mizar-items: Exploring fine-grained dependencies in the Mizar Mathematical Library

The Mizar Mathematical Library (MML) is a rich database of formalized mathematical proofs (see http://mizar.org). Owing to its large size (it contains more than 1100 "articles" summing to nearly 2.5 million lines of text, expressing more than 50000 theorems and 10000 definitions using more than 7000 symbols), the nature of its contents (the MML is slanted toward pure mathematics), and its classical foundations (first-order logic, set theory, natural deduction), the MML is an especially attractive target for research on foundations of mathematics. We have implemented a system, mizar-items, on which a variety of such foundational experiements can be based. The heart of mizar-items is a method for decomposing the contents of the MML into fine-grained "items" (e.g., theorem, definition, notation, etc.) and computing dependency relations among these items. mizar-items also comes equipped with a website for exploring these dependencies and interacting with them.Comment: Accepted at CICM 2011: Conferences in Intelligent Computer Mathematics, Track C: Systems and Project

Mean First Passage Time in Periodic Attractors

The properties of the mean first passage time in a system characterized by multiple periodic attractors are studied. Using a transformation from a high dimensional space to 1D, the problem is reduced to a stochastic process along the path from the fixed point attractor to a saddle point located between two neighboring attractors. It is found that the time to switch between attractors depends on the effective size of the attractors, $\tau$, the noise, $\epsilon$, and the potential difference between the attractor and an adjacent saddle point as: $~T = {c \over \tau} \exp({\tau \over \epsilon} \Delta {\cal{U}})~$; the ratio between the sizes of the two attractors affects $\Delta {\cal{U}}$. The result is obtained analytically for small $\tau$ and confirmed by numerical simulations. Possible implications that may arise from the model and results are discussed.Comment: 14 pages, 3 figures, submitted to journal of physics

Hydrodynamic mean field solutions of 1D exclusion processes with spatially varying hopping rates

We analyze the open boundary partially asymmetric exclusion process with smoothly varying internal hopping rates in the infinite-size, mean field limit. The mean field equations for particle densities are written in terms of Ricatti equations with the steady-state current $J$ as a parameter. These equations are solved both analytically and numerically. Upon imposing the boundary conditions set by the injection and extraction rates, the currents $J$ are found self-consistently. We find a number of cases where analytic solutions can be found exactly or approximated. Results for $J$ from asymptotic analyses for slowly varying hopping rates agree extremely well with those from extensive Monte Carlo simulations, suggesting that mean field currents asymptotically approach the exact currents in the hydrodynamic limit, as the hopping rates vary slowly over the lattice. If the forward hopping rate is greater than or less than the backward hopping rate throughout the entire chain, the three standard steady-state phases are preserved. Our analysis reveals the sensitivity of the current to the relative phase between the forward and backward hopping rate functions.Comment: 12 pages, 4 figure

The triple-mode pulsating variable V823 Cas

Based on extended multicolour CCD photometry of the triple-mode radial pulsator V823 Cas we studied the properties of the coupling frequencies invoked by nonlinear processes. Our results support that a resonance connection as suggested by Antonello & Aikawa (1998) affects the mode coupling behaviour. The P1/P0 period ratio of V823 Cas has an "out of range" value if compared with the period ratios of the known double mode pulsators, while the P2/P1 period ratio is normal. The periods and period ratios cannot be consistently interpret without conflict with pulsation and/or evolution models. We attempt to interpret this failure by the suggestion that at present, the periods of V823 Cas are in a transient, resonance affected state, thus do not reflect the true parameters of the object. The anomalous period change behaviour of the fundamental and second overtone modes supports this idea. We have also raised the possibility that a f0 + f2 = 2f1 resonance may act in triple mode pulsators.Comment: 10 pages, 7 figures, 5 tables. Accepted for publication in Astronomy and Astrophysic

Die Bedeutung von Metakognitionen für das Verständnis und die Psychotherapie von Zwang

The Importance of Metacognitions in the Understanding and Treatment of Obsessive Compulsive Disorder The present article discusses three cognitive approaches of Obsessive Compulsive Disorder (OCD): (1) Beck's theory of content-specificity, (2) Salkovskis' cognitive-behavioural approach and (3) Wells' more recent theory of metacognitions. Wells' approach is explained in more detail: the so called Self-Regulatory Executive Function model is presented as well as special aspects of thinking in OCD, for example the self-referential status of thinking, thinking in object mode and aspects of `thought-action fusion'. The relevance of Wells' metacognitive approach for the development and the maintenance of OCD is discussed. Furthermore, proposals are made on how to include these issues in the psychotherapy of OCD

Time-Dependent Density Functional Theory for Driven Lattice Gas Systems with Interactions

We present a new method to describe the kinetics of driven lattice gases with particle-particle interactions beyond hard-core exclusions. The method is based on the time-dependent density functional theory for lattice systems and allows one to set up closed evolution equations for mean site occupation numbers in a systematic manner. Application of the method to a totally asymmetric site exclusion process with nearest-neighbor interactions yields predictions for the current-density relation in the bulk, the phase diagram of non-equilibrium steady states and the time evolution of density profiles that are in good agreement with results from kinetic Monte Carlo simulations.Comment: 11 pages, 3 figure

Power spectra of TASEPs with a localized slow site

The totally asymmetric simple exclusion process (TASEP) with a localized defect is revisited in this article with attention paid to the power spectra of the particle occupancy N(t). Intrigued by the oscillatory behaviors in the power spectra of an ordinary TASEP in high/low density phase(HD/LD) observed by Adams et al. (2007 Phys. Rev. Lett. 99 020601), we introduce a single slow site with hopping rate q<1 to the system. As the power spectrum contains time-correlation information of the particle occupancy of the system, we are particularly interested in how the defect affects fluctuation in particle number of the left and right subsystems as well as that of the entire system. Exploiting Monte Carlo simulations, we observe the disappearance of oscillations when the defect is located at the center of the system. When the defect is off center, oscillations are restored. To explore the origin of such phenomenon, we use a linearized Langevin equation to calculate the power spectrum for the sublattices and the whole lattice. We provide insights into the interactions between the sublattices coupled through the defect site for both simulation and analytical results.Comment: 16 pages, 6 figures; v2: Minor revision

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600