There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

International Technology Roadmap for Semiconductors 2003の要求清浄度について － シリコンウエハ表面と雰囲気環境に要求される清浄度, 分析方法の現状について －

To alleviate the complex communication problems that arise as the number of on-chip components increases, network-on-chip (NoC) architectures have been recently proposed to replace global interconnects. In this paper, we first provide a general description of NoC architectures and applications. Then, we enumerate several related research problems organized under five main categories: Application characterization, communication paradigm, communication infrastructure, analysis, and solution evaluation. Motivation, problem description, proposed approaches, and open issues are discussed for each problem from system, microarchitecture, and circuit perspectives. Finally, we address the interactions among these research problems and put the NoC design process into perspective.

Outstanding Research Problems in NoC Design: System, Microarchitecture, and Circuit Perspectives

IEEE transactions on computer-aided design of integrated circuits and systems : a publication of the IEEE Circuits and Systems Society

Microarchitectural timing attacks are a type of information leakage attack, which exploit the time-shared microarchitectural components, such as caches, translation look-aside buffers (TLBs), branch prediction unit (BPU), and speculative execution, in modern processors to leak critical information from a victim process or thread. To mitigate such attacks, the mechanism for flushing the on-core state is extensively used by operating-system-level solutions, since on-core state is too expensive to partition. In these systems, the flushing operations are implemented in software (using cache maintenance instructions), which severely limit the efficiency of timing attack protection. 
To bridge this gap, we propose specialized hardware support, a single-instruction multiple-flush (SIMF) mechanism to flush the core-level state, which consists of L1 caches, BPU, TLBs, and register file. We demonstrate SIMF by implementing it as an ISA extension, i.e., flushx instruction, in scalar in-order RISC-V processor. The resultant processor is prototyped on Xilinx ZCU102 FPGA and validated with state-of-art seL4 microkernel, Linux kernel in multi-core scenarios, and a cache timing attack. Our evaluation shows that SIMF significantly alleviates the overhead of flushing by more than a factor of two in execution time and reduces dynamic instruction count by orders-of-magnitude.

SIMF: Single-Instruction Multiple-Flush Mechanism for Processor Temporal Isolation.

This paper presents UCloD, a novel random clock delay-based robust and scalable countermeasure against recently discovered remote power analysis (RPA) attacks. UCloD deploys very small clock delays (in the picosecond range) generated using the tapped delays lines (TDLs) to mitigate RPA attacks. UCloD provides the most robust countermeasures demonstrated thus far against RPA attacks. RPA attacks use delay sensors, such as Time to Digital Converters (TDC) or Ring Oscillators (ROs) to measure voltage fluctuations occurring in power delivery networks (PDNs) of Field Programmable Gate Arrays (FPGAs). These voltage fluctuations reveal secret information, such as secret keys of cryptographic circuits. The only countermeasure proposed thus far activates ROs to consume significant power and has managed to secure Advanced Encryption Standard (AES) circuits for up to 300,000 encryptions. Using TDLs available in FPGAs, UCloD randomly varies the clock to the cryptographic circuits under attack to induce noise in the adversary’s delay sensor(s). We demonstrate correlation power analysis (referred to as CPA) attack resistance of UCloD AES implementations for up to one million encryptions. Compared to an unprotected AES circuit, UCloD implementations have minimal overheads (0.2% Slice LUT overhead and 4.8% Slice register overhead for Xilinx implementations and 0.5% LogicCells overhead for Lattice Semiconductor implementations).

/pdf/uclod-small-clock-delays-to-mitigate-remote-power-analysis-4fbmnbuhvi.pdf

UCloD: Small Clock Delays to Mitigate Remote Power Analysis Attacks

Data integrity is important. One way to protect data integrity is attaching an identifying tag to individual data. The authenticity of the data can then be checked against its tag. If the data is altered by the adversary, the related tag becomes invalid and the attack will be detected. This paper studies an existing tag design (CETD) for memory data in embedded processor systems, where data that are stored in the memory or transferred over the bus can be tampered and need to be authenticated before use. Compared to other designs, this design offers the flexibility of tradeoff between the implementation cost and tag size (hence the level of security); the design is cost effective and can counter the data integrity attack with random values; namely the fake values used to replace the valid data in the attack are random. However, we find that the design is vulnerable when the fake data is not randomly selected. For some data, their tags are not distributed over the full tag value space but rather limited to a reduced set of values. When those values were chosen as the fake value, the data alteration would likely go undetected. In this paper, we analytically investigate this problem and propose a low cost enhancement to ensure the full-range distribution of tag values for each data, hence effectively removing the vulnerability of the original design.

Improving tag generation for memory data authentication in embedded processor systems

On-chip many-core systems are expected to be in common use in the future. A set of homogeneous processors in a many-core system can be used to implement multiple pipelines which execute simultaneously. Pipelines of processors use varying numbers of cores when their workloads vary at run time. In this paper, we show how such a system executing multiple pipelines with varying workloads can be implemented. We further show how the system can switch cores within a pipeline (intra-elasticity) and between pipelines (inter-elasticity). The method is named E-pipeline, and is implemented and evaluated in a commercial tool suite. Compared to reference design methods with clock gating, E-pipeline achieves the same power savings, maintains the throughput to meet throughput constraints and reduces core usage by an average of 37.7%. The adaptation overhead for switching cores is approximately 2μs.

E-pipeline: elastic hardware/software pipelines on a many-core fabric

Cache attacks have been described in the literature for over a decade now. Cache attacks are performed remotely by the use of time differences observed due to cache misses and hits, or by the use of power traces either by measuring power or by monitoring the bus between the processor and the memory to monitor the cache activity. In this paper, for the first time we have implemented a fast trace driven cache attack, and incorporated this attack into a flexible framework containing extensible processor(s). This simulator is modifiable and incorporates both Tensilica's [9] processor simulator environment along with DRAMsim, a DRAM simulator. Thus we are able to make changes to processor's instruction set, its cache architecture, and add additional hardware units. On this framework we have implemented a hardware / software countermeasure and shown that it is difficult to differentiate the cache misses for differing encryptions. The processor with the countermeasure is 30% more energy efficient, 17% more power efficient and 15% faster and when compared to processor without the countermeasure. The area of the processor with the countermeasure increases by 7.6%.

Sri Parameswaran

Papers

SIMF: Single-Instruction Multiple-Flush Mechanism for Processor Temporal Isolation.

UCloD: Small Clock Delays to Mitigate Remote Power Analysis Attacks

Improving tag generation for memory data authentication in embedded processor systems

E-pipeline: elastic hardware/software pipelines on a many-core fabric

A Hardware/Software Countermeasure and a Testing Framework for Cache Based Side Channel Attacks