Efficient Adaptive Mesh Refinement for MoM-based Package-Board 3D Full-wave Extraction

The accurate solution of 3D full-wave Method of Moments (MoM) on an arbitrary mesh of a package-board structure does not guarantee accuracy, since the discretizations may not be fine enough to capture rapid spatial changes in the solution variable. At the same time, uniform over-meshing on the entire structure generates large number of solution variables and therefore requires an unnecessarily large matrix solution. In this work, a suitable refinement criterion for MoM based electromagnetic package-board extraction is proposed and the advantages of the adaptive strategy are demonstrated from both accuracy and speed perspectives.

Learning-Based Fast Iterative Convergence of 3-D MoM via Eigen-AGMRES Method

Three-dimensional (3-D) full-wave electromagnetic simulation using method of moments (MoM) under the framework of fast solver algorithms like fast multipole method (FMM) is often bottlenecked by the speed of convergence of the Krylov-subspace-based iterative process. This is primarily because the electric field integral equation (EFIE) matrix, even with cutting-edge preconditioning techniques, often exhibits bad spectral properties arising from frequency or geometry-based ill-conditioning, which render iterative solvers slow to converge or stagnate occasionally. In this communication, a novel technique to expedite the convergence of MoMmatrix solution at a specific frequency is proposed, by extracting and applying Eigen-vectors from a previously solved neighboring frequency in an augmented generalized minimum residual (AGMRES) iterative framework. This technique can be applied in unison with any preconditioner. Numerical results demonstrate up to 40% speed-up in convergence using the proposed Eigen-AGMRES method.

Conformational Changes Triggered by Mg2+ Mediate Transactivator Function

Transactivator protein C of bacteriophage mu is essential for the transition from middle to late gene expression during the phage life cycle. The unusual, multistep activation of mom promoter (Pmom) by C protein involves activator-mediated promoter unwinding to recruit RNA polymerase and subsequent enhanced promoter clearance of the enzyme. To achieve this, C binds its site overlapping the -35 region of the mom promoter with a very high affinity, in Mg2+-dependent fashion. Mg2+-mediated conformational transition in C is necessary for its DNA binding and transactivation. We have determined the residues in C which coordinate Mg2+, to induce allosteric transition in the protein, required for the specific interaction with DNA. Residues E26 and D40 in the putative metal binding motif (E26X10D37X2D40) present toward the N-terminus of the protein are found to be important for Mg2+ ion binding. Mutations in these residues lead to altered Mg2+-induced conformation, compromised DNA binding, and reduced levels of transcription activation. Although Mg2+ is widely used in various DNA transaction reactions, this report provides the first insights on the importance of the metal ion-induced allosteric transitions in regulating transcription factor function.

Mutations in beta ` subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance

P>Transcription activator C employs a unique mechanism to activate mom gene of bacteriophage Mu. The activation process involves, facilitating the recruitment of RNA polymerase (RNAP) by altering the topology of the promoter and enhancing the promoter clearance by reducing the abortive transcription. To understand the basis of this multi-step activation mechanism, we investigated the nature of the physical interaction between C and RNAP during the process. A variety of assays revealed that only DNA-bound C contacts the beta' subunit of RNAP. Consistent to these results, we have also isolated RNAP mutants having mutations in the beta' subunit which were compromised in C-mediated activation. Mutant RNAPs show reduced productive transcription and increased abortive initiation specifically at the C-dependent mom promoter. Positive control (pc) mutants of C, defective in interaction with RNAP, retained the property of recruiting RNAP to the promoter but were unable to enhance promoter clearance. These results strongly suggest that the recruitment of RNAP to the mom promoter does not require physical interaction with C, whereas a contact between the beta' subunit and the activator, and the subsequent allosteric changes in the active site of the enzyme are essential for the enhancement of promoter clearance.

Silencing of toxic gene expression by Fis

Bacteria and bacteriophages have evolved DNA modification as a strategy to protect their genomes. Mom protein of bacteriophage Mu modifies the phage DNA, rendering it refractile to numerous restriction enzymes and in turn enabling the phage to successfully invade a variety of hosts. A strong fortification, a combined activity of the phage and host factors, prevents untimely expression of mom and associated toxic effects. Here, we identify the bacterial chromatin architectural protein Fis as an additional player in this crowded regulatory cascade. Both in vivo and in vitro studies described here indicate that Fis acts as a transcriptional repressor of mom promoter. Further, our data shows that Fis mediates its repressive effect by denying access to RNA polymerase at mom promoter. We propose that a combined repressive effect of Fis and previously characterized negative regulatory factors could be responsible to keep the gene silenced most of the time. We thus present a new facet of Fis function in Mu biology. In addition to bringing about overall downregulation of Mu genome, it also ensures silencing of the advantageous but potentially lethal mom gene.

Silencing of toxic gene expression by Fis

Bacteria and bacteriophages have evolved DNA modification as a strategy to protect their genomes. Mom protein of bacteriophage Mumodifies the phage DNA, rendering it refractile to numerous restriction enzymes and in turn enabling the phage to successfully invade a variety of hosts. A strong fortification, a combined activity of the phage and host factors, prevents untimely expression of mom and associated toxic effects. Here, we identify the bacterial chromatin architectural protein Fis as an additional player in this crowded regulatory cascade. Both in vivo and in vitro studies described here indicate that Fisacts as a transcriptional repressor of mom promoter. Further, our data shows that Fis mediates its repressive effect by denying access to RNA polymerase at mom promoter. We propose that a combined repressive effect of Fis and previously characterized negative regulatory factors could be responsible to keep the gene silenced most of the time. We thus present a new facet of Fis function in Mu biology. In addition to bringing about overall downregulation of Mu genome, it also ensures silencing of the advantageous but potentially lethal mom gene.

Hardware Accelerator for 3D Method of Moments based Parasitic Extraction

A Field Programmable Gate Array (FPGA) based hardware accelerator for multi-conductor parasitic capacitance extraction, using Method of Moments (MoM), is presented in this paper. Due to the prohibitive cost of solving a dense algebraic system formed by MoM, linear complexity fast solver algorithms have been developed in the past to expedite the matrix-vector product computation in a Krylov sub-space based iterative solver framework. However, as the number of conductors in a system increases leading to a corresponding increase in the number of right-hand-side (RHS) vectors, the computational cost for multiple matrix-vector products present a time bottleneck, especially for ill-conditioned system matrices. In this work, an FPGA based hardware implementation is proposed to parallelize the iterative matrix solution for multiple RHS vectors in a low-rank compression based fast solver scheme. The method is applied to accelerate electrostatic parasitic capacitance extraction of multiple conductors in a Ball Grid Array (BGA) package. Speed-ups up to 13x over equivalent software implementation on an Intel Core i5 processor for dense matrix-vector products and 12x for QR compressed matrix-vector products is achieved using a Virtex-6 XC6VLX240T FPGA on Xilinx's ML605 board.

Adaptive Mesh Refinement for Fast Convergence of EFIE-Based 3-D Extraction

3-D full-wave method of moments (MoM) based electromagnetic analysis is a popular means toward accurate solution of Maxwell's equations. The time and memory bottlenecks associated with such a solution have been addressed over the last two decades by linear complexity fast solver algorithms. However, the accurate solution of 3-D full-wave MoM on an arbitrary mesh of a package-board structure does not guarantee accuracy, since the discretization may not be fine enough to capture spatial changes in the solution variable. At the same time, uniform over-meshing on the entire structure generates a large number of solution variables and therefore requires an unnecessarily large matrix solution. In this paper, different refinement criteria are studied in an adaptive mesh refinement platform. Consequently, the most suitable conductor mesh refinement criterion for MoM-based electromagnetic package-board extraction is identified and the advantages of this adaptive strategy are demonstrated from both accuracy and speed perspectives. The results are also compared with those of the recently reported integral equation-based h-refinement strategy. Finally, a new methodology to expedite each adaptive refinement pass is proposed.

Different Modes of Transactivation of Bacteriophage Mu Late Promoters by Transcription Factor C

Transactivator protein C is required for the expression of bacteriophage Mu late genes from lys, I, P and mom promoters during lytic life cycle of the phage. The mechanism of transcription activation of mom gene by C protein is well understood. C activates transcription at Pmom by initial unwinding of the promoter DNA, thereby facilitating RNA polymerase (RNAP) recruitment. Subsequently, C interacts with the (sic) subunit of RNAP to enhance promoter clearance. The mechanism by which C activates other late genes of the phage is not known. We carried out promoter-polymerase interaction studies with all the late gene promoters to determine the individual step of C mediated activation. Unlike at P-mom, at the other three promoters, RNAP recruitment and closed complex formation are not C dependent. Instead, the action of C at P-lys, P-I, and P-P is during the isomerization from closed complex to open complex with no apparent effect at other steps of initiation pathway. The mechanism of transcription activation of mom and other late promoters by their common activator is different. This distinction in the mode of activation (promoter recruitment and escape versus isomerization) by the same activator at different promoters appears to be important for optimized expression of each of the late genes.

Accelerating method of moments based package-board 3D parasitic extraction using FPGA

In this article, a Field Programmable Gate Array (FPGA)-based hardware accelerator for 3D electromagnetic extraction, using Method of Moments (MoM) is presented. As the number of nets or ports in a system increases, leading to a corresponding increase in the number of right-hand-side (RHS) vectors, the computational cost for multiple matrix-vector products presents a time bottleneck in a linear-complexity fast solver framework. In this work, an FPGA-based hardware implementation is proposed toward a two-level parallelization scheme: (i) matrix level parallelization for single RHS and (ii) pipelining for multiple-RHS. The method is applied to accelerate electrostatic parasitic capacitance extraction of multiple nets in a Ball Grid Array (BGA) package. The acceleration is shown to be linearly scalable with FPGA resources and speed-ups over 10x against equivalent software implementation on a 2.4GHz Intel Core i5 processor is achieved using a Virtex-6 XC6VLX240T FPGA on Xilinx's ML605 board with the implemented design operating at 200MHz clock frequency. (c) 2016 Wiley Periodicals, Inc. Microwave Opt Technol Lett 58:776-783, 2016