Exact Stochastic Simulation of Chemical Reactions with Cycle Leaping

The stochastic simulation algorithm (SSA), first proposed by Gillespie, has become the workhorse of computational biology. It tracks integer quantities of the molecular species, executing reactions at random based on propensity calculations. An estimate for the resulting quantities of the different species is obtained by averaging the results of repeated trials. Unfortunately, for models with many reaction channels and many species, the algorithm requires a prohibitive amount of computation time. Many trials must be performed, each forming a lengthy trajectory through the state space. With coupled or reversible reactions, the simulation often loops through the same sequence of states repeatedly, consuming computing time, but making no forward progress. We propose a algorithm that reduces the simulation time through cycle leaping: when cycles are encountered, the exit probabilities are calculated. Then, in a single bound, the simulation leaps directly to one of the exit states. The technique is exact, sampling the state space with the expected probability distribution. It is a component of a general framework that we have developed for stochastic simulation based on probabilistic analysis and caching

The Synthesis of Cyclic Combinatorial Circuits

To be added

Cyclic Boolean circuits

A Boolean circuit is a collection of gates and wires that performs a mapping from Boolean inputs to Boolean outputs. The accepted wisdom is that such circuits must have acyclic (i.e., loop-free or feed-forward) topologies. In fact, the model is often defined this way – as a directed acyclic graph (DAG). And yet simple examples suggest that this is incorrect. We advocate that Boolean circuits should have cyclic topologies (i.e., loops or feedback paths). In other work, we demonstrated the practical implications of this view: digital circuits can be designed with fewer gates if they contain cycles. In this paper, we explore the theoretical underpinnings of the idea. We show that the complexity of implementing Boolean functions can be lower with cyclic topologies than with acyclic topologies. With examples, we show that certain Boolean functions can be implemented by cyclic circuits with as little as one-half the number gates that are required by equivalent acyclic circuits

Algorithmic Aspects of Cyclic Combinational Circuit Synthesis

Digital circuits are called combinational if they are memoryless: if they have outputs that depend only on the current values of the inputs. Combinational circuits are generally thought of as acyclic (i.e., feed-forward) structures. And yet, cyclic circuits can be combinational. Cycles sometimes occur in designs synthesized from high-level descriptions, as well as in bus-based designs [16]. Feedback in such cases is carefully contrived, typically occurring when functional units are connected in a cyclic topology. Although the premise of cycles in combinational circuits has been accepted, and analysis techniques have been proposed [7], no one has attempted the synthesis of circuits with feedback at the logic level. We have argued the case for a paradigm shift in combinational circuit design [10]. We should no longer think of combinational logic as acyclic in theory or in practice, since most combinational circuits are best designed with cycles. We have proposed a general methodology for the synthesis of multilevel networks with cyclic topologies and incorporated it in a general logic synthesis environment. In trials, benchmark circuits were optimized significantly, with improvements of up to 30%I n the area. In this paper, we discuss algorithmic aspects of cyclic circuit design. We formulate a symbolic framework for analysis based on a divide-and-conquer strategy. Unlike previous approaches, our method does not require ternary-valued simulation. Our analysis for combinationality is tightly coupled with the synthesis phase, in which we assemble a combinational network from smaller combinational components. We discuss the underpinnings of the heuristic search methods and present examples as well as synthesis results for benchmark circuits. In this paper, we discuss algorithmic aspects of cyclic circuit design. We formulate a symbolic framework for analysis based on a divide-and-conquer strategy. Unlike previous approaches, our method does not require ternary-valued simulation. Our analysis for combinationality is tightly coupled with the synthesis phase, in which we assemble a combinational network from smaller combinational components. We discuss the underpinnings of the heuristic search methods and present examples as well as synthesis results for benchmark circuits

Data report: Seismic structure beneath the North Cascadia drilling transect of IODP Expedition 311

Between 1999 and 2004, new seismic data became available for the study of gas hydrates on the northern Cascadia margin. These data consist of multi- and single-channel data with two- and partly three-dimensional subsurface coverage and were acquired and used in support of the proposal for Integrated Ocean Drilling Program (IODP) Expedition 311 carried out in 2005. The working area lies across the continental slope off the coast of central Vancouver Island, British Columbia, Canada, with water depths ranging from 2600 m in the trench to 500 m on the upper slope, where it is well above the minimum depth for gas hydrate stability. This paper gives the details of the data acquisition and conventional processing and then focuses on describing the new data at six individual sites along a transect across the gas hydrate zone. Five of the sites were drilled during the Expedition 311. The transect of sites commences at the almost undeformed incoming sediments seaward of the region where gas hydrates are observed; these ocean basin sediments were drilled at a site 40 km southeast during Ocean Drilling Program (ODP) Leg 146. The transect continues up the continental slope into the area of hydrate stability, with a site on top of the frontal accretionary ridge where normal faulting indicates margin parallel extension; a site in the first slope basin overlying a buried ridge near a reflectivity wipe-out zone; a site adjacent to Site 889 of Leg 146 and therefore acting as a tie hole; the most landward site at the shallowest end of the hydrate stability field; and a cold vent site at one of several blank zones close to a bright spot region in the seismic records

A low-loss, broadband antenna for efficient photon collection from a coherent spin in diamond

We report the creation of a low-loss, broadband optical antenna giving highly directed output from a coherent single spin in the solid-state. The device, the first solid-state realization of a dielectric antenna, is engineered for individual nitrogen vacancy (NV) electronic spins in diamond. We demonstrate a directionality close to 10. The photonic structure preserves the high spin coherence of single crystal diamond (T2>100us). The single photon count rate approaches a MHz facilitating efficient spin readout. We thus demonstrate a key enabling technology for quantum applications such as high-sensitivity magnetometry and long-distance spin entanglement.Comment: 5 pages, 4 figures and supplementary information (5 pages, 8 figures). Comments welcome. Further information under http://www.quantum-sensing.physik.unibas.c

Computing in the RAIN: a reliable array of independent nodes

The RAIN project is a research collaboration between Caltech and NASA-JPL on distributed computing and data-storage systems for future spaceborne missions. The goal of the project is to identify and develop key building blocks for reliable distributed systems built with inexpensive off-the-shelf components. The RAIN platform consists of a heterogeneous cluster of computing and/or storage nodes connected via multiple interfaces to networks configured in fault-tolerant topologies. The RAIN software components run in conjunction with operating system services and standard network protocols. Through software-implemented fault tolerance, the system tolerates multiple node, link, and switch failures, with no single point of failure. The RAIN-technology has been transferred to Rainfinity, a start-up company focusing on creating clustered solutions for improving the performance and availability of Internet data centers. In this paper, we describe the following contributions: 1) fault-tolerant interconnect topologies and communication protocols providing consistent error reporting of link failures, 2) fault management techniques based on group membership, and 3) data storage schemes based on computationally efficient error-control codes. We present several proof-of-concept applications: a highly-available video server, a highly-available Web server, and a distributed checkpointing system. Also, we describe a commercial product, Rainwall, built with the RAIN technology