Run-Time Adaptable On-Chip Predictive Thermal Triggers

With ever-increasing power densities, Dynamic Thermal Management (DTM) techniques have become mainstream in today’s systems. An important component of such techniques is the thermal trigger. It has been shown that predictive thermal triggers can outperform reactive ones. In this paper, we present a novel trade-off space of predictive thermal triggers, and identify run-time adaptability as a crucial parameter of interest. We identify the Neural Network (NN) simulator presented in [14] to have some key advantages over other predictive thermal triggers. We extend it to work for an arbitrary sensor layout configuration and to be run-time adaptable. We present experimental results on Niagara UltraSPARC T1 chip with real-life benchmark applications. Our results validate our proposed extension of the NN simulator. Our results also quantitatively establish the effectiveness of the proposed simulator for reducing, the otherwise unacceptably high errors, that can arise due to expected leakage current variation and design-time thermal modelling errors

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing.

Sequencing technologies have undergone a paradigm shift from bulk to single-cell resolution in response to an evolving understanding of the role of cellular heterogeneity in biological systems. However, single-cell sequencing of large populations has been hampered by limitations in processing genomes for sequencing. In this paper, we describe a method for single-cell genome sequencing (SiC-seq) which uses droplet microfluidics to isolate, amplify, and barcode the genomes of single cells. Cell encapsulation in microgels allows the compartmentalized purification and tagmentation of DNA, while a microfluidic merger efficiently pairs each genome with a unique single-cell oligonucleotide barcode, allowing >50,000 single cells to be sequenced per run. The sequencing data is demultiplexed by barcode, generating groups of reads originating from single cells. As a high-throughput and low-bias method of single-cell sequencing, SiC-seq will enable a broader range of genomic studies targeted at diverse cell populations

Securing Real-Time Internet-of-Things

Modern embedded and cyber-physical systems are ubiquitous. A large number of critical cyber-physical systems have real-time requirements (e.g., avionics, automobiles, power grids, manufacturing systems, industrial control systems, etc.). Recent developments and new functionality requires real-time embedded devices to be connected to the Internet. This gives rise to the real-time Internet-of-things (RT-IoT) that promises a better user experience through stronger connectivity and efficient use of next-generation embedded devices. However RT- IoT are also increasingly becoming targets for cyber-attacks which is exacerbated by this increased connectivity. This paper gives an introduction to RT-IoT systems, an outlook of current approaches and possible research challenges towards secure RT- IoT frameworks

Design and Operation of FACT -- The First G-APD Cherenkov Telescope

The First G-APD Cherenkov Telescope (FACT) is designed to detect cosmic gamma-rays with energies from several hundred GeV up to about 10 TeV using the Imaging Atmospheric Cherenkov Technique. In contrast to former or existing telescopes, the camera of the FACT telescope is comprised of solid-state Geiger-mode Avalanche Photodiodes (G-APD) instead of photomultiplier tubes for photo detection. It is the first full-scale device of its kind employing this new technology. The telescope is operated at the Observatorio del Roque de los Muchachos (La Palma, Canary Islands, Spain) since fall 2011. This paper describes in detail the design, construction and operation of the system, including hardware and software aspects. Technical experiences gained after one year of operation are discussed and conclusions with regard to future projects are drawn.Comment: Corresponding authors: T. Bretz and Q. Weitze

Design, Fabrication, and Run-time Strategies for Hardware-Assisted Security

Today, electronic computing devices are critically involved in our daily lives, basic infrastructure, and national defense systems. With the growing number of threats against them, hardware-based security features offer the best chance for building secure and trustworthy cyber systems. In this dissertation, we investigate ways of making hardware-based security into a reality with primary focus on two areas: Hardware Trojan Detection and Physically Unclonable Functions (PUFs). Hardware Trojans are malicious modifications made to original IC designs or layouts that can jeopardize the integrity of hardware and software platforms. Since most modern systems critically depend on ICs, detection of hardware Trojans has garnered significant interest in academia, industry, as well as governmental agencies. The majority of existing detection schemes focus on test-time because of the limited hardware resources available at run-time. In this dissertation, we explore innovative run-time solutions that utilize on-chip thermal sensor measurements and fundamental estimation/detection theory to expose changes in IC power/thermal profile caused by Trojan activation. The proposed solutions are low overhead and also generalizable to many other sensing modalities and problem instances. Simulation results using state-of-the-art tools on publicly available Trojan benchmarks verify that our approaches can detect Trojans quickly and with few false positives. Physically Unclonable Functions (PUFs) are circuits that rely on IC fabrication variations to generate unique signatures for various security applications such as IC authentication, anti-counterfeiting, cryptographic key generation, and tamper resistance. While the existence of variations has been well exploited in PUF design, knowledge of exactly how variations come into existence has largely been ignored. Yet, for several decades the Design-for-Manufacturability (DFM) community has actually investigated the fundamental sources of these variations. Furthermore, since manufacturing variations are often harmful to IC yield, the existing DFM tools have been geared towards suppressing them (counter-intuitive for PUFs). In this dissertation, we make several improvements over current state-of-the-art work in PUFs. First, our approaches exploit existing DFM models to improve PUFs at physical layout and mask generation levels. Second, our proposed algorithms reverse the role of standard DFM tools and extend them towards improving PUF quality without harming non-PUF portions of the IC. Finally, since our approaches occur after design and before fabrication, they are applicable to all types of PUFs and have little overhead in terms of area, power, etc. The innovative and unconventional techniques presented in this dissertation should act as important building blocks for future work in cyber security

Design of Autonomous Underwater Vehicle and Optimization of Hydrodynamic Properties and Control

Autonomous vehicles are becoming more and more prevalent in military, private industry and residential applications. Unfortunately, research currently being done in the area of autonomous underwater craft is often hindered by expense. It was desired to build a craft at WPI which could serve as an inexpensive test-bed for future research and implementation of control algorithms, etc. The vehicle\u27s construction required the design and manufacture of a number of components including water-jet stabilization thrusters, propeller driven main thrusters, a complete multi-hub electronic sensor and drive control system and individual sensors such as a tri-axial sonar unit as well as a capacitance based water-leak sensor. A Lexan heat forming process was also developed for hull construction

Doctor of Philosophy

dissertationThis project will produce an automated microfluidic system capable of extracting and purifying nucleic acids from raw samples for detection and analysis. The first step will be the development and characterization of microfluidic components and fabrication methods that will be implemented into the final device. The gas permeability properties of PDMS will be utilized to demonstrate integrated components for pumping, gas bubble trapping and removal, and enhanced mixing. Next, a three-layer PDMS with silicone membrane microfluidic platform will be developed to control fluid flow for nucleic acid purification processes. This microfluidic chip will be capable of taking a raw biological sample through the steps of cell lysis and solid phase nucleic acid extraction to deliver purified DNA or RNA for testing and analysis. The microfluidic chip will be mounted on a portable, desktop control system to allow automated device operation in clinics, laboratories, or the field. Finally, a disposable oscillatory flow PCR chip will be made from polycarbonate to amplify low concentrations of nucleic acid. The PCR module will also be controlled by the same instrument used for nucleic acid extraction. Temperature control will be provided by external heating blocks, and internal chip fluid temperature will be determined by numerical simulations. This device will be a step towards having a universal nucleic acid purification device to fill the much-needed niche in sample preparation for lab-on-a-chip applications

The peptide-break technology : a novel approach for protein post-translational modification assays in drug discovery

The work presented in this thesis describes the development of a universal platform for the biochemical detection of protein post-translational modifications (PTM) using the quenching resonance energy transfer (QRET) technique in an antibody-free system. The QRET technique employed is based on the difference in the luminescence signal produced by the target bound and unbound to a Ln3+-ligand in the presence of soluble quenchers. In the project, PTM monitoring was first demonstrated in a simple QRET tyrosine EGFR assay using antibodies to recognize the modified substrate peptide, a commonality in FRET assays, yet in a single-label approach. On the basis of this, a universal PTM detection method called “the peptide-break technology” was further developed as an antibody-free system. The approach relied on the peptide dimerization concept of leucine zipper (LZ) coiled-coils. The dimer was composed of an enzyme-substrate peptide and a detection Eu3+-peptide. In the assay, the PTM addition to the substrate peptide disrupted the dimer, leading to a low luminescence signal, whereas without PTM addition the dimer formation proceeds and provides Eu3+-chelate protection leading to a high luminescence. The peptide-break technology was successfully developed for a variety of enzymes for phosphorylation, dephosphorylation, deacetylation, and citrullination, using nanomolar concentrations without the need for antibodies or enzyme reporters. Later, the peptide-break technology was simplified and optimized to increase the freedom for substrate peptide selection and design. The peptide dimerization was mediated by the interaction between oppositely charged peptides. Finally, the technology was further studied in a thermal shift assay, allowing the use of high substrate peptide concentrations that are needed in assays with low affinity or activity enzymes. The reported data suggest that this technology is potentially applicable to other challenging PTM types, possibly providing new assay solutions within academia as well as for the pharmaceutical industry.Peptide-break teknologia: Uusi lääkeseulontaan soveltuva menetelmä proteiinien jälkitranslationaalisten modifikaatioiden Tämän tutkimuksen tavoitteena oli kehittää universaali biokemiallinen ja ilman vasta-aineita toteutettu määritysalusta proteiinien jälkitranslaationaalisten modifikaatioiden (PTM) havainnointiin. PTM-reaktion havainnoinnissa käytettiin sammutus-resonanssi-energiansiirtoa (QRET), joka perustuu sammuttajamolekyylin kykyyn erotella kohteeseen sitoutunut ja sitoutumaton lantanidikelaatin sisältämä reportterimolekyyli ja luoda tähän perustuva luminesenssi-signaalin muutos. Ensimmäisenä QRET teknologian soveltuvuus PTM havainnointiin osoitettiin käyttäen lyhyttä repotteripeptidiä ja leimaamatonta vasta-ainetta, joka tunnisti epidermaalisen kasvutekijäreseptorin (EGFR) luoman fosfotyrosiinin. Universaalin määritysalustan luomiseksi, PTM havainnointiin kehitettiin vasta-aineista riippumaton ”peptide-break” teknologia, joka perustuu luontaisiin kahden peptidin muodostamiin leusiinivetoketju-rakenteisiin. Perustilassaan sitoutuneet muokkaamattomat peptidit tuottavat korkean luminesenssi-signaalin, mutta aktiivisen entsyymin ollessa läsnä, muokkaamattoman reportteripeptidin ja entsyymin muokkaaman vasta-peptidin sitoutuminen estyy ja luminesenssi-signaali laskee. Menetelmän toiminnallisuus ja nanomolaarinen herkkyys havainnollistettiin lukuisien eri entsyymien ja entsyymiryhmien kanssa. Tämän jälkeen peptide-break teknologian toiminnallisuus ja monipuolisuus osoitettiin käyttämällä varauksellisia peptidejä leusiinivetoketju-peptidien sijasta. Näin helpotettiin peptidien suunnittelua, tinkimättä menetelmän suorituskyvystä. Lisäksi peptide-break teknologiasta kehitettiin lämpötilaan perustuva muunnos, jossa nostamalla entsymaattisesti muokattavan peptidin määrää kyettiin havainnoimaan huonon toiminnallisuuden omaavia entsyymejä. Tämän tutkimuksen perusteella, peptide-break teknologia soveltuu lukuisten PTM-ryhmien havainnointiin ja luo uudentyyppisen lähestymistavan, joka on hyödynnettävissä niin akateemisesti kuin teollisuudessakin

Design and operation of a field telescope for cosmic ray geophysical tomography

International audienceThe cosmic ray muon tomography gives an access to the density structure of geological targets. In the present article we describe a muon telescope adapted to harsh environmental conditions. In particular the design optimizes the total weight and power consumption to ease the deployment and increase the autonomy of the detector. The muon telescopes consist of at least two scintillator detection matrices readout by photosensors via optical fibres. Two photosensor options have been studied. The baseline option foresees one multianode photomultiplier (MAPM) per matrix. A second option using one multipixel photon counter (MPPC) per bar is under development. The readout electronics and data acquisition system developed for both options are detailed. We present a first data set acquired in open-sky conditions compared with the muon flux detected across geological objects