Airflow Model Testing to Determine the Distribution of Hot Gas Flow and O/F Ratio Across the Space Shuttle Main Engine Main Injector Assembly

Engine 0209, the certification engine for the new Phase 2+ Hot Gas Manifold (HGM), showed severe deterioration of the Main Combustion Chamber (MCC) liner during hot fire tests. One theory on the cause of the damage held that uneven local distribution of the fuel rich hot gas flow through the main injector assembly was producing regions of high oxidizer/fuel (O/F) ratio near the wall of the MCC liner. Airflow testing was proposed to measure the local hot gas flow rates through individual injector elements. The airflow tests were conducted using full scale, geometrically correct models of both the current Phase 2 and the new Phase 2+ HGMs. Different main injector flow shield configurations were tested for each HGM to ascertain their effect on the pressure levels and distribution of hot gas flow. Instrumentation located on the primary faceplate of the main injector measured hot gas flow through selected injector elements. These data were combined with information from the current space shuttle main engine (SSME) power balances to produce maps of pressure, hot gas flow rate, and O/F ratio near the main injector primary plate. The O/F distributions were compared for the different injector and HGM configurations

Authors' Rights to Share Scholarship: A Survey of IUPUI Faculty Attitudes

Faculty who take an active role in the dissemination of their research are more likely to make an impact on a field of scholarship. Online, full text archiving is a key component of being a self-advocate and for building a scholarly reputation. In fact, posting a version of a published article in an open access repository, such as IUPUI ScholarWorks, increases an author’s citation rate. Most journal publishers (72%) permit authors to upload a version of their article to IUPUI ScholarWorks; however, faculty may be unsure of how to exercise this right. Do IUPUI faculty self-archive their articles? Do they examine or negotiate the terms of their copyright transfer agreements? Would IUPUI faculty consider implementing a campus policy to maximize their rights as authors? To explore attitudes related to these questions, we conducted a campus-wide survey of IUPUI faculty in the Fall semester of 2013. The survey adapted an instrument used in similar campus-wide research conducted in 2006 at the University of California and in 2010 at the University of Toronto. This broad survey addressed attitudes regarding many factors relevant to publishing, peer review and scholarly communications. Here we report preliminary results pertaining to author’s rights, self-archiving practices and open access policies. Results: Complete responses (n=248); Partial responses (n=90). Author’s Rights: Most faculty (54%) consider the right to self-archive as a factor in selecting a journal for publication. A few have refused to sign a copyright transfer agreement (n=16) and a few have modified contracts (n=10). Most (68%) support a campus discussion of copyright management. Likewise, faculty would appreciate instructions and models for copyright negotiations (65%) as well as more formal institutional support for retaining rights (61%). Self-Archiving: Although nearly half had heard of IUPUI ScholarWorks (45%), only 25% of the respondents reported submitting a work to an institutional repository. Faculty were most influenced to self-archive by the motivation to support the dissemination of academic research in general (n=151), by increased exposure (n=149), and by the norms of their academic unit (n=102). Open Access Policies: The majority of faculty (72%) were unfamiliar with institutional open access policies such as those at Harvard, MIT, Duke and Kansas. When asked, however, if IUPUI should consider implementing a similar policy, 52% were unsure, 39% were supportive and only 9% disagreed

Faculty Attitudes toward Open Access and Scholarly Communications: Disciplinary Differences on an Urban and Health Science Campus

The Journal of Librarianship and Scholarly Communication seeks to share useful innovations, both in thought and in practice, with the aim of encouraging scholarly exchange and the subsequent benefits that are borne of scrutiny, experimentation and debate. As modes of scholarly communication, the technologies and economics of publishing and the roles of libraries evolve, it is our hope that the work shared in the journal will inform practices that strengthen librarianship and that increase access to the "common Stock of Knowledge."JLSC is particularly interested in the intersection of librarianship and publishing and the resulting role of libraries in both content dissemination and content creation. Related areas of interest include new methods for the dissemination of information and information exchange; the theory and practice of the organization, use and curation of information; and issues related to the review, credentialing, reputation and impact of scholarly work

Viscosity Dependence of the Folding Rates of Proteins

The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is given by the Langevin equation we show that the folding rates increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and have a maximum at intermediate values. The Kramers theory of barrier crossing provides a quantitative fit of the numerical results. By mapping the simulation results to real proteins we estimate that for optimized sequences the time scale for forming a four turn \alpha-helix topology is about 500 nanoseconds, whereas the time scale for forming a beta-sheet topology is about 10 microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical Review Letter

Refolding dynamics of stretched biopolymers upon force quench

Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench, using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, $\tau_F$, depends asymmetrically on $\delta f_S = f_S - f_m$ and $\delta f_Q = f_m - f_Q$ where $f_S$ ($f_Q$) is the stretch (quench) force, and $f_m$ is the transition mid-force of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension, $R(t)$, occurs in three stages: a rapid initial decrease in the extension is followed by a plateau, and finally an abrupt reduction in $R(t)$ that occurs as the native state is approached. The duration of the plateau increases as $\lambda =\tau_Q/\tau_F$ decreases (where $\tau_Q$ is the time in which the force is reduced from $f_S$ to $f_Q$). Variations in the mechanisms of force quench relaxation as $\lambda$ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in $R(t)$. The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding.Comment: 31 pages 11 figure

One-dimensional Ising ferromagnet frustrated by long-range interactions at finite temperatures

We consider a one-dimensional lattice of Ising-type variables where the ferromagnetic exchange interaction J between neighboring sites is frustrated by a long-ranged anti-ferromagnetic interaction of strength g between the sites i and j, decaying as |i-j|^-alpha, with alpha>1. For alpha smaller than a certain threshold alpha_0, which is larger than 2 and depends on the ratio J/g, the ground state consists of an ordered sequence of segments with equal length and alternating magnetization. The width of the segments depends on both alpha and the ratio J/g. Our Monte Carlo study shows that the on-site magnetization vanishes at finite temperatures and finds no indication of any phase transition. Yet, the modulation present in the ground state is recovered at finite temperatures in the two-point correlation function, which oscillates in space with a characteristic spatial period: The latter depends on alpha and J/g and decreases smoothly from the ground-state value as the temperature is increased. Such an oscillation of the correlation function is exponentially damped over a characteristic spatial scale, the correlation length, which asymptotically diverges roughly as the inverse of the temperature as T=0 is approached. This suggests that the long-range interaction causes the Ising chain to fall into a universality class consistent with an underlying continuous symmetry. The e^(Delta/T)-temperature dependence of the correlation length and the uniform ferromagnetic ground state, characteristic of the g=0 discrete Ising symmetry, are recovered for alpha > alpha_0.Comment: 12 pages, 7 figure

Finite size effects on thermal denaturation of globular proteins

Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of proteins and substantiates the earlier predictions that the efficient folding of two-state proteins requires the folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press

Timed Parity Games: Complexity and Robustness

We consider two-player games played in real time on game structures with clocks where the objectives of players are described using parity conditions. The games are \emph{concurrent} in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to play strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to \emph{turn-based} (i.e., not concurrent) \emph{finite-state} (i.e., untimed) parity games. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. The states of the resulting game are based on clock regions of the original game, and the state space of the finite game is linear in the size of the region graph. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, \emph{limit-robust} and \emph{bounded-robust} winning strategies. Using a limit-robust winning strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust winning. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust winning strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers

Exploring the Levinthal limit in protein folding

According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers. Furthermore, an enhancement of the degree of fluctuation of the non-native conformers can be explained by an insufficient relaxation to their local free energy minimum. These results favor Levinthal's hypothesis that protein folding is a kinetic non-equilibrium process.FCT - Foundation for Science and Technology, Portugal [UID/Multi/04326/2013]; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP); Conselho Nacional de Desenvolvimento Cientia co e Tecnologico (CNPq