Dynamics of a bouncing dimer

We investigate the dynamics of a dimer bouncing on a vertically oscillated plate. The dimer, composed of two spheres rigidly connected by a light rod, exhibits several modes depending on initial and driving conditions. The first excited mode has a novel horizontal drift in which one end of the dimer stays on the plate during most of the cycle, while the other end bounces in phase with the plate. The speed and direction of the drift depend on the aspect ratio of the dimer. We employ event-driven simulations based on a detailed treatment of frictional interactions between the dimer and the plate in order to elucidate the nature of the transport mechanism in the drift mode.Comment: 4 pages, 5 figures, Movies: http://physics.clarku.edu/~akudrolli/dime

Thermal collapse of a granular gas under gravity

Free cooling of a gas of inelastically colliding hard spheres represents a central paradigm of kinetic theory of granular gases. At zero gravity the temperature of a freely cooling homogeneous granular gas follows a power law in time. How does gravity, which brings inhomogeneity, affect the cooling? We combine molecular dynamics simulations, a numerical solution of hydrodynamic equations and an analytic theory to show that a granular gas cooling under gravity undergoes thermal collapse: it cools down to zero temperature and condenses on the bottom of the container in a finite time.Comment: 4 pages, 12 eps figures, to appear in PR

Partially fluidized shear granular flows: Continuum theory and MD simulations

The continuum theory of partially fluidized shear granular flows is tested and calibrated using two dimensional soft particle molecular dynamics simulations. The theory is based on the relaxational dynamics of the order parameter that describes the transition between static and flowing regimes of granular material. We define the order parameter as a fraction of static contacts among all contacts between particles. We also propose and verify by direct simulations the constitutive relation based on the splitting of the shear stress tensor into a``fluid part'' proportional to the strain rate tensor, and a remaining ``solid part''. The ratio of these two parts is a function of the order parameter. The rheology of the fluid component agrees well with the kinetic theory of granular fluids even in the dense regime. Based on the hysteretic bifurcation diagram for a thin shear granular layer obtained in simulations, we construct the ``free energy'' for the order parameter. The theory calibrated using numerical experiments with the thin granular layer is applied to the surface-driven stationary two dimensional granular flows in a thick granular layer under gravity.Comment: 20 pages, 19 figures, submitted to Phys. Rev.

Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions

During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus

Patterns and Collective Behavior in Granular Media: Theoretical Concepts

Granular materials are ubiquitous in our daily lives. While they have been a subject of intensive engineering research for centuries, in the last decade granular matter attracted significant attention of physicists. Yet despite a major efforts by many groups, the theoretical description of granular systems remains largely a plethora of different, often contradicting concepts and approaches. Authors give an overview of various theoretical models emerged in the physics of granular matter, with the focus on the onset of collective behavior and pattern formation. Their aim is two-fold: to identify general principles common for granular systems and other complex non-equilibrium systems, and to elucidate important distinctions between collective behavior in granular and continuum pattern-forming systems.Comment: Submitted to Reviews of Modern Physics. Full text with figures (2Mb pdf) avaliable at http://mti.msd.anl.gov/AransonTsimringReview/aranson_tsimring.pdf Community responce is appreciated. Comments/suggestions send to [email protected]

In-Silico Patterning of Vascular Mesenchymal Cells in Three Dimensions

Cells organize in complex three-dimensional patterns by interacting with proteins along with the surrounding extracellular matrix. This organization provides the mechanical and chemical cues that ultimately influence a cell's differentiation and function. Here, we computationally investigate the pattern formation process of vascular mesenchymal cells arising from their interaction with Bone Morphogenic Protein-2 (BMP-2) and its inhibitor, Matrix Gla Protein (MGP). Using a first-principles approach, we derive a reaction-diffusion model based on the biochemical interactions of BMP-2, MGP and cells. Simulations of the model exhibit a wide variety of three-dimensional patterns not observed in a two-dimensional analysis. We demonstrate the emergence of three types of patterns: spheres, tubes, and sheets, and show that the patterns can be tuned by modifying parameters in the model such as the degradation rates of proteins and chemotactic coefficient of cells. Our model may be useful for improved engineering of three-dimensional tissue structures as well as for understanding three dimensional microenvironments in developmental processes.National Institutes of Health (U.S.) (GM69811)United States. Dept. of Energy (DOE CSGF fellowship

Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression

The large variability in mRNA and protein levels found from both static and dynamic measurements in single cells has been largely attributed to random periods of transcription, often occurring in bursts. The cell cycle has a pronounced global role in affecting transcriptional and translational output, but how this influences transcriptional statistics from noisy promoters is unknown and generally ignored by current stochastic models. Here we show that variable transcription from the synthetic tetO promoter in S. cerevisiae is dominated by its dependence on the cell cycle. Real-time measurements of fluorescent protein at high expression levels indicate tetO promoters increase transcription rate ~2-fold in S/G2/M similar to constitutive genes. At low expression levels, where tetO promoters are thought to generate infrequent bursts of transcription, we observe random pulses of expression restricted to S/G2/M, which are correlated between homologous promoters present in the same cell. The analysis of static, single-cell mRNA measurements at different points along the cell cycle corroborates these findings. Our results demonstrate that highly variable mRNA distributions in yeast are not solely the result of randomly switching between periods of active and inactive gene expression, but instead largely driven by differences in transcriptional activity between G1 and S/G2/M.GM095733BBBE 103316MIT Startup Fun

Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans

Background: Examples of heterozygote advantage in humans are scarce and limited to protein-coding sequences. Here, we attempt a genome-wide functional inference of advantageous heterozygosity at cis-regulatory regions. Results: The single-nucleotide polymorphisms bearing the signatures of balancing selection are enriched in active cis-regulatory regions of immune cells and epithelial cells, the latter of which provide barrier function and innate immunity. Examples associated with ancient trans-specific balancing selection are also discovered. Allelic imbalance in chromatin accessibility and divergence in transcription factor motif sequences indicate that these balanced polymorphisms cause distinct regulatory variation. However, a majority of these variants show no association with the expression level of the target gene. Instead, single-cell experimental data for gene expression and chromatin accessibility demonstrate that heterozygous sequences can lower cell-to-cell variability in proportion to selection strengths. This negative correlation is more pronounced for highly expressed genes and consistently observed when using different data and methods. Based on mathematical modeling, we hypothesize that extrinsic noise from fluctuations in transcription factor activity may be amplified in homozygotes, whereas it is buffered in heterozygotes. While high expression levels are coupled with intrinsic noise reduction, regulatory heterozygosity can contribute to the suppression of extrinsic noise. Conclusions: This mechanism may confer a selective advantage by increasing cell population homogeneity and thereby enhancing the collective action of the cells, especially of those involved in the defense systems in humansope

Nuclear Power in Taiwan: A Clash of Views

Рукопись поступила в редакцию: 26.03.21. Принята к публикации: 23.07.21.Received: 26.03.21. Accepted: 23.07.21.В статье рассматривается проблема атомной энергетики Тайваня, ставшая особенно актуальной после выборов 2016 г., когда победившая Демократическая прогрессивная партия (ДПП), во главе с президентом Цай Инвэнь, объявила об отказе от использования атомной энергетики к 2025 г. Данный курс, принятый на фоне многотысячных протестов после аварии на Фукусиме-1, к 2020 году обрел немало как сторонников, так и противников, став предметом политической борьбы между ныне правящей ДПП и оппозиционным Гоминьданом. В работе анализируется аргументация сторон, описываются противоборствующие организационные структуры и их связь с политическими силами. Можно выделить 3 основных общих вопроса, по которым идут споры: безопасность, экология и экономика. В сфере безопасности противники атомной энергетики на Тайване используют в качестве примера аварию на Чернобыльской АЭС и Фукусиме-1, говоря об опасности атомной энергетики как таковой, невозможности ее контролировать и обеспечить надлежащий уровень безопасности ядерных объектов. Сторонники же доказывают, что системы безопасности АЭС на Тайване превосходят аналогичные на Фукусиме-1, а сама компания постоянно их модернизирует. В сфере экологии наиболее остро стоит вопрос утилизации низкоактивных ядерных отходов, уделяется большое внимание уменьшению выбросов CO2 в атмосферу. В сфере экономики отмечается недостаток резервных мощностей на Тайване, подчеркивается относительная дороговизна альтернативных экологически чистых источников энергии. Антиядерные активисты говорят о высокой стоимости строительства и эксплуатации АЭС, утверждая, что в долгосрочной перспективе АЭС проигрывает возобновляемым источникам энергии как экономически, так и технологически, и считая атомную энергетику устаревающей отраслью.The article addresses the issue of nuclear energy in Taiwan, which became particularly relevant after the 2016 elections, when the winning Democratic Progressive Party (DPP), led by President Tsai Ing-wen, announced the rejection of the use of nuclear energy by 2025. By 2020, adopted against the backdrop of thousands of protests after the Fukushima-1 accident, this course gained many supporters and opponents and became the subject of a political struggle between the currently ruling DPP and its rival Kuomintang. The paper analyzes the reasoning by the parties, describes the opposing organizational structures and their relations with political forces. Three main general issues are in the focus of debates: security, ecology and economics. In security matters, opponents of nuclear energy in Taiwan use the Chernobyl accident and Fukushima-1 as an example, talking about the danger of nuclear energy per se, the inability to control it and ensure an appropriate level of safety of nuclear facilities. Supporters argue that the safety systems of nuclear power plants in Taiwan are superior to those at Fukushima-1, and the company itself is constantly upgrading them. In the ecology sector, the most acute issue is low-level nuclear waste disposal, and the opponents pay much attention to reducing CO2 emissions into the atmosphere. In the area of economic matters, there is a lack of reserve capacity in Taiwan, and the parties emphasize the relatively high cost of alternative environmentally friendly energy sources. Anti-nuclear activists talk about the high costs of building and operating nuclear power plants, arguing that in the long run, nuclear power plants lose out to renewable energy sources both economically and technologically, considering atomic power as an outdated industry

Stochastic Coherence in an Oscillatory Gene Circuit Model

We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a purely stochastic molecular reaction description of the circuit dynamics. We compare the molecular reaction model behavior with that predicted by a rate equation version of the same system. In addition, we show that commonly used reduced models that ignore fast operator reactions do not capture the full stochastic behavior of the gene circuit. Stochastic coherence occurs under conditions that may be physiologically relevant