells or less. In a subset of the tissue samples tested, the HIV DNA mostly existed in a free unintegrated form. The V3-V5 envelope sequences, demonstrated a brain-specific compartmentalization in four of the ten subjects and a phylogenetic overlap between the neural and non-neural compartments in three other subjects. The envelope sequences phylogenetically belonged to subtype C and the majority of them were R5 tropic. To the best of our knowledge, the present study represents the first analysis of the proviral burden in subtype C postmortem human brain tissues. Future studies should determine the presence of the viral antigens, the viral transcripts, and the proviral DNA, in parallel, in different brain compartments to shed more light on the significance of the viral burden on neurologic consequences of HIV infection.

A Front end Switched Rectifier DC Source for Neutral Point Balancing of A NPC Three-Level Inverter for The Full Modulation Range

A switched DC voltage three level NPC is proposed in this paper to eliminate capacitor balancing problems in conventional three-level Neutral Point Clamped (NPC) inverter. The proposed configuration requires only one DC link with a voltage V-dc/2, where V-dc is the DC link voltage in a onventional NPC inverter. To get rated DC link voltage (V-dc), the voltage source is alternately onnected in parallel to one of the two series capacitors using two switches and two diodes with device voltage rating of V-dc/2. The frequency at which the voltage source is switched is independent and will not affect the operation of NPC inverter. The switched voltage source in this configuration balances the capacitors automatically. The proposed configuration can also be used as a conventional two level inverter in lower modulation range, thereby increases the reliability of the drive system. A space vector based PWM scheme is used to verify this proposed topology.

DFL: A Data Flow Language

Many novel computer architectures like array and multiprocessors which achieve high performance through the use of concurrency exploit variations of the von Neumann model of computation. The effective utilization of the machines makes special demands on programmers and their programming languages, such as the structuring of data into vectors or the partitioning of programs into concurrent processes. In comparison, the data flow model of computation demands only that the principle of structured programming be followed. A data flow program, often represented as a data flow graph, is a program that expresses a computation by indicating the data dependencies among operators. A data flow computer is a machine designed to take advantage of concurrency in data flow graphs by executing data independent operations in parallel. In this paper, we discuss the design of a high level language (DFL: Data Flow Language) suitable for data flow computers. Some sample procedures in DFL are presented. The implementation aspects have not been discussed in detail since there are no new problems encountered. The language DFL embodies the concepts of functional programming, but in appearance closely resembles Pascal. The language is a better vehicle than the data flow graph for expressing a parallel algorithm. The compiler has been implemented on a DEC 1090 system in Pascal.

A Generalized Approach to Multiresolution Complex SAR Signal Processing

Multiresolution synthetic aperture radar (SAR) image formation has been proven to be beneficial in a variety of applications such as improved imaging and target detection as well as speckle reduction. SAR signal processing traditionally carried out in the Fourier domain has inherent limitations in the context of image formation at hierarchical scales. We present a generalized approach to the formation of multiresolution SAR images using biorthogonal shift-invariant discrete wavelet transform (SIDWT) in both range and azimuth directions. Particularly in azimuth, the inherent subband decomposition property of wavelet packet transform is introduced to produce multiscale complex matched filtering without involving any approximations. This generalized approach also includes the formulation of multilook processing within the discrete wavelet transform (DWT) paradigm. The efficiency of the algorithm in parallel form of execution to generate hierarchical scale SAR images is shown. Analytical results and sample imagery of diffuse backscatter are presented to validate the method.

Redefine: Runtime Reconfigurable Polymorphic ASIC

Emerging embedded applications are based on evolving standards (e.g., MPEG2/4, H.264/265, IEEE802.11a/b/g/n). Since most of these applications run on handheld devices, there is an increasing need for a single chip solution that can dynamically interoperate between different standards and their derivatives. In order to achieve high resource utilization and low power dissipation, we propose REDEFINE, a polymorphic ASIC in which specialized hardware units are replaced with basic hardware units that can create the same functionality by runtime re-composition. It is a ``future-proof'' custom hardware solution for multiple applications and their derivatives in a domain. In this article, we describe a compiler framework and supporting hardware comprising compute, storage, and communication resources. Applications described in high-level language (e.g., C) are compiled into application substructures. For each application substructure, a set of compute elements on the hardware are interconnected during runtime to form a pattern that closely matches the communication pattern of that particular application. The advantage is that the bounded CEs are neither processor cores nor logic elements as in FPGAs. Hence, REDEFINE offers the power and performance advantage of an ASIC and the hardware reconfigurability and programmability of that of an FPGA/instruction set processor. In addition, the hardware supports custom instruction pipelining. Existing instruction-set extensible processors determine a sequence of instructions that repeatedly occur within the application to create custom instructions at design time to speed up the execution of this sequence. We extend this scheme further, where a kernel is compiled into custom instructions that bear strong producer-consumer relationship (and not limited to frequently occurring sequences of instructions). Custom instructions, realized as hardware compositions effected at runtime, allow several instances of the same to be active in parallel. A key distinguishing factor in majority of the emerging embedded applications is stream processing. To reduce the overheads of data transfer between custom instructions, direct communication paths are employed among custom instructions. In this article, we present the overview of the hardware-aware compiler framework, which determines the NoC-aware schedule of transports of the data exchanged between the custom instructions on the interconnect. The results for the FFT kernel indicate a 25% reduction in the number of loads/stores, and throughput improves by log(n) for n-point FFT when compared to sequential implementation. Overall, REDEFINE offers flexibility and a runtime reconfigurability at the expense of 1.16x in power and 8x in area when compared to an ASIC. REDEFINE implementation consumes 0.1x the power of an FPGA implementation. In addition, the configuration overhead of the FPGA implementation is 1,000x more than that of REDEFINE.

Semi-active vibration isolation using a near-zero-spring-rate device:steady state analysis of a single-degree-of-freedom model

A vibration isolator is described which incorporates a near-zero-spring-rate device within its operating range. The device is an assembly of a vertical spring in parallel with two inclined springs. A low spring rate is achieved by combining the equivalent stiffness in the vertical direction of the inclined springs with the stiffness of the vertical central spring. It is shown that there is a relation between the geometry and the stiffness of the individual springs that results in a low spring rate. Computer simulation studies of a single-degree-of-freedom model for harmonic base input show that the performance of the proposed scheme is superior to that of the passive schemes with linear springs and skyhook damping configuration. The response curves show that, for small to large amplitudes of base disturbance, the system goes into resonance at low frequencies of excitation. Thus, it is possible to achieve very good isolation over a wide low-frequency band. Also, the damper force requirements for the proposed scheme are much lower than for the damper force of a skyhook configuration or a conventional linear spring with a semi-active damper.