Now showing items 22-41 of 46

    • Mapping Network Motif Tunability and Robustness in the Design of Synthetic Signaling Circuits 

      Iadevaia, Sergio; Nakhleh, Luay K.; Azencott, Robert; Ram, Prahlad T. (2014)
      Cellular networks are highly dynamic in their function, yet evolutionarily conserved in their core network motifs or topologies. Understanding functional tunability and robustness of network motifs to small perturbations ...
    • The Mason Test: A Defense Against Sybil Attacks in Wireless Networks Without Trusted Authorities 

      Liu, Yue; Bild, David R.; Dick, Robert P.; Mao, Z. Morley; Wallach, Dan S. (2015)
      Wireless networks are vulnerable to Sybil attacks, in which a malicious node poses as many identities in order to gain disproportionate influence. Many defenses based on spatial variability of wireless channels exist, but ...
    • Mechanism of Graphene Oxide Formation 

      Dimiev, Ayrat M.; Tour, James M. (2014)
      Despite intensive research, the mechanism of graphene oxide (GO) formation remains unclear. The role of interfacial interactions between solid graphite and the liquid reaction medium, and transport of the oxidizing agent ...
    • Meniscus-Mask Lithography for Fabrication of Narrow Nanowires 

      Abramova, Vera; Slesarev, Alexander S.; Tour, James M. (2015)
      We demonstrate the efficiency of meniscus-mask lithography (MML) for fabrication of precisely positioned nanowires in a variety of materials. Si, SiO2, Au, Cr, W, Ti, TiO2, and Al nanowires are fabricated and characterized. ...
    • Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks 

      Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay (2013)
      The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each ...
    • Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments 

      Saxer, Gerda; Krepps, Michael D.; Merkley, Eric D.; Ansong, Charles; Deatherage Kaiser, Brooke L.; Valovska, Marie-Thérèse; Ristic, Nikola; Yeh, Ping T.; Prakash, Vittal P.; Leiser, Owen P.; Nakhleh, Luay; Gibbons, Henry S.; Kreuzer, Helen W.; Shamoo, You (2014)
      Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Adaptation to a new environment with abundant ...
    • ncDNA and drift drive binding site accumulation 

      Ruths, Troy; Nakhleh, Luay (2012)
      Background: The amount of transcription factor binding sites (TFBS) in an organism's genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise ...
    • Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology 

      Ruths, Troy; Nakhleh, Luay (2013-04)
      Cis-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive ...
    • Non-intrusive Persistence with a Backend NVM Controller 

      Pu, Libei; Doshi, Kshitij; Giles, Ellis; Varman, Peter (2015)
      By providing instruction-grained access to vast amounts of persistent data with ordinary loads and stores, byte-addressable storage class memory (SCM) has the potential to revolutionize system architecture. We describe a ...
    • On computing minimal independent support and its applications to sampling and counting 

      Ivrii, Alexander; Malik, Sharad; Meel, Kuldeep S.; Vardi, Moshe Y. (2015)
      Constrained sampling and counting are two fundamental problems arising in domains ranging from artificial intelligence and security, to hardware and software testing. Recent approaches to approximate solutions for these ...
    • Once and For All 

      Kupferman, Orna; Pnueli, Amir; Vardi, Moshe Y. (2012)
      It has long been known that past-time operators add no expressive power to linear temporal logics. In this paper, we consider the extension of branching temporal logics with past-time operators. Two possible views regarding ...
    • Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting 

      Yu, Yun; Barnett, R. Matthew; Nakhleh, Luay (2013)
      Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, ...
    • Performance Analysis and Optimization of a Hybrid Seismic Imaging Application 

      Paul, Sri Raj; Araya-Polo, Mauricio; Mellor-Crummey, John; Hohl, Detlef (2016)
      Applications to process seismic data are computationally expensive and, therefore, employ scalable parallel systems to produce timely results. Here we describe our experiences of using performance analysis tools to gain ...
    • Publication Culture in Computing Research 

      Mehlhorn, Kurt; Vardi, Moshe Y.; Herbstritt, Marc (2012)
      The dissemination of research results is an integral part of research and hence a crucial component for any scientific discipline. In the area of computing research, there have been raised concerns recently about its ...
    • Regular Real Analysis 

      Chaudhuri, Swarat; Sankaranarayanan, Sriram; Vardi, Moshe Y. (2013)
      We initiate the study of regular real analysis, or the analysis of real functions that can be encoded by automata on infinite words. It is known that ω-automata can be used to represent {relations} between real ...
    • Relentful Strategic Reasoning in 1 Alternating-Time Temporal Logic 

      Mogavero, Fabio; Murano, Aniello; Vardi, Moshe Y. (2014)
      Temporal logics are a well investigated formalism for the specification, verification, and synthesis of reactive systems. Within this family, Alternating-Time Temporal Logic (ATL , for short) has been introduced as a ...
    • SIMS: A Hybrid Method for Rapid Conformational Analysis 

      Gipson, Bryant; Moll, Mark; Kavraki, Lydia E. (2013)
      Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a ...
    • Solving Partial-Information Stochastic Parity Games 

      Nain, Sumit; Vardi, Moshe Y. (2013)
      We study one-sided partial-information 2-player concurrent stochastic games with parity objectives. In such a game, one of the players has only partial visibility of the state of the game, while the other player has complete ...
    • Structure-guided selection of specificity determining positions in the human Kinome 

      Moll, Mark; Finn, Paul W; Kavraki, Lydia E (2016-08-18)
      Abstract Background The human kinome contains many important drug targets. It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. ...