The cell cycle program of polypeptide labeling in Chlamydomonas reinhardtii

The cell cycle program of polypeptide labeling in syndhronous cultures of wild-type Chlamydomonas reinhardtii was analyzed by pulse-labeling cells with 35SO4 = or [3H]arginine at different cell cycle stages. Nearly 100 labeled membrane and soluble polypeptides were resolved and studied using one-dimensional sodium dodecyl sulfate (SDS)- polyacrylamide gel electrophoresis. The labeling experiments produced the following results. (a) Total 35SO4 = and [3H]arginine incorporation rates varied independently throughout the cell cycle. 35SO4 = incorporation was highest in the mid-light phase, while [3H]arginine incorporation peaked in the dark phase just before cell division. (b) The relative labeling rate for 20 of 100 polypeptides showed significant fluctuations (3-12 fold) during the cell cycle. The remaining polypeptides were labeled at a rate commensurate with total 35SO4 = or [3H]arginine incorporation. The polypeptides that showed significant fluctuations in relative labeling rates served as markers to identify cell cycle stages. (c) The effects of illumination conditions on the apparent cell cycle stage-specific labeling of polypeptides were tested. Shifting light-grown asynchronous cells to the dark had an immediate and pronounced effect on the pattern of polypeptide labeling, but shifting dark-phase syndhronous cells to the light had little effect. The apparent cell cycle variations in the labeling of ribulose 1,5-biphosphate (RUBP)-carboxylase were strongly influenced by illumination effects. (d) Pulse-chase experiments with light-grown asynchronous cells revealed little turnover or inter- conversion of labeled polypeptides within one cell generation, meaning that major polypeptides, whether labeled in a stage-specific manner or not, do not appear transiently in the cell cycle of actively dividing, light-grown cells. The cell cycle program of labeling was used to analyze effects of a temperature-sensitive cycle blocked (cb) mutant. A synchronous culture of ts10001 was shifted to restrictive temperature before its block point to prevent it from dividing. The mutant continued its cell cycle program of polypeptide labeling for over a cell generation, despite its inability to divide

A VERY FAST CONSTRAINT SOLVER INTERPRETER FOR EVALUATING MODEL CONSTRAINTS

Poster and poster abstractModel-Driven Engineering (MDE) facilitates building solutions in many enterprise application domains through the systematic use of graphical languages called domain-specific modeling languages (DSMLs). MDE tools, such as the Generic Modeling Environment (GME) and the Generic Eclipse Modeling System (GEMS), enable end-users to rapidly create such custom DSMLs. One advantage of using DSMLs is its correct-by-construction characteristics, which is provided by domain-specific constraints defined within these custom languages. The constraints, written in Object Constraint Language (OCL), are evaluated during and after model construction using a constraint checker. For example, GME provides a Constraint Manager (CM) that evaluate the constraints defined by a DSMLs against its models. Unfortunately, our experience has shown that the constraint checkers provided by MDE tools do not scale to large models (i.e., models that have 10s of 1000s of model elements and 10s of 100s of constraints). Our research therefore focuses on developing a very fast OCL constraint solver that can address the current shortcomings of existing OCL constraint solvers in the context of GME. Our design approach leverages best practices in software design patterns, caching, and multi-threading to improve its performance and scalability. Initial results of our work show that for small models (e.g., 10s to 100s of elements), the traditional constraint solvers run slightly faster than our approach. For models with more than 1000s of elements, our approach is twice as fast, and performs exponential better as the size and complexity of the models increase

Realtime Dynamic Binary Instrumentation

poster abstractAbstract: We present a novel technique and framework for decreasing instrumentation overhead in software systems that utilize dynamic binary instrumentation. First, we introduce a lightweight networking framework combined with an easily extensible BSON implementation as a heavy analysis routine replacement. Secondly, we bind instrumentation and analysis threads to non-overlapping cpu cores---allowing analysis threads to execute faster. Lastly, we utilize a lock-free buffering system to bridge the gap between instrumentation and analysis threads, and minimize the overhead to the instrumentation threads. Using this combination, we managed to write a dynamic binary instrumentation tool (DBI) in Pin using Pin++ that is 1100% faster than its counterpart DBI tool with no buffering, and less than 500% slower than a similar tool with no analysis routine

AUTO-GENERATING MODELS FROM THEIR SEMANTICS AND CONSTRAINTS

poster abstractModel-Driven Engineering (MDE) facilitates building solutions in many en-terprise application domains through the systematic use of graphical lan-guages called domain-specific modeling languages (DSMLs). MDE tools, such as the Generic Modeling Environment (GME) and the Generic Eclipse Modeling System (GEMS), enable end-users to rapidly create such custom DSMLs. When DSMLs are coupled with constraint solvers, it is possible for DSML end-users to auto-generate solutions (i.e., models) based on the goals of the constraint solver (e.g., finding the optimal deployment for a set of software components given resource availability and resource needs). One requirement of using a constraint solver with a DSML, however, is that mod-elers have to create an initial model, also known as a “partial model”. This implies that it is the end-users responsibility to (1) understand how to use the DSML and (2) understand when they have created an appropriate partial model that is a candidate for completion using a constraint solver. Our research therefore focuses on addressing the two problems men-tioned above. We address the problems by analyzing the semantics and con-straints of the DSML (i.e., the meta-model). Based on our analysis, we then auto-generate as much of the model until we reach a point that requires us-er intervention. At that point, we present a set of operations (or moves) to the user and continue the process until the model is complete, or is solvable using a constraint solver

Pin++: An Object-oriented Framework for Writing Pintools

This paper presents a framework named Pin++. Pin++ is an object-oriented framework that uses template metaprogramming to implement Pintools, which are analysis tools for the dynamic binary instrumentation tool named Pin. The goal of Pin++ is to simplify programming a Pintool and promote reuse of its components across different Pintools. Our results show that Pintools implemented using Pin++ can have a 54% reduction in complexity, increase its modularity, and up to 60% reduction in instrumentation overhead

An experimental comparison of several current viscoplastic constitutive models at elevated temperature

Four current viscoplastic models are compared experimentally for Inconel 718 at 593 C. This material system responds with apparent negative strain rate sensitivity, undergoes cyclic work softening, and is susceptible to low cycle fatigue. A series of tests were performed to create a data base from which to evaluate material constants. A method to evaluate the constants is developed which draws on common assumptions for this type of material, recent advances by other researchers, and iterative techniques. A complex history test, not used in calculating the constants, is then used to compare the predictive capabilities of the models. The combination of exponentially based inelastic strain rate equations and dynamic recovery is shown to model this material system with the greatest success. The method of constant calculation developed was successfully applied to the complex material response encountered. Backstress measuring tests were found to be invaluable and to warrant further development

Simultaneous Multithreading and Hard Real Time: Can It Be Safe?

The applicability of Simultaneous Multithreading (SMT) to real-time systems has been hampered by the difficulty of obtaining reliable execution costs in an SMT-enabled system. This problem is addressed by introducing a scheduling framework, called CERT-MT, that combines scheduling-aware timing analysis with a cyclic-executive scheduler in a way that minimizes SMT-related timing variations. The proposed scheduling-aware timing analysis is based on maximum observed execution times and accounts for the uncertainty inherent in measurement-based timing analysis. The timing analysis is found to work for tasks with and without SMT, though some adjustments are required in the former case. A large-scale schedulability study is presented that shows CERT-MT can schedule systems with total utilizations approaching 1.4 times the core count, without sacrificing safety

An automated procedure for material parameter evaluation for viscoplastic constitutive models

An automated procedure is presented for evaluating the material parameters in Walker's exponential viscoplastic constitutive model for metals at elevated temperature. Both physical and numerical approximations are utilized to compute the constants for Inconel 718 at 1100 F. When intermediate results are carefully scrutinized and engineering judgement applied, parameters may be computed which yield stress output histories that are in agreement with experimental results. A qualitative assessment of the theta-plot method for predicting the limiting value of stress is also presented. The procedure may also be used as a basis to develop evaluation schemes for other viscoplastic constitutive theories of this type

The Lennard-Jones-Devonshire cell model revisited

We reanalyse the cell theory of Lennard-Jones and Devonshire and find that in addition to the critical point originally reported for the 12-6 potential (and widely quoted in standard textbooks), the model exhibits a further critical point. We show that the latter is actually a more appropriate candidate for liquid-gas criticality than the original critical point.Comment: 5 pages, 3 figures, submitted to Mol. Phy