A Scalable High Throughput Firewall in FPGA

High end network security applications demand high speed operation and large rule set support. Packet classification is the core functionality that demands high throughput in such applications. This paper proposes a packet classification architecture to meet such high throughput. We have implemented a Firewall with this architecture in reconflgurable hardware. We propose an extension to Distributed Crossproducting of Field Labels (DCFL) technique to achieve scalable and high performance architecture. The implemented Firewall takes advantage of inherent structure and redundancy of rule set by using our DCFL Extended (DCFLE) algorithm. The use of DCFLE algorithm results in both speed and area improvement when it is implemented in hardware. Although we restrict ourselves to standard 5-tuple matching, the architecture supports additional fields. High throughput classification invariably uses Ternary Content Addressable Memory (TCAM) for prefix matching, though TCAM fares poorly in terms of area and power efficiency. Use of TCAM for port range matching is expensive, as the range to prefix conversion results in large number of prefixes leading to storage inefficiency. Extended TCAM (ETCAM) is fast and the most storage efficient solution for range matching. We present for the first time a reconfigurable hardware implementation of ETCAM. We have implemented our Firewall as an embedded system on Virtex-II Pro FPGA based platform, running Linux with the packet classification in hardware. The Firewall was tested in real time with 1 Gbps Ethernet link and 128 sample rules. The packet classification hardware uses a quarter of logic resources and slightly over one third of memory resources of XC2VP30 FPGA. It achieves a maximum classification throughput of 50 million packet/s corresponding to 16 Gbps link rate for the worst case packet size. The Firewall rule update involves only memory re-initialization in software without any hardware change.

A Scalable High Throughput Firewall in FPGA

High end network security applications demand high speed operation and large rule set support. Packet classification is the core functionality that demands high throughput in such applications. This paper proposes a packet classification architecture to meet such high throughput. We have Implemented a Firewall with this architecture in reconfigurable hardware. We propose an extension to Distributed Crossproducting of Field Labels (DCFL) technique to achieve scalable and high performance architecture. The implemented Firewall takes advantage of inherent structure and redundancy of rule set by using, our DCFL Extended (DCFLE) algorithm. The use of DCFLE algorithm results In both speed and area Improvement when It is Implemented in hardware. Although we restrict ourselves to standard 5-tuple matching, the architecture supports additional fields.High throughput classification Invariably uses Ternary Content Addressable Memory (TCAM) for prefix matching, though TCAM fares poorly In terms of area and power efficiency. Use of TCAM for port range matching is expensive, as the range to prefix conversion results in large number of prefixes leading to storage inefficiency. Extended TCAM (ETCAM) is fast and the most storage efficient solution for range matching. We present for the first time a reconfigurable hardware Implementation of ETCAM. We have implemented our Firewall as an embedded system on Virtex-II Pro FPGA based platform, running Linux with the packet classification in hardware. The Firewall was tested in real time with 1 Gbps Ethernet link and 128 sample rules. The packet classification hardware uses a quarter of logic resources and slightly over one third of memory resources of XC2VP30 FPGA. It achieves a maximum classification throughput of 50 million packet/s corresponding to 16 Gbps link rate for file worst case packet size. The Firewall rule update Involves only memory re-initialiization in software without any hardware change.

A scalable network port scan detection system on FPGA

With ever increasing network speed, scalable and reliable detection of network port scans has become a major challenge. In this paper, we present a scalable and flexible architecture and a novel algorithm, to detect and block port scans in real time. The proposed architecture detects fast scanners as well as stealth scanners having large inter-probe periods. FPGA implementation of the proposed system gives an average throughput of 2 Gbps with a system clock frequency of 100 MHz on Xilinx Virtex-II Pro FPGA. Experimental results on real network trace show the effectiveness of the proposed system in detecting and blocking network scans with very low false positives and false negatives.

Polypeptide models of collagen. II. Solution properties of (Pro-Gly-Phe)n

The conformation of (Pro-Gly-Phe)n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro-Gly-Phe)n can exist in a partially triple-helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly-R2-R3, in collagen.

Conformational transitions in a Pro-Pro peptide on dissolution of single crystals

The peptide t-butyloxycarbonyl-α-aminoisobutyryl-L-prolyl-L-prolyl-N-methylamide has been shown to adopt an extended structure in the solid state. The Pro-Pro segment occurs in the poly-proline II conformation. On dissolution of single crystals at not, vert, similar 233°K, a single species corresponding to the all Image peptide backbone is observed by 270 MHz 1H NMR. On warming, Image to Image isomerization about the Pro-Pro bond is facilitated. Both Image (ψ not, vert, similar−50°) and Image (ψ not, vert, similar 130°) rotamers about the Pro3 Cα---CO bond are detectable in the Pro-Pro Image conformer, at low temperature. These observations demonstrate unambiguously the large differences in the solid state and solution conformations of a Pro-Pro sequence.

Type II beta-turn conformation of pivaloyl-L-prolyl-alpha-aminoisobutyryl-N-methylamide: Theoretical, spectroscopic, and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H-nmr methods, suggesting the existence of beta -turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II beta-turn conformations are about 2 kcal mol-1 more stable than Type III structures. A crystallographic study has established the Type II beta-turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, beta = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II -turn conformation is stabilized by an intramolecular 4 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are Pro = -57.8°, Pro = 139.3°, Aib = 61.4°, and Aib = 25.1°. The Type II beta-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.

Acyclic peptides as conformational models Crystal structure of Boc-Aib-Leu-Pro-NHMe± 2H2O

The tripeptide Boc-Aib-Leu-Pro-NHMe crystallizes in the orthorhombic space group P212121 with a = 9.542, b = 15.200, c = 18.256 Å and Z = 4. Each peptide is associated wth two water molecules in the asymmetric unit of the crystal. The structure has been solved by direct methods and refined to an R-value of 0.069. The peptide adopts a structure without any intramolecular hydrogen bond. The three residues occupy distinctly different regions of the Ramachandran map: Aib in the left-handed 310-helical region (± = 67°, ± = 23°), Leu in the β-sheet region (± = - 133°, ± = 142°) and Pro in the poly (Pro) II region (± = - 69°, ± = 151°). An interesting observation is that each water molecule participates in four hydrogen bonds with distorted tetrahedral coordination about the oxygen atom.

Cytotoxicity of half sandwich ruthenium(II) complexes with strong hydrogen bond acceptor ligands and their mechanism of action

Neutral and cationic organometallic ruthenium(II) piano stool complexes of the type [(eta(6)-cymene)R-uCl(X)(Y)] (complexes R1-R8) has been synthesized and characterized. In cationic complexes, X, Y is either a eta(2) phosphorus ligand such as 1,1-bis(diphenylphosphino)methane (DPPM) and 1,2-bis(diphenylphosphino)ethane (DPPE) or partially oxidized ligands such as 1,2-bis(diphenylphosphino)methane monooxide (DPPMO) and 1,2-bis(diphenylphosphino)ethane monooxide (DPPEO) which are strong hydrogen bond acceptors. In neutral complexes. X is chloride and Y is a monodentate phosphorous donor. Complexes with DPPM and DPPMO ligands ([(eta(6)-cymene)Ru(eta(2)-DPPM)Cl]PF6 (R2), [(eta(6)-cymene)Ru(eta(2)-DPPMO)Cl]PF6 (R3), [(eta(6)-cymene)Ru(eta(1)-DPPM)Cl-2] (R5) and [(eta(6)-cymene)Ru(eta(1)-DPPMO)Cl-2] (R6) show good cytotoxicity. Growth inhibition study of several human cancer cell lines by these complexes has been carried out. Mechanistic studies for R5 and R6 show that inhibition of cancer cell growth involves both cell cycle arrest and apoptosis induction. Using an apoptosis PCR array, we identified the sets of antiapoptotic genes that were down regulated and pro-apoptotic genes that were up regulated. These complexes were also found to be potent metastasis inhibitors as they prevented cell invasion through matrigel. The complexes were shown to bind DNA in a non intercalative fashion and cause unwinding of plasmid DNA in cell-free medium by competitive ethidium bromide binding, viscosity measurements, thermal denaturation and gel mobility shift assays.

Type II beta-turn conformation of pivaloyl-L-prolyl-a-aminoiso-butyryl-N-methylamide: Theoretical, spectroscopic and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamihdaes been shown to possess one intramolecular hydrogen bond in (CD&SO solution, by 'H-nmr methods, suggesting the existence of p-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II P-turn conformations are about 2 kcal mol-' more stable than Type 111 structures. A crystallographic study has established the Type I1 /%turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 8, b = 11.421 A, c = 12.966 A, /3 = 97.55", and 2 = 2. The structure has been refined to a final R value of 0.061. The Type I1 p-turn conformation is stabilized by an intramolecular 4 - 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are @pro= -57.8", $pro = 139.3', @Aib = 61.4', and $Ajb = 25.1'. The Type 11 /%turn conformation for Pro-Aib in this peptide is compared with the Type I11 structures observed for the same segment in larger peptides.

Conformational restrictions of peptides via backbone modification: Solution and crystal-state analysis of Boc-L-Pro-DZPhe-Gly-NH2

An N-alpha-protected model tripeptide amide containing, in the central position, an alpha,beta-dehydrophenylalanine (Z-configurational isomer), Boc-L-Pro-DELTA-Z-Phe-Gly-NH2 (Boc, tert-butyloxycarbonyl), has been synthesized by solution methods and fully characterized. IR absorption and H-1 NMR studies provided evidence for the occurrence of a significant population of a conformer containing two consecutive, intramolecularly H-bonded (type II-III') beta-bends in solution. However, an X-ray diffraction analysis clearly indicates that only the type-II beta-bend structure survives in the crystal state.

Conformations of peptides containing Z-alpha,beta-dehydroleucine (delta ZLeu). A comparison of Boc-Pro-delta ZLeu-Gly-NHEt and Boc-Pro-delta ZPhe-Gly-NHEt.

Two tripeptides of the type Boc-Pro-ΔZX-Gly-NHEt (where X = Leu, Phe) have been synthesized and their solution conformations investigated by 270 MHz 1H n.m.r. and i.r. spectroscopy. These conformational studies indicated that ΔZLeu, similar to ΔZPhe, has a strong tendency to stabilize folded Type II β-turn conformations when present at i + 2 position.

Stabilization of unusual structures in peptides using alpha,beta-dehydrophenylalanine: Crystal and solution structures of Boc-Pro-Delta Phe-Val-Delta Phe-Ala-OMe and Boc-Pro-Delta Phe-Gly-Delta Phe-Ala-OMe

The structures of two dehydropentapeptides, Boc-Pro-Delta Phe-Val-Delta Phe-Ala-OMe (I) and Boc-Pro-Delta Phe-Gly-Delta Phe-Ala-OMe (II) (Boc: t-butoxycarbonyl), have been determined by nuclear magnentic resonance (NMR), circular dichroism (CD), and X-ray, crystallographic studies. The peptide I assumes a S-shaped flat beta-bend structure, characterized by two partially overlapping type II beta-bends and absence of a second 1 <- 4 (N4-H center dot center dot center dot O1') intramolecular hydrogen bond. This is in contrast to the generally observed 3(10)-helical conformation in peptides with Delta Phe at alternate positions. This report describes the novel conformation assumed by peptide I and compares it with that of the conserved tip of the V3 loop of the HIV-1 envelope glycoprotein gp120 (sequence, G:P319 to F:P324, PDB code IACY). The tip of the V3 loop also assumes a S-shaped conformation with Arg:P322, making an intramolecular side-chain-backbone interaction with the carbonyl oxygen of Gly:P319. Interestingly, in peptide I, C(gamma)HVal(3) makes a similar side-chain-backbone C-H center dot center dot center dot O hydrogen bond with the carbonyl oxygen of the Boc group. The observed overall similarity indicates the possible use of the peptide as a viral antagonist or synthetic antigen. Peptide 11 adopts a unique turn followed by a 3(10)-helix. Both peptides I and II are classical examples of stabilization of unusual structures in oligopeptides.

Diproline Templates as Folding Nuclei in Designed Peptides. Conformational Analysis of Synthetic Peptide Helices Containing Amino Terminal Pro-Pro Segments

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (RR) conformation for the segment residues 2 to 5, stabilized by one 4 -> 1 hydrogen bond and two 5 -> 1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P-II) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alpha(R)-alpha(R) conformation, whereas in the latter, a P-II-alpha(R) structure is established. The conformational equilibrium shifts in favor of the P-II-alpha(R) structure in solvents like methanol and DMSO. A significant population of the Pro(1)- Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro- Pro segment: trans alpha(R)-alpha(R), trans P-II-alpha(R) and cis P-II-alpha(R). Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alpha(R)-alpha(R) conformation followed by a helix. Modeling and energy minimization studies suggest that both P-II-alpha(R) and alpha(R)-alpha(R) conformations have very similar energies in the model hexapeptide 1

Structure and conformation of the calcium complex of cyclo(Ala-Leu-Pro-Gly)2 in two crystal forms

Crystal structures of two different forms of the calcium perchlorate complex of cyclo(Ala-Leu-Pro-Gly)2 have been determined and refined using X-ray crystallographic techniques. Orthorhombic form: C32H52N8O8.Ca(ClO4)2.7H2O.2CH3OH, space group C222(1), a = 14.366, b = 18.653, c = 19.824 A, Z = 4, R = 0.068 for 2208 observed reflections. Monoclinic form: C32H52N8O8.Ca(ClO4)2.4H2O, space group C2, a = 21.096, b = 10.182, c = 11.256 A, beta = 103.33 degrees, Z = 2, R = 0.075 for 2165 observed reflections. The cyclic peptide molecule in both the structures has the form of a twofold symmetric, slightly elongated bowl. Type II' beta-turns, involving Gly and Ala at the corners, exist at the two ends of the molecule. The interior of the molecule is substantially hydrophilic, and the external surface of the bowl is largely hydrophobic. The calcium ion is located at the centre of the mouth of the bowl-like molecule. In both crystal forms, four peptide carbonyl oxygens from the cyclic peptide and two solvent oxygens coordinate to the metal ion. The mode of complexation may be described as incomplete encapsulation as, for example, in the case of metal complexes of antamanide. In the crystal structures the complex ions are held together by hydrogen bonds involving perchlorate ions and water molecules. The molecular structure observed in the crystals is entirely consistent with the results of solution studies, which also indicate the conformation of the cyclic peptide in the complex to be similar to that of the uncomplexed molecule.

Epithelial atrophy in oral submucous fibrosis is mediated by copper (II) and arecoline of areca nut

Exposure of oral cavity to areca nut is associated with several pathological conditions including oral submucous fibrosis (OSF). Histopathologically OSF is characterized by epithelial atrophy, chronic inflammation, juxtaepithelial hyalinization, leading to fibrosis of submucosal tissue and affects 0.5% of the population in the Indian subcontinent. As the molecular mechanisms leading to atrophied epithelium and fibrosis are poorly understood, we studied areca nut actions on human keratinocyte and gingival fibroblast cells. Areca nut water extract (ANW) was cytotoxic to epithelial cells and had a pro-proliferative effect on fibroblasts. This opposite effect of ANW on epithelial and fibroblast cells was intriguing but reflects the OSF histopathology such as epithelial atrophy and proliferation of fibroblasts. We demonstrate that the pro-proliferative effects of ANW on fibroblasts are dependent on insulin-like growth factor signalling while the cytotoxic effects on keratinocytes are dependent on the generation of reactive oxygen species. Treatment of keratinocytes with arecoline which is a component of ANW along with copper resulted in enhanced cytotoxicity which becomes comparable to IC50 of ANW. Furthermore, studies using cyclic voltammetry, mass spectrometry and plasmid cleavage assay suggested that the presence of arecoline increases oxidation reduction potential of copper leading to enhanced cleavage of DNA which could generate an apoptotic response. Terminal deoxynucleotidyl transferase dUTP Nick End Labeling assay and Ki-67 index of OSF tissue sections suggested epithelial apoptosis, which could be responsible for the atrophy of OSF epithelium.