23 papers · ranked by Valyu relevance
Matthias Heizmann, Dominik Klumpp, Frank Schüssele, Lars Nitzke
We address the verification problem for concurrent program that dynamically create (fork) new threads or destroy (join) existing threads. We present a reduction to the verification problem for concurrent programs with a fixed number of threads. More precisely, we present petrification, a transformation from programs…
Daniel Ortíz-Arroyo, B. Lee
This paper presents the Dynamic Simultaneous Multithreaded Architecture (DSMT). DSMT efficiently executes multiple threads from a single program on a SMT processor core. To accomplish this, threads are generated dynamically from a predictable flow of control and then executed speculatively. Data obtained during the…
Ohad Kammar, Jack Liell-Cock, Sam Lindley, Cristina Matache + 1 more
Our programs are built from the key primitives 'fork' and 'wait'. 'Fork' creates a child thread and passes its name (thread ID) to the parent thread. 'Wait' allows us to wait for given child threads to finish. We provide a parameterized algebraic theory built from fork and wait, together with basic atomic actions and…
Aleksandra Prążyńska, Zbigniew Mikołajczyk, Maciej Kuchar, Alexey Smolin
'Alexey Smolin'] This publication presents the results of research aimed at analyzing the dynamic stretching process of multifilament polyester and polyamide threads with medium linear densities. Building virtual design tools for the mechanical properties of textiles under dynamic impact conditions on their structures…
Yatish Turakhia, Guangshuo Liu, Siddharth Garg, Diana Marculescu
—Dynamically adaptive multi-core architectures have been proposed as an effective solution to optimize performance for peak power constrained processors. In processors, the micro-architectural parameters or voltage/frequency of each core to be changed at run-time, thus providing a range of power/performance operating…
Rogelio Hernández-Tamayo, Niklas Steube, Thomas Heimerl, Georg Hochberg + 1 more
RecA plays a central role in DNA repair and is a main actor involved in homologous recombination (HR). In vivo, RecA forms filamentous structures termed “threads”, which are essential for HR, but whose nature is still ill defined. We show that RecA from Bacillus subtilis having lower ATP binding activity can still form…
Xing Liu, Kun Mean Hou, Christophe de Vaulx, Jun Xu + 4 more
'Haiying Zhou' 'Hongling Shi' 'Peng Zhou'] Memory and energy optimization strategies are essential for the resource-constrained wireless sensor network (WSN) nodes. In this article, a new memory-optimized and energy-optimized multithreaded WSN operating system (OS) LiveOS is designed and implemented. Memory cost of…
Alessandro Garbo, Stefano Quer
This paper presents a system for moving object exposure, focusing on pedestrian detection, in external, unfriendly, and heterogeneous environments. The system manipulates and accurately merges information coming from subsequent video frames, making small computational efforts in each single frame. Its main…
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread…
Hananel Hazan, Noam E. Ziv
There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for…
Aishwarya Upadhyay, Vijay Laxmi, Smita Naval
—As technology continues to advance and we usher in the era of Industry 5.0, there has been a profound paradigm shift in operating systems, file systems, web, and network applications. The conventional utilization of multiprocessing and multicore systems has made concurrent programming increasingly pervasive. However…
Xiandong Meng, Yanqing Ji
This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications-hidden Markov models (HMM). We show the detailed performance…
Rishi Tulsyan, Rekha Pai, Deepak D’Souza
We present a static analysis technique for detecting data races in Real-Time Operating System (RTOS) applications. These applications are often employed in safety-critical tasks and the presence of races may lead to erroneous behaviour with serious consequences. Analyzing these applications is challenging due to the…
Andrew C. Payne, Michael Andregg, Kent Kemmish, Mark Hamalainen + 11 more
'Charlotte Bowell' 'Andrew Bleloch' 'Nathan Klejwa' 'Wolfgang Lehrach' 'Ken Schatz' 'Heather Stark' 'Adam Marblestone' 'George Church' 'Christopher S. Own' 'William Andregg' 'Jerome Mathe'] We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Suyash Gupta, Rahul Shrivastava, V. Krishna Nandivada
In this paper, we present two symbiotic optimizations to optimize recursive task parallel (RTP) programs by reducing the task creation and termination overheads. Our first optimization Aggressive Finish-Elimination (AFE) helps reduce the redundant join operations to a large extent. The second optimization Dynamic…
Lisa Thomson, Daniel McDowall, Libby Marshall, Olivia Marshall + 8 more
Hierarchical self-assembly is an effective means of preparing useful materials. However, control over assembly across length scales is a difficult challenge, often confounded by the perceived need to re-design the molecular building blocks when new material properties are needed. Here, we show that we can treat a…
Colin Graber, Yurii Vlasov, Alexander Schwing
We introduce a probabilistic model to discover the dynamic connectivity structure in a network of spiking cortical neurons. The model is evaluated on ground truth synthetic data and compared to alternative methods to ensure quality and quantification of model predictions. When applied to large-scale recordings of…
Fabian Späth, Michele Stasi, Héctor Soria-Carrera, Judit Sastre + 2 more
Dynamic combinatorial chemistry (DCC) creates libraries of molecules that are constantly interchanging in a dynamic combinatorial library. When a library member self-assembles, it can displace the equilibria, leading to emergent phenomena like its selection or even its replication. However, such dynamic combinatorial…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
M. Alexander Ardagh, Omar A. Abdelrahman, Paul Dauenhauer
Acceleration of catalytic transformation of molecules via heterogeneous materials occurs through design of active binding sites to optimally balance the requirements of all steps in a catalytic cycle. In accordance with the Sabatier principle, the characteristics of a single binding site are balanced between at least…
Shumpei Morita, Jay T. Groves
T cells can recognize a few molecules of cognate antigen amongst vastly outnumbering non-cognate ligands. The T cell receptor (TCR) differentiates antigens based on antigen-TCR binding dwell time through a kinetic proofreading process. Historically, this has been modeled as the ligated receptor undergoing a series of…
Tomoya Maruyama, Jing Gong, Masahiro Takinoue
Bio-soft matter droplets formed via liquid-liquid phase separation (LLPS) of biopolymers have been found in living cells. Synthetic LLPS droplets have recently been employed in nanobiotechnology for artificial cell construction, molecular robotics, molecular computing, diagnosis, and therapeutics. Controlling the…