Folding and Misfolding of Designed Heteropolymer Chains with Mutations

We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native conformation on a cubic lattice. It is found that quite a large fraction, between one half and one third of the substitutions, which we call 'cold errors', make important contributions to the dynamics of the folding process, increasing folding times typically by a factor of two, the altered chain still folding into the native structure. Few mutations ('hot errors'), have quite dramatic effects, leading to protein misfolding. Our analysis reveals that mutations affect primarily the energetics of the native conformation and to a much lesser extent the ensemble of unfolded conformations, corroborating the utility of the ``energy gap'' concept for the analysis of folding properties of protein-like heteropolymers.Comment: 12 pages, Latex (Revtex

Critical dimensions for random walks on random-walk chains

The probability distribution of random walks on linear structures generated by random walks in $d$-dimensional space, $P_d(r,t)$, is analytically studied for the case $\xi\equiv r/t^{1/4}\ll1$. It is shown to obey the scaling form $P_d(r,t)=\rho(r) t^{-1/2} \xi^{-2} f_d(\xi)$, where $\rho(r)\sim r^{2-d}$ is the density of the chain. Expanding $f_d(\xi)$ in powers of $\xi$, we find that there exists an infinite hierarchy of critical dimensions, $d_c=2,6,10,\ldots$, each one characterized by a logarithmic correction in $f_d(\xi)$. Namely, for $d=2$, $f_2(\xi)\simeq a_2\xi^2\ln\xi+b_2\xi^2$; for $3\le d\le 5$, $f_d(\xi)\simeq a_d\xi^2+b_d\xi^d$; for $d=6$, $f_6(\xi)\simeq a_6\xi^2+b_6\xi^6\ln\xi$; for $7\le d\le 9$, $f_d(\xi)\simeq a_d\xi^2+b_d\xi^6+c_d\xi^d$; for $d=10$, $f_{10}(\xi)\simeq a_{10}\xi^2+b_{10}\xi^6+c_{10}\xi^{10}\ln\xi$, {\it etc.\/} In particular, for $d=2$, this implies that the temporal dependence of the probability density of being close to the origin $Q_2(r,t)\equiv P_2(r,t)/\rho(r)\simeq t^{-1/2}\ln t$.Comment: LATeX, 10 pages, no figures submitted for publication in PR

Probability Distribution of the Shortest Path on the Percolation Cluster, its Backbone and Skeleton

We consider the mean distribution functions Phi(r|l), Phi(B)(r|l), and Phi(S)(r|l), giving the probability that two sites on the incipient percolation cluster, on its backbone and on its skeleton, respectively, connected by a shortest path of length l are separated by an Euclidean distance r. Following a scaling argument due to de Gennes for self-avoiding walks, we derive analytical expressions for the exponents g1=df+dmin-d and g1B=g1S-3dmin-d, which determine the scaling behavior of the distribution functions in the limit x=r/l^(nu) much less than 1, i.e., Phi(r|l) proportional to l^(-(nu)d)x^(g1), Phi(B)(r|l) proportional to l^(-(nu)d)x^(g1B), and Phi(S)(r|l) proportional to l^(-(nu)d)x^(g1S), with nu=1/dmin, where df and dmin are the fractal dimensions of the percolation cluster and the shortest path, respectively. The theoretical predictions for g1, g1B, and g1S are in very good agreement with our numerical results.Comment: 10 pages, 3 figure

A FLAMINGOS Deep Near Infrared Imaging Survey of the Rosette Complex I: Identification and Distribution of the Embedded Population

We present the results of a deep near-infrared imaging survey of the Rosette Complex. We studied the distribution of young embedded sources using a variation of the Nearest Neighbor Method applied to a carefully selected sample of near-infrared excess (NIRX) stars which trace the latest episode of star formation in the complex. Our analysis confirmed the existence of seven clusters previously detected in the molecular cloud, and identified four more clusters across the complex. We determined that 60% of the young stars in the complex and 86% of the stars within the molecular cloud are contained in clusters, implying that the majority of stars in the Rosette formed in embedded clusters. We compare the sizes, infrared excess fractions and average extinction towards individual clusters to investigate their early evolution and expansion. We found that the average infrared excess fraction of clusters increases as a function of distance from NGC 2244, implying a temporal sequence of star formation across the complex. This sequence appears to be primordial, possibly resulting from the formation and evolution of the molecular cloud and not from the interaction with the HII region.Comment: Accepted by Astrophysical Journa

A Shared Dataspace Language Supporting Larger-Scale Concurrency

Our ultimate goal is to develop the software support needed for the design, analysis, understanding, and testing of programs involving many thousands of concurrent processes running on a highly parallel multiprocessor. We are currently evaluating the use of a shared dataspace paradigm as the basis for a new programming language supporting large-scale concurrency. The language is called SDL (Shared Dataspace Language). In SDL, a content-addressable dataspace is examined and altered by concurrent processes using atomic transactions much like those in a traditional database. Associated with each process is a programmer-defined view. The view is a mechanism which allows processes to interrogate the dataspace at a level of abstraction convenient for the task they are pursuing. This paper provides an overview of the key SDL features. Small examples are used to illustrate the power and flexibility of the language. They also serve as a backdrop against which we discuss programming style implications of the shared dataspace paradigm

Microbial Characterization of Internal Active Thermal Control System (IATCS) Hardware Surfaces after Five Years of Operation in the International Space Station

A flex hose assembly containing aqueous coolant from the International Space Station (ISS) Internal Active Thermal Control System (IATCS) consisting of a 2 foot section of Teflon hose and quick disconnects (QDs) and a Special Performance Checkout Unit (SPCU) heat exchanger containing separate channels of IATCS coolant and iodinated water used to cool spacesuits and Extravehicular Mobility Units (EMUS) were returned for destructive analyses on Shuttle return to flight mission STS-114. The original aqueous IATCS coolant used in Node 1, the Laboratory Module, and the Airlock consisted of water, borate (pH buffer), phosphate (corrosion control), and silver sulfate (microbiological control) at a pH of 9.5 +/- 0.5. Chemical changes occurred after on-orbit implementation including a decrease to pH 8.4 due to the diffusion of carbon dioxide through the Teflon hoses, an increase in nickel ions due to general corrosion of heat exchanger braze coatings, a decrease in phosphate concentration due to precipitation of nickel phosphate, and the rapid disappearance of silver ions due to deposition on hardware surfaces. Also associated with the coolant chemistry changes was an increase in planktonic microorganisms from less than 100 colony forming units (CFU) per 100 ml to approximately 1 million CFU per 100 ml. Attachment and growth of microorganisms to the system surfaces (biofilm) was suspected due to the levels of planktonic microorganisms in the coolant. Biofilms can reduce coolant flow, reduce heat transfer, amplify degradation of system materials initiated by chemical corrosion, and enhance mineral scale formation

Fractional derivatives of random walks: Time series with long-time memory

We review statistical properties of models generated by the application of a (positive and negative order) fractional derivative operator to a standard random walk and show that the resulting stochastic walks display slowly-decaying autocorrelation functions. The relation between these correlated walks and the well-known fractionally integrated autoregressive (FIGARCH) models, commonly used in econometric studies, is discussed. The application of correlated random walks to simulate empirical financial times series is considered and compared with the predictions from FIGARCH and the simpler FIARCH processes. A comparison with empirical data is performed.Comment: 10 pages, 14 figure

A Superluminal Subway: The Krasnikov Tube

The ``warp drive'' metric recently presented by Alcubierre has the problem that an observer at the center of the warp bubble is causally separated from the outer edge of the bubble wall. Hence such an observer can neither create a warp bubble on demand nor control one once it has been created. In addition, such a bubble requires negative energy densities. One might hope that elimination of the first problem might ameliorate the second as well. We analyze and generalize a metric, originally proposed by Krasnikov for two spacetime dimensions, which does not suffer from the first difficulty. As a consequence, the Krasnikov metric has the interesting property that although the time for a one-way trip to a distant star cannot be shortened, the time for a round trip, as measured by clocks on Earth, can be made arbitrarily short. In our four dimensional extension of this metric, a ``tube'' is constructed along the path of an outbound spaceship, which connects the Earth and the star. Inside the tube spacetime is flat, but the light cones are opened out so as to allow superluminal travel in one direction. We show that, although a single Krasnikov tube does not involve closed timelike curves, a time machine can be constructed with a system of two non-overlapping tubes. Furthermore, it is demonstrated that Krasnikov tubes, like warp bubbles and traversable wormholes, also involve unphysically thin layers of negative energy density, as well as large total negative energies, and therefore probably cannot be realized in practice.Comment: 20 pages, LATEX, 5 eps figures, uses \eps