CiteULike: Author Bagchi

Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model

Kimberly Stark — 2008-05-29T11:11:33-00:00

Nat Genet, Vol. 40, No. 6. (June 2008), pp. 751-760.

Energy Landscape, Antiplasticization, and Polydispersity Induced Crossover of Heterogeneity in Supercooled Polydisperse Liquids

Sneha Abraham — 2008-05-05T20:40:53-00:00

Physical Review Letters, Vol. 100, No. 16. (2008)

Polydispersity is found to have a significant effect on the potential energy landscape; the average inherent structure energy decreases with polydispersity. Increasing polydispersity at a fixed volume fraction decreases the glass transition temperature and the fragility of glass formation analogous to the antiplasticization seen in some polymeric melts. An interesting temperature dependent crossover of heterogeneity with polydispersity is observed at low temperature due to the faster buildup of dynamic heterogeneity at lower polydispersity.

A molecular explanation of the transition from viscous to hopping mechanism of mass transport in the supercooled liquid near the glass transition

Biman Bagchi — 2008-06-18T15:45:47-00:00

The Journal of Chemical Physics, Vol. 101, No. 11. (1994), pp. 9946-9955.

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Adaptive correctness monitoring for wireless sensor networks using hierarchical distributed run-time invariant checking

Douglas Herbert — 2008-06-16T01:56:36-00:00

ACM Trans. Auton. Adapt. Syst., Vol. 2, No. 3. (September 2007)

Best-First Search Methods for Constrained Two-Dimensional Cutting Stock Problems

KV Viswanathan — 2008-06-14T17:39:14-00:00

Operations Research, Vol. 41, No. 4. (1993), pp. 768-776.

Best-first search is a widely used problem solving technique in the field of artificial intelligence. The method has useful applications in operations research as well. Here we describe an application to constrained two-dimensional cutting stock problems of the following type: A stock rectangle S of dimensions (L, W) is supplied. There are n types of demanded rectangles r1,r2,...,rn, with the ith type having length li, width wi, value vi, and demand constraint bi. It is required to produce, from the stock rectangle S, ai copies of ri, 1≤ i≤ n, to maximize a1v1+a2v2+... +anvn subject to the constraints ai≤ bi. Only orthogonal guillotine cuts are permitted. All parameters are integers. A best-first tree search algorithm based on Wang's bottom-up approach is described that guarantees optimal solutions and is more efficient than existing methods.

Combinatorial triangulations of homology spheres

Bhaskar Bagchi — 2008-05-15T12:01:13-00:00

Discrete Mathematics, Vol. 305, No. 1-3. (6 December 2005), pp. 1-17.

Let M be an n-vertex combinatorial triangulation of a -homology d-sphere. In this paper we prove that if n[less-than-or-equals, slant]d+8 then M must be a combinatorial sphere. Further, if n=d+9 and M is not a combinatorial sphere then M cannot admit any proper bistellar move. Existence of a 12-vertex triangulation of the lens space L(3,1) shows that the first result is sharp in dimension three. In the course of the proof we also show that any -acyclic simplicial complex on [less-than-or-equals, slant]7 vertices is necessarily collapsible. This result is best possible since there exist 8-vertex triangulations of the Dunce Hat which are not collapsible.

The Quest for the 1p36 Tumor Suppressor

Anindya Bagchi — 2008-05-05T15:22:47-00:00

Cancer Res, Vol. 68, No. 8. (15 April 2008), pp. 2551-2556.

Genomic analyses of late-stage human cancers have uncovered deletions encompassing 1p36, thereby providing an extensive body of literature supporting the idea that a potent tumor suppressor resides in this interval. Although several genes have been proposed as 1p36 candidate tumor suppressors, convincing evidence that their encoded products protect from cancer has been scanty. A recent functional study identified chromodomain helicase DNA-binding protein 5 (CHD5) as a novel tumor suppressor mapping to 1p36. Here, we discuss evidence supporting the tumor-suppressive role of CHD5. Together, these findings suggest that strategies designed to enhance CHD5 activity could provide novel approaches for treating a broad range of human malignancies. [Cancer Res 2008;68(8):2551-6] 10.1158/0008-5472.CAN-07-2095

Constructing disjoint paths for secure communication

A Bagchi — 2008-04-24T18:26:19-00:00

Lecture Notes in Computer Science, Vol. 2848 (2003)

We propose a bandwidth-e#cient algorithmic solution for perfectly-secure communication in the absence of secure infrastructure.

Mesoscale Simulation of Blood Flow in Small Vessels

Prosenjit Bagchi — 2008-02-11T19:32:12-00:00

Biophys. J., Vol. 92, No. 6. (15 March 2007), pp. 1858-1877.

Computational modeling of blood flow in microvessels with internal diameter 20-500 microm is a major challenge. It is because blood in such vessels behaves as a multiphase suspension of deformable particles. A continuum model of blood is not adequate if the motion of individual red blood cells in the suspension is of interest. At the same time, multiple cells, often a few thousands in number, must also be considered to account for cell-cell hydrodynamic interaction. Moreover, the red blood cells (RBCs) are highly deformable. Deformation of the cells must also be considered in the model, as it is a major determinant of many physiologically significant phenomena, such as formation of a cell-free layer, and the Fahraeus-Lindqvist effect. In this article, we present two-dimensional computational simulation of blood flow in vessels of size 20-300 microm at discharge hematocrit of 10-60%, taking into consideration the particulate nature of blood and cell deformation. The numerical model is based on the immersed boundary method, and the red blood cells are modeled as liquid capsules. A large RBC population comprising of as many as 2500 cells are simulated. Migration of the cells normal to the wall of the vessel and the formation of the cell-free layer are studied. Results on the trajectory and velocity traces of the RBCs, and their fluctuations are presented. Also presented are the results on the plug-flow velocity profile of blood, the apparent viscosity, and the Fahraeus-Lindqvist effect. The numerical results also allow us to investigate the variation of apparent blood viscosity along the cross-section of a vessel. The computational results are compared with the experimental results. To the best of our knowledge, this article presents the first simulation to simultaneously consider a large ensemble of red blood cells and the cell deformation. 10.1529/biophysj.106.095042

Hydrogen-Bond Dynamics near a Micellar Surface: Origin of the Universal Slow Relaxation at Complex Aqueous Interfaces

Sundaram Balasubramanian — 2008-04-03T21:04:30-00:00

Physical Review Letters, Vol. 89, No. 11. (2002), 115505.

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules; and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.

Characterization of proteases in guts of Daphnia magna and their inhibition by Microcystis aeruginosa PCC 7806.

MK Agrawal — 2008-03-05T16:12:21-00:00

Environ Toxicol, Vol. 20, No. 3. (June 2005), pp. 314-322.

Many cyanobacteria produce peptides that inhibit mammalian proteases. The hypothesis that inhibitors of mammalian proteases produced by cyanobacteria also interfere with digestive proteases of natural cladoceran grazers was tested by comparing the effects of cyanobacterial protease inhibitors on digestive proteases from Daphnia magna and on commercially available bovine proteases. The major digestive proteases of D. magna are trypsins and chymotrypsins, which differ from those of bovine origin in substrate specificity and susceptibility to synthetic inhibitors. An extract from Microcystis aeruginosa strain PCC 7806 inhibited both types of D. magna proteases. Subsequent fractionation of the extract by high-performance liquid chromatography indicated that several inhibitors are produced by M. aeruginosa that differ in their specificity for the trypsins and chymotrypsins of D. magna. Two fractions differed in their inhibitory effect on proteases of D. magna and bovine origin; therefore, assessment of the impact of cyanobacterial protease inhibitors on natural communities requires the use of digestive proteases from ecologically relevant grazers.

Diffusion and viscosity in a supercooled polydisperse system

Rajesh Murarka — 2008-03-01T21:03:11-00:00

Physical Review E, Vol. 67, No. 5. (23 May 2003), 051504.

We have carried out extensive molecular dynamics simulations of a supercooled polydisperse Lennard-Jones liquid with large variations in temperature at a fixed pressure. The particles in the system are considered to be polydisperse in both size and mass. The temperature dependence of dynamical properties such as the viscosity (η) and the self-diffusion coefficients ( D i ) of different size particles is studied. Both viscosity and diffusion coefficients show super-Arrhenius temperature dependence and fit well to the well-known Vogel-Fulcher-Tammann equation. Within the temperature range investigated; the value of Angell’s fragility parameter ( D ≈1.4) classifies the present system as a very fragile liquid. The critical temperature for diffusion ( T o D i ) increases with the size of the particles. The critical temperature for viscosity ( T o η ) is larger than that for diffusion; and sizable deviations appear for the smaller size particles; implying a decoupling of translational diffusion from viscosity in deeply supercooled liquids. Indeed; the diffusion shows markedly non-Stokesian behavior at low temperatures where a highly nonlinear dependence on size is observed. An inspection of the trajectories of the particles shows that at low temperatures the motions of both the smallest and largest size particles are discontinuous (jump type). However; the crossover from continuous Brownian to large length hopping motion takes place at shorter time scales for the smaller size particles.

Overview of a compiler for synthesizing MATLAB programs onto FPGAs

P Banerjee — 2008-01-29T15:33:44-00:00

Very Large Scale Integration (VLSI) Systems, IEEE Transactions on, Vol. 12, No. 3. (2004), pp. 312-324.

This paper describes a behavioral synthesis tool called AccelFPGA which reads in high-level descriptions of digital signal processing (DSP) applications written in MATLAB, and automatically generates synthesizable register transfer level (RTL) models and simulation testbenches in VHDL or Verilog. The RTL models can be synthesized using commercial logic synthesis tools and place and route tools onto field-programmable gate arrays (FPGAs). This paper describes how powerful directives are used to provide high-level architectural tradeoffs for the DSP designer. Experimental results are reported on a set of eight MATLAB benchmarks that are mapped onto the Xilinx Virtex II and Altera Stratix FPGAs.

Automatic conversion of floating point MATLAB programs into fixed point FPGA based hardware design

P Banerjee — 2008-01-29T15:40:47-00:00

Field-Programmable Custom Computing Machines, 2003. FCCM 2003. 11th Annual IEEE Symposium on (2003), pp. 263-264.

This paper describes how the floating point computations in MATLAB can be automatically converted to a fixed point MATLAB version of specific precision for hardware design. The techniques have been incorporated in the AcelFPGA behavioral synthesis tool (Banerjee et al., 2003) that reads in high-level descriptions of DSP applications written in MATLAB, and automatically generate synthesizable RTL models in VHDL or Verilog. Experimental results are reported with the AccelFPGA version 1.5 compiler on a set of five MATLAB benchmarks that are mapped onto the Xilinx Virtex II FPGAs (field programmable gate arrays).

Computational Fluid Dynamic Simulation of Aggregation of Deformable Cells in a Shear Flow

Prosenjit Bagchi — 2008-02-11T19:33:32-00:00

Journal of Biomechanical Engineering, Vol. 127, No. 7. (2005), pp. 1070-1080.

We present computational fluid dynamic (CFD) simulation of aggregation of two deformable cells in a shear flow. This work is motivated by an attempt to develop computational models of aggregation of red blood cells (RBCs). Aggregation of RBCs is a major determinant of blood viscosity in microcirculation under physiological and pathological conditions. Deformability of the RBCs plays a major role in determining their aggregability. Deformability depends on the viscosity of the cytoplasmic fluid and on the rigidity of the cell membrane, in a macroscopic sense. This paper presents a computational study of RBC aggregation that takes into account the rheology of the cells as well as cell-cell adhesion kinetics. The simulation technique considered here is two dimensional and based on the front tracking/immersed boundary method for multiple fluids. Results presented here are on the dynamic events of aggregate formation between two cells, and its subsequent motion, rolling, deformation, and breakage. We show that the rheological properties of the cells have significant effects on the dynamics of the aggregate. A stable aggregate is formed at higher cytoplasmic viscosity and membrane rigidity. We also show that the bonds formed between the cells change in a cyclic manner as the aggregate rolls in a shear flow. The cyclic behavior is related to the rolling orientation of the aggregate. The frequency and amplitude of oscillation in the number of bonds also depend on the rheological properties.

Flow Past a Sphere With Surface Blowing and Suction

Prosenjit Bagchi — 2008-02-11T19:28:57-00:00

Journal of Fluids Engineering, Vol. 129, No. 12. (2007), pp. 1547-1558.

The effect of uniform surface blowing and suction on the wake dynamics and the drag and lift forces on a sphere is studied using a high-resolution direct numerical simulation technique. The sphere Reynolds number Re, based on its diameter and the freestream velocity, is in the range 1–300. The onset of recirculation in the sphere wake occurs at higher Re, and the transition to nonaxisymmetry and unsteadiness occurs at lower Re in the presence of blowing. The size of the recirculation region increases with blowing, but it nearly disappears in the case of suction. Wake oscillation also increases in the presence of blowing. The drag coefficient in the presence of blowing is reduced compared to that in uniform flow, in the range 10<Re<250, whereas it is increased in the presence of suction. The reduction in the wake pressure minimum associated with the enhanced vortical structures is the primary cause for drag reduction in the case of blowing. In the case of suction, it is the increased surface vorticity associated with the reduction of the boundary layer that results into increased drag. The fluctuations in the instantaneous lift and drag coefficients are significant for blowing, and they result from the asymmetric movement of the wake pressure minimum associated with the shedding process.

Biased Skip Lists

Amitabha Bagchi — 2008-01-31T20:33:47-00:00

We design a variation of skip lists that performs well for generally biased access sequences.

MOBIWORP: Mitigation of the Wormhole Attack in Mobile Multihop Wireless Networks

Issa Khalil — 2007-12-18T00:35:18-00:00

Securecomm and Workshops, 2006 (2006), pp. 1-12.

In multihop wireless systems, the need for cooperation among nodes to relay each other's packets exposes them to a wide range of security attacks. A particularly devastating attack is the wormhole attack, where a malicious node records control traffic at one location and tunnels it to a colluding node, possibly far away, which replays it locally. This can have an adverse effect on route establishment by preventing nodes from discovering legitimate routes that are more than two hops away. Previous works on tolerating wormhole attacks have focused only on detection and used specialized hardware, such as directional antennas or extremely accurate clocks. More recent work has addressed the problem of locally isolating the malicious nodes. However, all of this work has been done in the context of static networks due to the difficulty of secure neighbor verification with mobile nodes. The existing work on secure neighbor verification has limitations in accuracy, resource requirements, and applicability to ad-hoc and sensor networks. In this paper, we present a countermeasure for the wormhole attack, called MOBIWORP, which alleviates these drawbacks and efficiently mitigates the wormhole attack in mobile networks. MOBIWORP uses a secure central authority (CA) for global tracking of node positions. Local monitoring is used to detect and isolate malicious nodes locally. Additionally, when sufficient suspicion builds up at the CA, it enforces a global isolation of the malicious node from the whole network. The effect of MOBIWORP on the data traffic and the fidelity of detection is brought out through extensive simulation using ns-2

Intelligent robotic systems in service of the disabled

K Kawamura — 2007-12-03T16:17:13-00:00

Rehabilitation Engineering, IEEE Transactions on [see also IEEE Trans. on Neural Systems and Rehabilitation], Vol. 3, No. 1. (1995), pp. 14-21.

The authors argue that intelligence is necessary in robots used for rehabilitation in order to reduce the amount of mental activity needed by the user of these robots. With this in mind, the areas of research relevant to imparting robotic systems with the capability of assuming a more intelligent role are identified. The authors describe their implementation of functionalities such as fuzzy command interpretation, object recognition, face tracking, and task planning and learning, which are part of the ISAC, an intelligent system designed to feed individuals with physical disabilities

Correlated orientational and translational motions in supercooled liquids

Sarika Bhattacharyya — 2007-11-28T00:55:12-00:00

The Journal of Chemical Physics, Vol. 117, No. 6. (2002), pp. 2741-2746.

We have carried out NPT molecular dynamics simulations of isolated ellipsoids in a glass forming binary mixture to gain insight into the nature of orientational relaxation (OR) in a viscous liquid. At high pressures when the liquid is highly viscous, the OR is found to occur mainly via correlated hopping, sometimes involving participation of several neighboring atoms, placed in a ring like tunnel. In the glassy state, hopping is found to be accompanied by larger fluctuations in the total energy and the volume of the system. Both orientational and translational hopping are found to be gated, restricted primarily by the entropic bottlenecks, with the orientational motion becoming increasingly slower than the translation as the pressure is increased. Orientational relaxation is found to occur with a wide distribution of decay times.

Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres

S Ravichandran — 2007-11-28T00:50:06-00:00

The Journal of Chemical Physics, Vol. 111, No. 16. (1999), pp. 7505-7511.

Detailed molecular dynamics simulations of the rotational and the translational motions of Gay–Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier–Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased.

LiteWorp: Detection and isolation of the wormhole attack in static multihop wireless networks

Issa Khalil — 2007-09-19T07:19:15-00:00

Comput. Networks, Vol. 51, No. 13. (September 2007), pp. 3750-3772.

DICAS: Detection, Diagnosis and Isolation of Control Attacks in Sensor Networks

Issa Khalil — 2007-09-19T07:15:10-00:00

(2005), pp. 89-100.

Supersymmetry In Quantum and Classical Mechanics

Bijan Bagchi — 2007-05-10T16:47:31-00:00

(21 September 2000)

<P>Following Witten's remarkable discovery of the quantum mechanical scheme in which all the salient features of supersymmetry are embedded, SCQM (supersymmetric classical and quantum mechanics) has become a separate area of research, and in recent years has made dramatic progress. This Monograph summarizes the major developments of the last decade, provides an up-to-date review of the literature, and offers a detailed exposition of the underlying SCQM principles.</P>

Graph-Based Logic and Sketches II: Finite-Product Categories and Equational Logic (Preliminary Report)

A Bagchi — 2007-08-02T13:09:02-00:00

ArXiv Mathematics e-prints (December 1996)

It is shown that the proof theory for sketches and forms provided in Part I of this paper (see http://www.cwru.edu/1/class/mans/math/pub/wells) is strong enough to produce all the theorems of the entailment system for multisorted equational logic provided in Goguen and Meseguer's article “Completeness of many-sorted equational logic” (Technical Report CSL-135, SRI International Computer Science Laboratory, 333 Ravenswood Ave., Menlo Park, CA 94025, USA, 1982).

Graph-Based Logic and Sketches 1: The General Framework

A Bagchi — 2007-08-02T13:04:47-00:00

ArXiv Mathematics e-prints (October 1994)

Traditional treatments of formal logic provide: 1. A syntax for formulas. 2. An inference relation between sets of formulas. 3. A rule for assigning meaning to formulas (semantics) that is sound with respect to the inference relation. First order logic, the logic and semantics of programming languages, and the languages that have been formulated for various kinds of categories are all commonly described in this way. The formulas in those logics are strings of symbols that are ultimately modeled on the sentences mathematicians speak and write when proving theorems. Mathematicians with a categorial orientation frequently state and prove theorems using graphs and diagrams. The theory of sketches provides a formal way to describe mathematical structures and impose requirements (such as equations) on them using graphs, diagrams and similar structures. The graphs, diagrams and other data of a sketch are formal objects that correspond to the graphs and diagrams used by such mathematicians in much the same way as the formulas of traditional logic correspond to the sentences mathematicians use in proofs. Sketch theory has a well-known and well-developed functorial semantics corresponding to item 3 in the description of logic above. The content of this paper is to propose a structure in sketch theory that corresponds to items 1 and 2 in that description.

Biodiversity and ecosystem multifunctionality

Andy Hector — 2007-07-12T00:29:19-00:00

Nature, Vol. 448, No. 7150. (2007), pp. 188-190.

Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid.

A Mukherjee — 2005-08-29T20:10:44-00:00

J Chem Phys, Vol. 120, No. 3. (15 January 2004), pp. 1602-1612.

The folding of an extended protein to its unique native state requires establishment of specific, predetermined, often distant, contacts between amino acid residue pairs. The dynamics of contact pair formation between various hydrophobic residues during folding of two different small proteins, the chicken villin head piece (HP-36) and the Alzheimer protein beta-amyloid (betaA-40), are investigated by Brownian dynamics (BD) simulations. These two proteins represent two very different classes-HP-36 being globular while betaA-40 is nonglobular, stringlike. Hydropathy scale and nonlocal helix propensity of amino acids are used to model the complex interaction potential among the various amino acid residues. The minimalistic model we use here employs a connected backbone chain of atoms of equal size while an amino acid is attached to each backbone atom as an additional atom of differing sizes and interaction parameters, determined by the characteristics of each amino acid. Even for such simple models, we find that the low-energy structures obtained by BD simulations of both the model proteins mimic the native state of the real protein rather well, with a best root-mean-square deviation of 4.5 A for HP-36. For betaA-40 (where a single well-defined structure is not available), the simulated structures resemble the reported ensemble rather well, with the well-known beta-bend correctly reproduced. We introduce and calculate a contact pair distance time correlation function, C(P) (ij)(t), to quantify the dynamical evolution of the pair contact formation between the amino acid residue pairs i and j. The contact pair time correlation function exhibits multistage dynamics, including a two stage fast collapse, followed by a slow (microsecond long) late stage dynamics for several specific pairs. The slow late stage dynamics is in accordance with the findings of Sali et al. Analysis of the individual trajectories shows that the slow decay is due to the attempt of the protein to form energetically more favorable pair contacts to replace the less favorable ones. This late stage contact formation is a highly cooperative process, involving participation of several pairs and thus entropically unfavorable and expected to face a large free energy barrier. This is because any new pair contact formation among hydrophobic pairs will require breaking of several contacts, before the favorable ones can be formed. This aspect of protein folding dynamics is similar to relaxation in glassy liquids, where also alpha relaxation requires highly cooperative process of hopping. The present analysis suggests that waiting time for the necessary pair contact formation may obey the Poissonian distribution. We also study the dynamics of Forster energy transfer during folding between two tagged amino acid pairs. This dynamics can be studied by fluorescence resonance energy transfer (FRET). It is found that suitably placed donor-acceptor pairs can capture the slow dynamics during folding. The dynamics probed by FRET is predicted to be nonexponential.

Automated adaptive intrusion containment in systems of interacting services

Yu-Sung Wu — 2007-05-06T01:58:08-00:00

Computer Networks, Vol. 51, No. 5. (11 April 2007), pp. 1334-1360.

Large scale distributed systems typically have interactions among different services that create an avenue for propagation of a failure from one service to another. The failures being considered may be the result of natural failures or malicious activity, collectively called disruptions. To make these systems tolerant to failures it is necessary to contain the spread of the occurrence automatically once it is detected. The objective is to allow certain parts of the system to continue to provide partial functionality in the system in the face of failures. Real world situations impose several constraints on the design of such a disruption tolerant system of which we consider the following - the alarms may have type I or type II errors; it may not be possible to change the service itself even though the interaction may be changed; attacks may use steps that are not anticipated a priori; and there may be bursts of concurrent alarms. We present the design and implementation of a system named Adepts as the realization of such a disruption tolerant system. Adepts uses a directed graph representation to model the spread of the failure through the system, presents algorithms for determining appropriate responses and monitoring their effectiveness, and quantifies the effect of disruptions through a high level survivability metric. Adepts is demonstrated on a real e-commerce testbed with actual attack patterns injected into it.

A Synechococcus sp. PCC 7942 mutant with a higher tolerance towards bentazone.

SN Bagchi — 2007-04-18T10:51:34-00:00

Photosynth Res, Vol. 75, No. 2. (2003), pp. 171-182.

In this article we describe the partial characterization of a Synechococcus sp. PCC 7942 mutant Mu1 with an enhanced resistance towards the herbicide bentazone (3-isopropyl-1H-2,1,3-benzothiadiazine-4(3H)-one 2,2-dioxide). The mutant was derived from a random mutagenesis with N-methyl-N'-nitro-N-nitrosoguanidine (NSG) and exhibited superior growth rates, pigment content and overall photosynthetic activities under regular growth conditions compared to wild type. Whereas Synechococcus PCC 7942 wild type showed significant photoinhibition, especially in the presence of lincomycin, Mu1 was much more robust. A comparative analysis of the content of several photosynthesis-associated proteins revealed that Mu1 had an increased expression of PsbO on mRNA and protein level and that PsbO is tightly bound to Photosystem II, relative to wild type. This result was substantiated by mass spectrometer measurements of photosynthetic water oxidation revealing a higher stability and integrity of the water oxidizing complex in Mu1 cells grown under regular or calcium deficient conditions. Therefore, our results give rise to the possibility that the overexpression of PsbO in mutant Mu1 confers resistance to reactive oxygen species (ROS) formed as a consequence of bentazone binding to the acceptor side of PS II. In addition, we observed a significantly higher tolerance towards bentazone in iron depleted wild type cells, conditions under which the IdiA protein becomes expressed in highly elevated amounts. As we have previously shown, IdiA preferentially protects the acceptor site of PS II against oxidative stress, especially under iron limitation. Thus, it is likely that IdiA due to its topology interferes with bentazone binding or protects PS II against ROS generated in the presence of bentazone.

Graph-based logic and sketches ii: Finite product categories and equational logic

A Bagchi — 2007-04-06T22:17:40-00:00

(1997)

It is shown that the proof theory for sketches and forms provided in [Bagchi and Wells, 1997] is strong enough to produce all the theorems of the entailment system for multisorted equational logic provided in [Goguen and Meseguer, 1982]. 1.

Bioavailability, antioxidant and immune-enhancing properties of zinc methionine.

XX Chien — 2007-01-13T21:45:07-00:00

Biofactors, Vol. 27, No. 1-4. (2006), pp. 231-244.

Although a large number of transition metals and cations remarkably induce oxidative deterioration of biological macromolecules including lipids, proteins and DNA, the trace element zinc acts as a novel dietary supplement and an essential micronutrient, and serves a wide range of biological functions in human and animal health. Zinc promotes antioxidant and immune functions, stabilizes and maintains the structural integrity of biological membranes, and plays a pivotal role in skin and connective tissue metabolism and repair. Zinc is an integral constituent of a large number of enzymes including antioxidant enzymes, and hormones including glucagon, insulin, growth hormone, and sex hormones. High concentrations of zinc are found in the prostate gland and choroids of the eye. Zinc deficiency leads to biochemical abnormalities including the impairments of growth, dermal, gastrointestinal, neurologic and immunologic systems. Given its superior bioavailability, antioxidant and immune-enhancing properties, zinc methionine may serve as a novel dietary supplement to promote health benefits in humans and animals.

LITEWORP: a lightweight countermeasure for the wormhole attack in multihop wireless networks

I Khalil — 2006-11-29T18:44:56-00:00

Dependable Systems and Networks, 2005. DSN 2005. Proceedings. International Conference on (2005), pp. 612-621.

In multihop wireless systems, such as ad-hoc and sensor networks, the need for cooperation among nodes to relay each other's packets exposes them to a wide range of security attacks. A particularly devastating attack is known as the wormhole attack, where a malicious node records control and data traffic at one location and tunnels it to a colluding node, which replays it locally. This can have an adverse effect in route establishment by preventing nodes from discovering routes that are more than two hops away. In this paper, we present a lightweight countermeasure for the wormhole attack, called LITEWORP, which does not require specialized hardware. LITEWORP is particularly suitable for resource-constrained multihop wireless networks, such as sensor networks. Our solution allows detection of the wormhole, followed by isolation of the malicious nodes. Simulation results show that every wormhole is detected and isolated within a very short period of time over a large range of scenarios. The results also show that the fraction of packets lost due to the wormhole when LITEWORP is applied is negligible compared to the loss encountered when the method is not applied.

Giant Ringlike Radio Structures Around Galaxy Cluster Abell 3376

Joydeep Bagchi — 2006-11-22T01:20:02-00:00

(9 Nov 2006)

In the current paradigm of cold dark matter cosmology, large-scale structures are assembling through hierarchical clustering of matter. In this process, an important role is played by megaparsec (Mpc)-scale cosmic shock waves, arising in gravity-driven supersonic flows of intergalactic matter onto dark matter-dominated collapsing structures such as pancakes, filaments, and clusters of galaxies. Here, we report Very Large Array telescope observations of giant (~2 Mpc by 1.6 Mpc), ring-shaped nonthermal radio-emitting structures, found at the outskirts of the rich cluster of galaxies Abell 3376. These structures may trace the elusive shock waves of cosmological large-scale matter flows, which are energetic enough to power them. These radio sources may also be the acceleration sites where magnetic shocks are possibly boosting cosmic-ray particles with energies of up to 10^18 to 10^19 electron volts.

Theory of the time development of the stokes shift in polar media

Biman Bagchi — 2006-11-20T14:03:51-00:00

Chemical Physics, Vol. 86, No. 3. (1984), pp. 257-267.

We present a theory for the time evolution of the Stokes shift of a polar molecule in a polar solvent. The time-dependent solute--solvent interaction is calculated in a continuum model by replacing the surrounding solvent by a frequency-dependent dielectric continuum. An expression for the time dependence of the fluorescence maximum is derived. This expression can be considered a direct generalization of the well-known Ooshika--Lippert--Mataga equation to the time domain. We also present an approximate expression for the wavelength dependence of the dynamics of the Stokes shift, and find it to be consistent with recent experimental results. We have investigated the effect of polarizability of the solute molecule and found that for many molecules this effect is not negligible.

On Nyman, Beurling and Baez-Duarte's Hilbert space reformulation of the Riemann hypothesis

Bhaskar Bagchi — 2006-07-31T07:05:51-00:00

(28 Jul 2006)

There has been a surge of interest of late in an old result of Nyman and Beurling giving a Hilbert space formulation of the Riemann hypothesis. Many authors have contributed to this circle of ideas, culminating in a beautiful refinement due to Baez-Duarte. The purpose of this little survey is to dis-entangle the resulting web of complications, and reveal the essential simplicity of the main results.

Cul4A and DDB1 associate with Skp2 to target p27Kip1 for proteolysis involving the COP9 signalosome.

T Bondar — 2006-07-27T13:23:27-00:00

Mol Cell Biol, Vol. 26, No. 7. (April 2006), pp. 2531-2539.

DDB1, a subunit of the damaged-DNA binding protein DDB, has been shown to function also as an adaptor for Cul4A, a member of the cullin family of E3 ubiquitin ligase. The Cul4A-DDB1 complex remains associated with the COP9 signalosome, and that interaction is conserved from fission yeast to human. Studies with fission yeast suggested a role of the Pcu4-Ddb1-signalosome complex in the proteolysis of the replication inhibitor Spd1. Here we provide evidence that the function of replication inhibitor proteolysis is conserved in the mammalian DDB1-Cul4A-signalosome complex. We show that small interfering RNA-mediated knockdown of DDB1, CSN1 (a subunit of the signalosome), and Cul4A in mammalian cells causes an accumulation of p27Kip1. Moreover, expression of DDB1 reduces the level of p27Kip1 by increasing its decay rate. The DDB1-induced proteolysis of p27Kip1 requires signalosome and Cul4A, because DDB1 failed to increase the decay rate of p27Kip1 in cells deficient in CSN1 or Cul4A. Surprisingly, the DDB1-induced proteolysis of p27Kip1 also involves Skp2, an F-box protein that allows targeting of p27Kip1 for ubiquitination by the Skp1-Cul1-F-box complex. Moreover, we provide evidence for a physical association between Cul4A, DDB1, and Skp2. We speculate that the F-box protein Skp2, in addition to utilizing Cul1-Skp1, utilizes Cul4A-DDB1 to induce proteolysis of p27Kip1.

Hierarchical error detection in a software implemented fault tolerance (SIFT) environment

S Bagchi — 2006-07-06T15:29:53-00:00

Knowledge and Data Engineering, IEEE Transactions on, Vol. 12, No. 2. (2000), pp. 203-224.

Proposes a hierarchical error detection framework for a software-implemented fault tolerance (SIFT) layer of a distributed system. A four-level error detection hierarchy is proposed in the context of Chameleon, a software environment for providing adaptive fault tolerance in an environment of commercial off-the-shelf (COTS) system components and software. The design and implementation of a software-based distributed signature monitoring scheme, which is central to the proposed four-level hierarchy, is described. Both intra-level and inter-level optimizations that minimize the overhead of detection and are capable of adapting to runtime requirements are proposed. The paper presents results from a prototype implementation of two levels of the error detection hierarchy and results of a detailed simulation of the overall environment. The results indicate a substantial increase in availability due to the detection framework and help in understanding the tradeoffs between overhead and coverage for different combinations of techniques

Collapse of stiff conjugated polymers with chemical defects into ordered, cylindrical conformations

D Hu — 2006-05-11T04:05:55-00:00

Nature, Vol. 405, No. 6790. (29 June 2000), pp. 1030-1033.

The optical, electronic and mechanical properties of synthetic and biological materials consisting of polymer chains depend sensitively on the conformation adopted by these chains. The range of conformations available to such systems has accordingly been of intense fundamental as well as practical interest, and distinct conformational classes have been predicted, depending on the stiffness of the polymer chains and the strength of attractive interactions between segments within a chain. For example, flexible polymers should adopt highly disordered conformations resembling either a random coil or, in the presence of strong intrachain attractions, a so-called 'molten globule'. Stiff polymers with strong intrachain interactions, in contrast, are expected to collapse into conformations with long-range order, in the shape of toroids or rod-like structures. Here we use computer simulations to show that the anisotropy distribution obtained from polarization spectroscopy measurements on individual poly[2-methoxy-5-(2'-ethylhexyl)oxy-1,4-phenylenevinylene] polymer molecules is consistent with this prototypical stiff conjugated polymer adopting a highly ordered, collapsed conformation that cannot be correlated with ideal toroid or rod structures. We find that the presence of so-called 'tetrahedral chemical defects', where conjugated carbon-carbon links are replaced by tetrahedral links, divides the polymer chain into structurally identifiable quasi-straight segments that allow the molecule to adopt cylindrical conformations. Indeed, highly ordered, cylindrical conformations may be a critical factor in dictating the extraordinary photophysical properties of conjugated polymers, including highly efficient intramolecular energy transfer and significant local optical anisotropy in thin films.

Molecular analysis of the dormancy response in Mycobacterium smegmatis: expression analysis of genes encoding the DevR-DevS two-component system, Rv3134c and chaperone alpha-crystallin homologues.

Mayuri — 2006-02-20T20:02:41-00:00

FEMS Microbiol Lett, Vol. 211, No. 2. (4 June 2002), pp. 231-237.

Mycobacteria adapt to a decrease in oxygen tension by entry into a non-replicative persistent phase. It was shown earlier that the two-component system, DevR-DevS, was induced in Mycobacterium tuberculosis and Mycobacterium bovis BCG cultures during hypoxia, suggesting that it may play a regulatory role in their adaptation to oxygen limitation. The presence of a homologous genetic system in Mycobacterium smegmatis was predicted by scanning its unfinished genome sequence with devR and devS genes of M. tuberculosis. Rv3134c, which is cotranscribed with devR-devS in M. tuberculosis, was also present in M. smegmatis at a similar location upstream from devR. The expression of all three genes was induced at the RNA and protein levels in M. smegmatis cultures grown under microaerobic and anaerobic conditions. The M. smegmatis genome also contained the hspX gene, encoding chaperone alpha-crystallin, Acr, that was induced during hypoxia. The similarity in sequences and hypoxia-responsive behaviour of devR-devS, Rv3134c and hspX genes in M. smegmatis and M. tuberculosis suggests that the molecular mechanisms involved in the dormancy response are likely conserved in these two species. M. smegmatis could therefore serve as a useful model for the delineation of the hypoxia response in general and DevR-DevS regulated pathways in particular.

SCIDIVE: a stateful and cross protocol intrusion detection architecture for voice-over-IP environments

Yu-Sung Wu — 2005-09-12T13:52:04-00:00

Dependable Systems and Networks, 2004 International Conference on (2004), pp. 433-442.

Voice-over-IP (VoIP) systems are gaining in popularity as the technology for transmitting voice traffic over IP networks. As the popularity of VoIP systems increases, they are being subjected to different kinds of intrusions some of which are specific to such systems and some of which follow a general pattern. VoIP systems pose several new challenges to intrusion detection system (IDS) designers. First, these systems employ multiple protocols for call management (e.g., SIP) and data delivery (e.g., RTP). Second, the systems are distributed in nature and employ distributed clients, servers and proxies. Third, the attacks to such systems span a large class, from denial of service to billing fraud attacks. Finally, the systems are heterogeneous and typically under several different administrative domains. In this paper, we propose the design of an intrusion detection system targeted to VoIP systems, called SCIDIVE (pronounced "Skydive"). SCIDIVE is structured to detect different classes of intrusions, including, masquerading, denial of service, and media stream-based attacks. It can operate with both classes of protocols that compose VoIP systems - call management protocols (CMP), e.g., SIP, and media delivery protocols (MDP), e.g., RTP. SCIDIVE proposes two abstractions for VoIP IDS - stateful detection and cross-protocol detection. Stateful detection denotes assembling state from multiple packets and using the aggregated state in the rule-matching engine. Cross protocol detection denotes matching rules that span multiple protocols. SCIDIVE is demonstrated on a sample VoIP system that comprises SIP clients and SIP proxy servers with RTP as the data delivery protocol. Four attack scenarios are created and the accuracy and the efficiency of the system evaluated with rules meant to catch these attacks.

A study on managing the performance requirements of a distributed service delivery software system

Ashutosh Bagchi — 2005-02-10T22:25:48-00:00

Information and Software Technology, Vol. In Press, Corrected Proof

Like other non-functional requirements (NFR), performance requirements can have global impact on a system. This article presents a preliminary study on the management of performance requirements of a distributed service delivery (DSD) system using the 'Performance Requirement Framework (PeRF)' developed by Nixon [B.A. Nixon, Management of performance requirements for information systems, IEEE Transactions on Software Engineering 20 (12), (2000)]. Various steps in the framework are explained in the context of the DSD system, and the effects of some design decisions on the performance have been evaluated. PeRF was originally developed for information systems. The article shows how the framework can be adapted to a distributed system. However, additional studies on a number of distributed systems need to be carried out in order to develop a full framework for performance requirements for distributed systems, or perhaps for different categories of such systems.