arjun singh - Academia.edu (original) (raw)

Papers by arjun singh

IEEE Computer Architecture Letters, 2004

We apply recent results in queueing theory to propose a methodology for bounding the buffer depth... more We apply recent results in queueing theory to propose a methodology for bounding the buffer depth and packet delay in high radix interconnection networks. While most work in interconnection networks has been focused on the throughput and average latency in such systems, few studies have been done providing statistical guarantees for buffer depth and packet delays. These parameters are key in the design and performance of a network. We present a methodology for calculating such bounds for a practical high radix network and through extensive simulations show its effectiveness for both bursty and non-bursty injection traffic. Our results suggest that modest speedups and buffer depths enable reliable networks without flow control to be constructed.

ACM Sigarch Computer Architecture News, 2003

We introduce a load-balanced adaptive routing algorithm for torus networks, GOAL -Globally Oblivi... more We introduce a load-balanced adaptive routing algorithm for torus networks, GOAL -Globally Oblivious Adaptive Locally -that provides high throughput on adversarial traffic patterns, matching or exceeding fully randomized routing and exceeding the worst-case performance of Chaos , RLB [14], and minimal routing [8] by more than 40%. GOAL also preserves locality to provide up to 4.6× the throughput of fully randomized routing [19] on local traffic. GOAL achieves global load balance by randomly choosing the direction to route in each dimension. Local load balance is then achieved by routing in the selected directions adaptively. We compare the throughput, latency, stability and hot-spot performance of GOAL to six previously published routing algorithms on six specific traffic patterns and 1,000 randomly generated permutations.

The trypanosome zinc finger protein ZC3H11 binds to AU-rich elements in mRNAs. It is essential fo... more The trypanosome zinc finger protein ZC3H11 binds to AU-rich elements in mRNAs. It is essential for survival of the mammalian-infective bloodstream form, where it stabilizes several mRNAs including some encoding chaperones, and is also required for stabilization of chaperone mRNAs during the heat-shock response in the vector-infective procyclic form. When ZC3H11 was artificially 'tethered' to a reporter mRNA in bloodstream forms it increased reporter expression. We here show that ZC3H11 interacts with trypanosome MKT1 and PBP1, and that domains required for both interactions are necessary for function in the bloodstream-form tethering assay. PBP1 interacts with MKT1, LSM12 and poly(A) binding protein, and localizes to granules during parasite starvation. All of these proteins are essential for bloodstream-form trypanosome survival and increase gene expression in the tethering assay. MKT1 is cytosolic and polysome associated. Using a yeast two-hybrid screen and tandem affinity purification we found that trypanosome MKT1 interacts with multiple RNA-binding proteins and other potential RNA regulators, placing it at the centre of a post-transcriptional regulatory network. A consensus interaction sequence, H(E/D/ N/Q)PY, was identified. Recruitment of MKT1containing regulatory complexes to mRNAs via sequence-specific mRNA-binding proteins could thus control several different post-transcriptional regulons.

RNA interference has already proven itself to be a highly versatile molecular biology tool for un... more RNA interference has already proven itself to be a highly versatile molecular biology tool for understanding gene function in a limited number of insect species, but its widespread use in other species will be dependent on the development of easier methods of double-stranded RNA (dsR-NA) delivery. This study demonstrates that RNA interference can be induced in the mosquito Aedes aegypti L. (Diptera: Culicidae) simply by soaking larvae in a solution of dsRNA for two hours. The mRNA transcripts for β-tubulin, chitin synthase-1 and -2, and heat shock protein 83 were reduced between 30 and 50% three days post-dsRNA treatment. The dsRNA was mixed with a visible dye to identify those individuals that fed on the dsRNA, and based on an absence of RNA interference in those individuals that contained no dye within their guts, the primary route of entry of dsRNA is likely through the gut epithelium. RNA interference was systemic in the insects, inducing measurable knock down of gene expression in tissues beyond the gut. Silencing of the β-tubulin and chitin synthase-1 genes resulted in reduced growth and/or mortality of the larvae, demonstrating the utility of dsRNA as a potential mosquito larvicide. Silencing of chitin synthase-2 did not induce mortality in the larvae, and silencing of heat shock protein 83 only induced mortality in the insects if they were subsequently subjected to a heat stress. Drosophila melanogaster Meigen (Diptera: Drosophilidae) larvae were also soaked in dsRNA designed to specifically target either their own β-tubulin gene, or that of A. aegypti, and significant mortality was only seen in larvae treated with dsRNA targeting their own gene, which suggests that dsRNA pesticides could be designed to be species-limited.

We present a model for the steady dynamic friction of a block of an elastomer, sliding steadily o... more We present a model for the steady dynamic friction of a block of an elastomer, sliding steadily on a hard surface. The model uses population balance of the bonds between the hard surface and the polymer chains of the elastomer to estimate the force of friction. Although the basic premises of the present model are the same as those of the Schallamach model for dynamic friction (1963), the present formulation is a clearer representation of the phenomena involved. Moreover, the model is not based on the ergodic hypothesis and is therefore more versatile. It also allows us to correct the error in the expression for the force of friction in the Schallamach model. The present model exhibits the same qualitative trends as the Schallamach model. However, there are significant quantitative differences between the two models. We also show that our expression for the force of friction is equivalent to that obtained by the Chernyak and Leonov (1986) model, which is based on the ergodic hypothesis. The model is further modified to account for both the non-Hookean extension of the bonded chains and the viscous retardation effect. The model is validated using the experimental data of Vorvolakos and Chaudhury (2003) on sliding of crosslinked PDMS solid on silane coated silicon wafer. From this analysis, scaling laws, which relate the model parameters to the molecular weight of the polymer chains and the temperature, are derived and justified.

In most organisms, the heat-shock response involves increased heat-shock gene transcription. In K... more In most organisms, the heat-shock response involves increased heat-shock gene transcription. In Kinetoplastid protists, however, virtually all control of gene expression is post-transcriptional. Correspondingly, Trypanosoma brucei heat-shock protein 70 (HSP70) synthesis after heat shock depends on regulation of HSP70 mRNA turnover. We here show that the T. brucei CCCH zinc finger protein ZC3H11 is a post-transcriptional regulator of trypanosome chaperone mRNAs. ZC3H11 is essential in bloodstream-form trypanosomes and for recovery of insect-form trypanosomes from heat shock. ZC3H11 binds to mRNAs encoding heat-shock protein homologues, with clear specificity for the subset of trypanosome chaperones that is required for protein refolding. In procyclic forms, ZC3H11 was required for stabilisation of target chaperone-encoding mRNAs after heat shock, and the HSP70 mRNA was also decreased upon ZC3H11 depletion in bloodstream forms. Many mRNAs bound to ZC3H11 have a consensus AUU repeat motif in the 3'-untranslated region. ZC3H11 bound preferentially to AUU repeats in vitro, and ZC3H11 regulation of HSP70 mRNA in bloodstream forms depended on its AUU repeat region. Tethering of ZC3H11 to a reporter mRNA increased reporter expression, showing that it is capable of actively stabilizing an mRNA. These results show that expression of trypanosome heat-shock genes is controlled by a specific RNA-protein interaction. They also show that heat-shock-induced chaperone expression in procyclic trypanosome enhances parasite survival at elevated temperatures.

The special type of general linear method known as a DIMSIM can be specialized to parallel comput... more The special type of general linear method known as a DIMSIM can be specialized to parallel computation for stiff initial value problems by considering type 4 methods. In this paper we consider an implementation of type 4 methods with A = λI and p = s. We also consider some generalizations of the type 4 DIMSIMs in an effort to make these methods more efficient.

IEEE Computer Architecture Letters, 2004

We apply recent results in queueing theory to propose a methodology for bounding the buffer depth... more We apply recent results in queueing theory to propose a methodology for bounding the buffer depth and packet delay in high radix interconnection networks. While most work in interconnection networks has been focused on the throughput and average latency in such systems, few studies have been done providing statistical guarantees for buffer depth and packet delays. These parameters are key in the design and performance of a network. We present a methodology for calculating such bounds for a practical high radix network and through extensive simulations show its effectiveness for both bursty and non-bursty injection traffic. Our results suggest that modest speedups and buffer depths enable reliable networks without flow control to be constructed.

ACM Sigarch Computer Architecture News, 2003

We introduce a load-balanced adaptive routing algorithm for torus networks, GOAL -Globally Oblivi... more We introduce a load-balanced adaptive routing algorithm for torus networks, GOAL -Globally Oblivious Adaptive Locally -that provides high throughput on adversarial traffic patterns, matching or exceeding fully randomized routing and exceeding the worst-case performance of Chaos , RLB [14], and minimal routing [8] by more than 40%. GOAL also preserves locality to provide up to 4.6× the throughput of fully randomized routing [19] on local traffic. GOAL achieves global load balance by randomly choosing the direction to route in each dimension. Local load balance is then achieved by routing in the selected directions adaptively. We compare the throughput, latency, stability and hot-spot performance of GOAL to six previously published routing algorithms on six specific traffic patterns and 1,000 randomly generated permutations.

The trypanosome zinc finger protein ZC3H11 binds to AU-rich elements in mRNAs. It is essential fo... more The trypanosome zinc finger protein ZC3H11 binds to AU-rich elements in mRNAs. It is essential for survival of the mammalian-infective bloodstream form, where it stabilizes several mRNAs including some encoding chaperones, and is also required for stabilization of chaperone mRNAs during the heat-shock response in the vector-infective procyclic form. When ZC3H11 was artificially 'tethered' to a reporter mRNA in bloodstream forms it increased reporter expression. We here show that ZC3H11 interacts with trypanosome MKT1 and PBP1, and that domains required for both interactions are necessary for function in the bloodstream-form tethering assay. PBP1 interacts with MKT1, LSM12 and poly(A) binding protein, and localizes to granules during parasite starvation. All of these proteins are essential for bloodstream-form trypanosome survival and increase gene expression in the tethering assay. MKT1 is cytosolic and polysome associated. Using a yeast two-hybrid screen and tandem affinity purification we found that trypanosome MKT1 interacts with multiple RNA-binding proteins and other potential RNA regulators, placing it at the centre of a post-transcriptional regulatory network. A consensus interaction sequence, H(E/D/ N/Q)PY, was identified. Recruitment of MKT1containing regulatory complexes to mRNAs via sequence-specific mRNA-binding proteins could thus control several different post-transcriptional regulons.

RNA interference has already proven itself to be a highly versatile molecular biology tool for un... more RNA interference has already proven itself to be a highly versatile molecular biology tool for understanding gene function in a limited number of insect species, but its widespread use in other species will be dependent on the development of easier methods of double-stranded RNA (dsR-NA) delivery. This study demonstrates that RNA interference can be induced in the mosquito Aedes aegypti L. (Diptera: Culicidae) simply by soaking larvae in a solution of dsRNA for two hours. The mRNA transcripts for β-tubulin, chitin synthase-1 and -2, and heat shock protein 83 were reduced between 30 and 50% three days post-dsRNA treatment. The dsRNA was mixed with a visible dye to identify those individuals that fed on the dsRNA, and based on an absence of RNA interference in those individuals that contained no dye within their guts, the primary route of entry of dsRNA is likely through the gut epithelium. RNA interference was systemic in the insects, inducing measurable knock down of gene expression in tissues beyond the gut. Silencing of the β-tubulin and chitin synthase-1 genes resulted in reduced growth and/or mortality of the larvae, demonstrating the utility of dsRNA as a potential mosquito larvicide. Silencing of chitin synthase-2 did not induce mortality in the larvae, and silencing of heat shock protein 83 only induced mortality in the insects if they were subsequently subjected to a heat stress. Drosophila melanogaster Meigen (Diptera: Drosophilidae) larvae were also soaked in dsRNA designed to specifically target either their own β-tubulin gene, or that of A. aegypti, and significant mortality was only seen in larvae treated with dsRNA targeting their own gene, which suggests that dsRNA pesticides could be designed to be species-limited.

We present a model for the steady dynamic friction of a block of an elastomer, sliding steadily o... more We present a model for the steady dynamic friction of a block of an elastomer, sliding steadily on a hard surface. The model uses population balance of the bonds between the hard surface and the polymer chains of the elastomer to estimate the force of friction. Although the basic premises of the present model are the same as those of the Schallamach model for dynamic friction (1963), the present formulation is a clearer representation of the phenomena involved. Moreover, the model is not based on the ergodic hypothesis and is therefore more versatile. It also allows us to correct the error in the expression for the force of friction in the Schallamach model. The present model exhibits the same qualitative trends as the Schallamach model. However, there are significant quantitative differences between the two models. We also show that our expression for the force of friction is equivalent to that obtained by the Chernyak and Leonov (1986) model, which is based on the ergodic hypothesis. The model is further modified to account for both the non-Hookean extension of the bonded chains and the viscous retardation effect. The model is validated using the experimental data of Vorvolakos and Chaudhury (2003) on sliding of crosslinked PDMS solid on silane coated silicon wafer. From this analysis, scaling laws, which relate the model parameters to the molecular weight of the polymer chains and the temperature, are derived and justified.

In most organisms, the heat-shock response involves increased heat-shock gene transcription. In K... more In most organisms, the heat-shock response involves increased heat-shock gene transcription. In Kinetoplastid protists, however, virtually all control of gene expression is post-transcriptional. Correspondingly, Trypanosoma brucei heat-shock protein 70 (HSP70) synthesis after heat shock depends on regulation of HSP70 mRNA turnover. We here show that the T. brucei CCCH zinc finger protein ZC3H11 is a post-transcriptional regulator of trypanosome chaperone mRNAs. ZC3H11 is essential in bloodstream-form trypanosomes and for recovery of insect-form trypanosomes from heat shock. ZC3H11 binds to mRNAs encoding heat-shock protein homologues, with clear specificity for the subset of trypanosome chaperones that is required for protein refolding. In procyclic forms, ZC3H11 was required for stabilisation of target chaperone-encoding mRNAs after heat shock, and the HSP70 mRNA was also decreased upon ZC3H11 depletion in bloodstream forms. Many mRNAs bound to ZC3H11 have a consensus AUU repeat motif in the 3'-untranslated region. ZC3H11 bound preferentially to AUU repeats in vitro, and ZC3H11 regulation of HSP70 mRNA in bloodstream forms depended on its AUU repeat region. Tethering of ZC3H11 to a reporter mRNA increased reporter expression, showing that it is capable of actively stabilizing an mRNA. These results show that expression of trypanosome heat-shock genes is controlled by a specific RNA-protein interaction. They also show that heat-shock-induced chaperone expression in procyclic trypanosome enhances parasite survival at elevated temperatures.

The special type of general linear method known as a DIMSIM can be specialized to parallel comput... more The special type of general linear method known as a DIMSIM can be specialized to parallel computation for stiff initial value problems by considering type 4 methods. In this paper we consider an implementation of type 4 methods with A = λI and p = s. We also consider some generalizations of the type 4 DIMSIMs in an effort to make these methods more efficient.