μ\mu-Limit Sets of Cellular Automata from a Computational Complexity Perspective

This paper concerns $\mu$-limit sets of cellular automata: sets of configurations made of words whose probability to appear does not vanish with time, starting from an initial $\mu$-random configuration. More precisely, we investigate the computational complexity of these sets and of related decision problems. Main results: first, $\mu$-limit sets can have a $\Sigma\_3^0$-hard language, second, they can contain only $\alpha$-complex configurations, third, any non-trivial property concerning them is at least $\Pi\_3^0$-hard. We prove complexity upper bounds, study restrictions of these questions to particular classes of CA, and different types of (non-)convergence of the measure of a word during the evolution.Comment: 41 page

The Relationship Between DNA\u27s Physical Properties and the DNA Molecule\u27s Harmonic Signature, and Related Motion in Water--A Computational Investigation

This research investigates through computational methods whether the physical properties of DNA contribute to its harmonic signature, the uniqueness of that signature if present, and motion of the DNA molecule in water. When DNA is solvated in water at normal \u27room temperature\u27, it experiences a natural vibration due to the Brownian motion of the particles in the water colliding with the DNA. The null hypothesis is that there is no evidence to suggest a relationship between DNA\u27s motion and strand length, while the alternative hypothesis is that there is evidence to suggest a relationship between DNA\u27s vibrational motion and strand length. In a similar vein to the first hypothesis, a second hypothesis posits that DNA\u27s vibrational motion may be dependent on strand content. The nature of this relationship, whether linear, exponential, logarithmic or non-continuous is not hypothesized by this research but will be discovered by testing if there is evidence to suggest a relationship between DNA\u27s motion and strand length. The research also aims to discover whether the motion of DNA, when it varies by strand length and/or content, is sufficiently unique to allow that DNA to be identified in the absence of foreknowledge of the type of DNA that is present in a manner similar to a signature. If there is evidence to suggest that there is a uniqueness in DNA\u27s vibrational motion under varying DNA strand content or length, then additional experimentation will be needed to determine whether these variances are unique across small changes as well as large changes, or large changes only. Finally, the question of whether it might be possible to identify a strand of unique DNA by base pair configuration solely from its vibrational signature, or if not, whether it might be possible to identify changes existing inside of a known DNA strand (such as a corruption, transposition or mutational error) is explored. Given the computational approach to this research, the NAMD simulation package (released by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign) with the CHARMM force field would be the most appropriate set of tools for this investigation (Phillips et al., 2005), and will therefore be the toolset used in this research. For visualization and manipulation of model data, the VMD (Visual Molecular Dynamics) package will be employed. Further, these tools may be optimized and/or be aware of nucleic acid structures, and are free. These tools appear to be sufficient for this task, with validated fidelity of the simulation to provide vibrational and pressure profile data that could be analyzed; sufficient capabilities to do what is being asked of it; speed, so that runs can be done in a reasonable period of time (weeks versus months); and parallelizability, so that the tool could be run over a clustered network of computers dedicated to the task to increase the speed and capacity of the simulations. The computer cluster enabled analysis of 30,000 to 40,000 atom systems spending more than 410,000 CPU computational hours of hundreds of nano second duration, experimental runs each sampled 500,000 times with two-femtosecond “frames.” Using Fourier transforms of run pressure readings into frequencies, the simulation investigation could not reject the null hypotheses that the frequencies observed in the system runs are independent on the DNA strand length or content being studied. To be clear, frequency variations were present in the in silicon replications of the DNA in ionized solutions, but we were unable to conclude that those variations were not due to other system factors. There were several tests employed to determine alternative factors that caused these variations. Chief among the factors is the possibility that the water box itself is the source of a large amount of vibrational noise that makes it difficult or impossible with the tools that we had at our disposal to isolate any signals emitted by the DNA strands. Assuming the water-box itself was a source of large amounts of vibrational noise, an emergent hypothesis was generated and additional post-hoc testing was undertaken to attempt to isolate and then filter the water box noise from the rest of the system frequencies. With conclusive results we found that the water box is responsible for the majority of the signals being recorded, resulting in very low signal amplitudes from the DNA molecules themselves. Using these low signal amplitudes being emitted by the DNA, we could not be conclusively uniquely associate either DNA length or content with the remaining observed frequencies. A brief look at a future possible isolation technique, wavelet analysis, was conducted. Finally, because these results are dependent on the tools at our disposal and hence by no means conclusive, suggestions for future research to expand on and further test these hypothesis are made in the final chapter

Topological dragging of solitons

We put forward properties of solitons supported by optical lattices featuring topological dislocations, and show that solitons experience attractive and repulsive forces around the dislocations. Suitable arrangements of dislocations are even found to form soliton traps, and the properties of such solitons are shown to crucially depend on the trap topology. The uncovered phenomenon opens a new concept for soliton control and manipulation, e.g., in disk-shaped Bose-Einstein condensates.Comment: 15 pages, 5 figures, to appear in Physical Review Letter

Application of two-color LIF thermometry to nucleate boiling

International audienceThe laser-induced fluorescence (LIF) thermometry is applied to measure the temperature field surrounding a single vapor bubble growing at an artificial nucleation site. In order to correct measurement errors due to the non-uniformity of the incident laser intensity, the two-color LIF thermometry technique is used in this nucleate boiling experiment. This technique is based on the use of two fluorescent dyes: the temperature sensitive dye Rhodamine B and the temperature insensitive dye Sulforhodamine-101. The concentration of the dyes is optimized by analyzing the behavior of fluorescence intensities. The mapping between the two images is determined through a geometrical calibration procedure. This technique presents a success in correcting the non uniformities due to the reflection of the light at the bubble surface and to the temperature gradient. The obtained temperature fields show that the two-color LIF is a promising technique in the investigation of nucleate boiling

The Grizzly, November 23, 1993

Dr. Davidson to Receive Cottrel Award • U.C.\u27s Questions are Answered • It\u27s Yes to NAFTA • A Dose of Reality • Touch my Flugel! • Exam Schedule • The Way to a Student\u27s Heart is Through His Stomach • Beer: A Historical Precedent? • A Dissatisfied Sanitation Worker Tells Ursinus to Clean Up its Act • Literary Society • Manning Retires as Soccer Coachhttps://digitalcommons.ursinus.edu/grizzlynews/1326/thumbnail.jp

The Grizzly, November 16, 1993

A Message From the Class of \u2797: The Freshmen Finally Surface • The Crunch is On • Fundraiser to Benefit Cancer Patients • Whitman Denies Allegations • Does Date Rape Exist at Ursinus? • ProTheatre to Present Henry Play • Freeze Tag and Organ Music? • Date Auction / Lease / Rental • Silenced by Shame • In Defense of Greek Life, Part Two • Anesthetizing of Literature • Bears Finish Stronghttps://digitalcommons.ursinus.edu/grizzlynews/1325/thumbnail.jp

Pennsylvania Folklife Vol. 10, No. 1

• Tramp Work : Penknife Plus Cigar Boxes • Tramps of My Youth • The German Broadside Songs of Pennsylvania • The Rise of Interest in Folk Art • Dutch Treats for Breakfast • The Amish, Citizens of Heaven and America • Collectanea • My Great-Grandmother • Old Sweitzer\u27s Ghost • Pastimes of My Youth • Battalion Day • Seven Days Make One Weekhttps://digitalcommons.ursinus.edu/pafolklifemag/1004/thumbnail.jp

The Grizzly, February 8, 1994

Ursinus Celebrates 125 Years of Academics • An Evaluation of the 128 Credit System • In Celebration of Black History Month: Al Eaton Brings on His One-Man Show • Ursinus Crimes Reported • Who Freed South Africa? • Guys Pledging Begins on Friday • Suite Etiquette • Senior Profile: Craig Faucher • Airband \u2794 • Come out and Support a U.C. Senior • Berman to Receive Preservation Grant • Woodward Exhibit on Display • Bright Moments to Perform • An Internal Compass Spinning • Eats & Seats • Wrestlers Up to 9-1 • Ursinus Gymnastics Sets New Records • Personal Interest Workshops to be Held • UC Student Almost Becomes Phillies\u27 Biggest Phanhttps://digitalcommons.ursinus.edu/grizzlynews/1329/thumbnail.jp

Deconvoluting kinase inhibitor induced cardiotoxicity

Many drugs designed to inhibit kinases have their clinical utility limited by cardiotoxicity-related label warnings or prescribing restrictions. While this liability is widely recognized, designing safer kinase inhibitors (KI) requires knowledge of the causative kinase(s). Efforts to unravel the kinases have encountered pharmacology with nearly prohibitive complexity. At therapeutically relevant concentrations, KIs show promiscuity distributed across the kinome. Here, to overcome this complexity, 65 KIs with known kinome-scale polypharmacology profiles were assessed for effects on cardiomyocyte (CM) beating. Changes in human iPSC-CM beat rate and amplitude were measured using label-free cellular impedance. Correlations between beat effects and kinase inhibition profiles were mined by computation analysis (Matthews Correlation Coefficient) to identify associated kinases. Thirty kinases met criteria of having (1) pharmacological inhibition correlated with CM beat changes, (2) expression in both human-induced pluripotent stem cell-derived cardiomyocytes and adult heart tissue, and (3) effects on CM beating following single gene knockdown. A subset of these 30 kinases were selected for mechanistic follow up. Examples of kinases regulating processes spanning the excitation–contraction cascade were identified, including calcium flux (RPS6KA3, IKBKE) and action potential duration (MAP4K2). Finally, a simple model was created to predict functional cardiotoxicity whereby inactivity at three sentinel kinases (RPS6KB1, FAK, STK35) showed exceptional accuracy in vitro and translated to clinical KI safety data. For drug discovery, identifying causative kinases and introducing a predictive model should transform the ability to design safer KI medicines. For cardiovascular biology, discovering kinases previously unrecognized as influencing cardiovascular biology should stimulate investigation of underappreciated signaling pathways