Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon

Transcriptional attenuation at E.coli\u27s tryptophan operon is a prime example of RNA-mediated gene regulation. In this paper, we present a discrete stochastic model for this phenomenon based on chemical reactions. Our model is compact and intelligible, due to n-ary reactions (which preclude object-centric approaches) and to rule schemas that define finite sets of chemical reactions. Stochastic simulations with our model confirm results that were previously obtained by master equations or differential equations. In addition, our approach permits to reflect mutation experiments by simple model modifications, and to re-use model components for transcriptional attenuation in other genes and organisms

Estimating cross-industry cross-country models using benchmark industry characteristics

International industry data permits testing whether the industry-specific impact of cross-country differences in institutions or policies is consistent with economic theory. Empirical implementation requires specifying the industry characteristics that determine impact strength. Most of the literature has been using US proxies of the relevant industry characteristics. We show that using industry characteristics in a benchmark country as a proxy of the relevant industry characteristics can result in an attenuation bias or an amplification bias. We also describe circumstances allowing for an alternative approach that yields consistent estimates. As an application, we reexamine the influential conjecture that financial development facilitates the reallocation of capital from declining to expanding industries.

Optimization Techniques for the Power Beaming Analysis of Microwave Transmissions from a Space-Based Solar Power Satellite

In the 21st century, the development of technologies to produce carbon free power sources remains paramount. In this paper, we study an optimal power transmission strategy from a space-based satellite generation station to Earth using scalar diffraction theory. The resulting model is then solved via a spectral method that guarantees a compactly supposed profile from the transmitting antenna. Finally, the problem is then solved via a more general pseudo-spectral method using control theory

Active Noise Control at low frequencies for Open Air events

Щороку в місті, поблизу житлових районів, проводяться все більше і більше open air заходів та великих концертів. Головною проблемою цього є шумове забруднення прилежних районів. З іншого боку, невід'ємною частиною таких концертів є високий рівень звукового тиску. Створення звукових зон є одним з можливих шляхів вирішення цієї проблеми. У даній роботі ми розглянемо та охарактеризуємо основні способи створення звукових зон: акустичний контраст, pressure matching та комбінований метод. Розглянуто також класичний метод активного контролю шуму на основі алгоритму найменших квадратів. Для всіх методів отримані кінцеві вирази для розрахунку оптимальних комплексних об'ємних швидкостей гучномовців. Описано значення параметрів регуляції цих методів. Для обчислення звукових зон використовуються виміряні або змодельовані передатні характеристики розповсюдження звуку. У цій роботі вивчається вплив навколишнього середовища та атмосферних умов. Моделювання всіх методів проводилося у середовищі MATLAB. Порівняння результатів проводилося за розрахунковими показниками продуктивності та за частотною характеристикою розрахованих оптимальних ваг. Важливість параметрів регулювання показана при моделюванні різних методів. Для досліджуваної системи обраний оптимальний метод. В цілому метою цієї роботи є порівняння та пошук оптимального методу створення звукових зон, який використовується для управління великими зонами в межах open air події; а також зробити оцінку можливого впливу атмосферних умов на точність і надійність цих методів.Every year more and more open-air events and large concerts are held in the city, near residential areas. The main problem of this is noise pollution in nearby areas. On the other hand, an integral part of such concerts is a high SPL. Creating sound zones is one possible solution to this problem. In this paper, we examine and characterize the main methods of creating sound zones: Acoustic Contrast, Pressure Matching and combined method. The classical method of active noise control based on the LMS algorithm is also considered. For all methods, final expressions are derived for calculating the optimal complex volume velocities of the loudspeakers. The meaning of regularization parameters of these methods is described. To calculate the sound zones, measured or modeled propagation transfer functions are used. The effect of the environment and atmospheric conditions is studied in this work and their impact is evaluated. Simulations of all methods were performed at MATLAB. Comparison of the results was carried out on the calculated performance metrics and on the frequency response of the calculated optimal weights. The importance of the regulation parameters has been shown when simulating various methods. The optimal method was chosen for the system under study. In general, this work aimed to make a comparison and search for the optimal method for creating sound zones, which is used to control large zones within an open air event; and also make an assessment of the possible influence of atmospheric conditions on the accuracy and robustness of these methods.Ежегодно в городе, вблизи жилых районов, проводятся все больше и больше open air мероприятий и больших концертов. Главной проблемой этого является шумовое загрязнение прилегающей районов. С другой стороны, неотъемлемой частью таких концертов является высокий уровень звукового давления. Создание звуковых зон является одним из возможных путей решения этой проблемы. В данной работе мы рассмотрим и охарактеризуем основные способы создание звуковых зон: акустический контраст, pressure matching и комбинированный метод. Рассмотрены также классический метод активного контроля шума на основе алгоритма наименьших квадратов. Для всех методов полученные конечные выражения для расчета оптимальных комплексных объемных скоростей громкоговорителей. Описаны значения параметров регуляции этих методов. Для вычисления звуковых зон используются измеренные или смоделированы передаточные характеристики распространения звука. В этой работе изучается влияние окружающей среды и атмосферных условий. Моделирование всех методов проводилось в среде MATLAB. Сравнение результатов проводилось по расчетным показателям производительности и по частотной характеристикой рассчитанных оптимальных весов. Важность параметров регулирования показана при моделировании различных методов. Для исследуемой системы выбран оптимальный метод. В целом целью этой работы является сравнение и поиск оптимального метода создания звуковых зон, который используется для управления большими зонами в пределах open air события; а также сделать оценку возможного воздействию атмосферных условий на точность и надежность этих методов

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.

BackgroundRewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems.ResultsHere, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9.ConclusionsThese data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type

Coherence in Large-Scale Networks: Dimension-Dependent Limitations of Local Feedback

We consider distributed consensus and vehicular formation control problems. Specifically we address the question of whether local feedback is sufficient to maintain coherence in large-scale networks subject to stochastic disturbances. We define macroscopic performance measures which are global quantities that capture the notion of coherence; a notion of global order that quantifies how closely the formation resembles a solid object. We consider how these measures scale asymptotically with network size in the topologies of regular lattices in 1, 2 and higher dimensions, with vehicular platoons corresponding to the 1 dimensional case. A common phenomenon appears where a higher spatial dimension implies a more favorable scaling of coherence measures, with a dimensions of 3 being necessary to achieve coherence in consensus and vehicular formations under certain conditions. In particular, we show that it is impossible to have large coherent one dimensional vehicular platoons with only local feedback. We analyze these effects in terms of the underlying energetic modes of motion, showing that they take the form of large temporal and spatial scales resulting in an accordion-like motion of formations. A conclusion can be drawn that in low spatial dimensions, local feedback is unable to regulate large-scale disturbances, but it can in higher spatial dimensions. This phenomenon is distinct from, and unrelated to string instability issues which are commonly encountered in control problems for automated highways.Comment: To appear in IEEE Trans. Automat. Control; 15 pages, 2 figure

SELF-STEERING BEHAVIOUR OF HIGH-SPEED TRACTOR-SEMITRAILER AND ITS CONTROL

The loss of the stability of heavy highway tractor-semitrailer combinations is the usual cause of several serious traffic accidents. One of the reasons is the different behaviour of the vehicle under changed conditions (e.g. different loading conditions, abrupt side wind gust acting on the vehicle, etc.) which is not expected by the driver or it differs from the usual one. The authors of the paper study the behaviour of the articulated vehicle from the point of view of the steerability and define the conditions of self-steering characteristics of articulated vehicles. In the paper, linear model of the articulated vehicle is used, but the simulations are carried out for more realistic non-linear two-track model including real tyre model. On the basis of the results of the above written examination, the authors deal with the improvement of the lateral stability of the tractor-semi trailer combination using controlled elements in the vehicle chassis, namely the steering of the rear axle of the tractor is examined, however, the practical realization is complicated. Possible solution is proposed instead of the steering of the rear wheels of the tractor based on control of their side slip angles. Results are shown on controlled steering of the wheels on the axle(s) of the trailer. In both mentioned cases, new method of the robust control design is used called Robust LQR (RLQR). Design of the anti-jackknifing device is demonstrated, which means the semi-active control of the switchable damper in the joint