Mathematical Modeling of a Bioluminescent E. Coli Based Biosensor

In this work we present a mathematical model for the bioreporter activity of an E. coli based bioluminescent bioreporter. This bioreporter is based on a genetically modified E. coli which harbors the recA promoter, a member of the bacterial SOS response, fused to the bacterial luminescence (lux) genes. This bioreporter responds to the presence of DNA damaging agents such as heavy metals, H2O2 and Nalidixic Acid (NA) that activate the SOS response. In our mathematical model we implemented basic physiological mechanisms such as: the penetration of the NA into the biosensor; gyrase enzyme inhibition by the NA; gyrase level regulation; creation of chromosomal DNA damage; DNA repair and release of ssDNA into the cytoplasm; SOS induction and chromosomal DNA repair; activation of lux genes by the fused recA promoter carried on a plasmidal DNA; transcription and translation of the luminescence responsible enzymes; luminescence cycle; energy molecules level regulation and the regulation of the O2 consumption. The mathematical model was defined using a set of ordinary differential equations (ODE) and solved numerically. We simulated the system for different concentrations of NA in water for specific biosensors concentration, and under limited O2 conditions. The simulated results were compared to experimental data and satisfactory matching was obtained. This manuscript presents a proof of concept showing that real biosensors can be modeled and simulated. This sets the ground to the next stage of implementing a comprehensive physiological model using experimentally extracted parameters. Following the completion of the next stage, it will be possible to construct a “Computer Aided Design” tool for the simulation of the genetically engineered biosensors. We define a term “bioCAD” for a Biological System Computer Aided Design. The specific bioCAD that is described here is aimed towards whole cell biosensors which are under investigation today for functional sensing. Usage of the bioCAD will improve the biosensors design process and boost their performance. It will also reduce Non Recurring Engineering (NRE) cost and time. Finally, using a parameterized solution will allow fair and quick evaluation of whole cell biosensors for various applications

Local crystallographic texture and voiding in passivated copper interconnects

A correlation between local crystallographic texture and stress‐induced void formation in tantalum‐encapsulated, copper interconnects was revealed by electron backscattering diffraction studies in a scanning electron microscope. Lines exhibiting an overall stronger 〈111〉 texture showed better resistance to void formation. Furthermore, grains adjacent to voids exhibited weaker 〈111〉 texture than grains in unvoided regions of the same line. The locally weaker 〈111〉 texture at voided locations suggests the presence of higher diffusivity, twist boundaries. This work, which represents the first characterization of local texture in stress voided, copper lines, helps to elucidate the relative importance of the thermodynamic and kinetic factors which govern void formation and growth. © 1996 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70319/2/APPLAB-69-26-4017-1.pd

In-vivo monitoring for electrical expression of plant living parameters by an impedance lab system

We present a complete in-lab system to monitor the plant and its surrounding environment. The plant impedance is directly measured in a continuous manner, while, simultaneously surrounding environment parameters known to affect plant status, are monitored. This is done combining a new in-vivo direct measurement of the plant together with an embedded system using available sensor technology and a designated interface for continuous data acquisition. Furthermore, the next versions this system can be deployed as a field monitoring device, with simple adaptations

CoWBP capping barrier layer for sub 90 nm Cu interconnects

Abstract Electroless cobalt films have been obtained by deposition using a plating bath containing two reducing agents: dimethylamineborane (DMAB) and sodium hypophosphite. This formulation allows spontaneous activation on copper followed by auto catalytic electroless plating. CoWBP and CoBP films are proposed as diffusion barriers and encapsulation layers, for copper lines and via contacts for ULSI interconnect applications. The crystalline structure, chemical composition and oxidation states of the elements were studied, as well as the electrical resistivity, topography and morphology of the films. The film composition was characterized as a function of the solution composition; the barrier properties of the films were tested and an oxidation resistance study was conducted. The films were characterized and the results show that they can be applied as capping layers for ULSI copper metallization

Faster linearizability checking via PP-compositionality

Linearizability is a well-established consistency and correctness criterion for concurrent data types. An important feature of linearizability is Herlihy and Wing's locality principle, which says that a concurrent system is linearizable if and only if all of its constituent parts (so-called objects) are linearizable. This paper presents $P$-compositionality, which generalizes the idea behind the locality principle to operations on the same concurrent data type. We implement $P$-compositionality in a novel linearizability checker. Our experiments with over nine implementations of concurrent sets, including Intel's TBB library, show that our linearizability checker is one order of magnitude faster and/or more space efficient than the state-of-the-art algorithm.Comment: 15 pages, 2 figure

Regular Topologies for Gigabit Wide-Area Networks

In general terms, this project aimed at the analysis and design of techniques for very high-speed networking. The formal objectives of the project were to: (1) Identify switch and network technologies for wide-area networks that interconnect a large number of users and can provide individual data paths at gigabit/s rates; (2) Quantitatively evaluate and compare existing and proposed architectures and protocols, identify their strength and growth potentials, and ascertain the compatibility of competing technologies; and (3) Propose new approaches to existing architectures and protocols, and identify opportunities for research to overcome deficiencies and enhance performance. The project was organized into two parts: 1. The design, analysis, and specification of techniques and protocols for very-high-speed network environments. In this part, SRI has focused on several key high-speed networking areas, including Forward Error Control (FEC) for high-speed networks in which data distortion is the result of packet loss, and the distribution of broadband, real-time traffic in multiple user sessions. 2. Congestion Avoidance Testbed Experiment (CATE). This part of the project was done within the framework of the DARTnet experimental T1 national network. The aim of the work was to advance the state of the art in benchmarking DARTnet's performance and traffic control by developing support tools for network experimentation, by designing benchmarks that allow various algorithms to be meaningfully compared, and by investigating new queueing techniques that better satisfy the needs of best-effort and reserved-resource traffic. This document is the final technical report describing the results obtained by SRI under this project. The report consists of three volumes: Volume 1 contains a technical description of the network techniques developed by SRI in the areas of FEC and multicast of real-time traffic. Volume 2 describes the work performed under CATE. Volume 3 contains the source code of all software developed under CATE

Analysis of in Vivo Plant Stem Impedance Variations in Relation with External Conditions Daily Cycle

World population growth and desertification are the most severe issue to agricultural food production. Smart agriculture is a promising solution to ensure food security. The use of sensors to monitor crop production can help farmers improve the yield and reduce water consumption. Here we propose a study where the electrical impedance of green plants' stem is analyzed in vivo, along with environmental conditions. In particular, the variations associated with the daily cycle are highlighted. These analyses lead to the possibility of understanding plant status directly from stem impedance

Auditable Compressed Storage

Outsourcing data to the cloud for personal use is becoming an everyday trend rather than an extreme scenario. The frequent outsourcing of data increases the possible attack window because users do not fully control their personal files. Typically, once there are established secure channels between two endpoints, communication is considered secure. However, in the cloud model the receiver–the cloud–cannot be fully trusted, either because it has been under adversarial control, or because it acts maliciously to increase its revenue by deleting infrequent accessed file blocks. One approach used by current literature to address the aforementioned security concerns is via Remote Data Integrity Checking (RDIC) protocols, whereby a data owner can challenge an untrusted cloud service provider (CSP) to prove faithful storage of its data. Current RDIC protocols assume that the original data format remains unchanged. However, users may wish to compress their data in order to enjoy less charges. In that case, current RDIC protocols become impractical because, each time compression happens on a file, the user has to run a new RDIC protocol. In this work we initiate the study for Auditable Compressed Storage (ACS). After defining the new model we instantiate two protocols for different widely used compression techniques: run length encoding and Huffman encoding. In contrast with conventional RDIC, our protocols allow a user to delegate the compression to the cloud in a provably secure way: The client can verify correctness of compression without having to download the entire uncompressed file and check it against the compressed one

Secure Code Update for Embedded Devices via Proofs of Secure Erasure

Abstract. Remote attestation is the process of verifying internal state of a remote embedded device. It is an important component of many security protocols and applications. Although previously proposed re-mote attestation techniques assisted by specialized secure hardware are effective, they not yet viable for low-cost embedded devices. One no-table alternative is software-based attestation, that is both less costly and more efficient. However, recent results identified weaknesses in some proposed software-based methods, thus showing that security of remote software attestation remains a challenge. Inspired by these developments, this paper explores an approach that relies neither on secure hardware nor on tight timing constraints typi-cal of software-based technqiques. By taking advantage of the bounded memory/storage model of low-cost embedded devices and assuming a small amount of read-only memory (ROM), our approach involves a new primitive – Proofs of Secure Erasure (PoSE-s). We also show that, even though it is effective and provably secure, PoSE-based attestation is not cheap. However, it is particularly well-suited and practical for two other related tasks: secure code update and secure memory/storage erasure. We consider several flavors of PoSE-based protocols and demonstrate their feasibility in the context of existing commodity embedded devices.

Antileukemic Activity of Nuclear Export Inhibitors that Spare Normal Hematopoietic Cells

Drugs that target the chief mediator of nuclear export, chromosome region maintenance 1 protein (CRM1) have potential as therapeutics for leukemia, but existing CRM1 inhibitors show variable potencies and a broad range of cytotoxic effects. Here, we report the structural analysis and antileukemic activity of a new generation of small-molecule inhibitors of CRM1. Designated selective inhibitors of nuclear export (SINE), these compounds were developed using molecular modeling to screen a small virtual library of compounds against the nuclear export signal (NES) groove of CRM1. The 2.2-Å crystal structure of the CRM1-Ran-RanBP1 complex bound to KPT-251, a representative molecule of this class of inhibitors, shows that the drug occupies part of the groove in CRM1 that is usually occupied by the NES, but penetrates much deeper into the groove and blocks CRM1-directed protein export. SINE inhibitors exhibit potent antileukemic activity, inducing apoptosis at nanomolar concentrations in a panel of 14 human acute myeloid leukemia (AML) cell lines representing different molecular subtypes of the disease. When administered orally to immunodeficient mice engrafted with human AML cells, KPT-251 had potent antileukemic activity with negligible toxicity to normal hematopoietic cells. Thus, KPT-SINE CRM1 antagonists represent a novel class of drugs that warrant further testing in AML patients