Dynamics and stationary configurations of heterogeneous foams.
Ontology highlight
ABSTRACT:
SUBMITTER: Wang D
PROVIDER: S-EPMC6488059 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
Publications
Dynamics and stationary configurations of heterogeneous foams.
Wang Dong D Cherkaev Andrej A Osting Braxton B
PloS one 20190429 4
We consider the variational foam model, where the goal is to minimize the total surface area of a collection of bubbles subject to the constraint that the volume of each bubble is prescribed. We apply sharp interface methods to develop an efficient computational method for this problem. In addition to simulating time dynamics, we also report on stationary states of this flow for ≤ 21 bubbles in two dimensions and ≤ 17 bubbles in three dimensions. For small numbers of bubbles, we recover known an ...[more]
Similar Datasets
Project description:The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force field produces the chain inequivalence with sn-1 as leading chain that is characteristic of glycerolipid packing in fluid bilayers. The exposure and high partial charge of the backbone carbonyls in Berger lipids leads to artifactual binding of Na+ ions reported in the literature. Both force fields predict coupled, near-symmetrical distributions of headgroup dihedral angles, which is compatible with models of interconverting mirror-image conformations used originally to interpret NMR order parameters. The Berger force field produces rotamer populations that correspond to the headgroup conformation found in a phosphatidylcholine lipid bilayer crystal, whereas CHARMM36 rotamer populations are closer to the more relaxed crystal conformations of phosphatidylethanolamine and glycerophosphocholine. CHARMM36 alone predicts the correct relative signs of the time-average headgroup order parameters, and reasonably reproduces the full range of NMR data from the phosphate diester to the choline methyls. There is strong motivation to seek further experimental criteria for verifying predicted conformational distributions in the choline headgroup, including the 31P chemical shift anisotropy and 14N and CD3 NMR quadrupole splittings.
| S-EPMC5937052 | biostudies-literature
Project description:Foams are viscoelastic soft materials with complex mechanical properties. Here, we evaluated the friction dynamics of foams between acrylic plates using a sinusoidal motion friction evaluation system and we found some interesting characteristics under accelerated conditions. On a typical solid surface, a symmetrical friction profile, in which static and kinetic frictions are observed, is obtained under reciprocating nonlinear motion. Meanwhile, significant lubricant effects and velocity-dependent friction profiles without static friction were observed in foams. The friction force in foams increased in proportion to the power of velocity, with a power index of <1. These characteristic and dynamic phenomena in foams were observed in this study. They had been caused by the formation of a thick lubricant film and various dissipative modes including surfactant diffusion, viscous dissipation, and wall slip of bubbles. Moreover, the addition of a thickener increased the friction force and the delay time of friction response and improved the foam durability against normal force and shear. These findings are useful for understanding dynamic phenomena in soft materials.
| S-EPMC9118422 | biostudies-literature
Project description:Chromatin dynamics are mediated by remodeling enzymes and play crucial roles in gene regulation, as established in a paradigmatic model, the Saccharomyces cerevisiae PHO5 promoter. However, effective nucleosome dynamics, that is, trajectories of promoter nucleosome configurations, remain elusive. Here, we infer such dynamics from the integration of published single-molecule data capturing multi-nucleosome configurations for repressed to fully active PHO5 promoter states with other existing histone turnover and new chromatin accessibility data. We devised and systematically investigated a new class of 'regulated on-off-slide' models simulating global and local nucleosome (dis)assembly and sliding. Only seven of 68,145 models agreed well with all data. All seven models involve sliding and the known central role of the N-2 nucleosome, but regulate promoter state transitions by modulating just one assembly rather than disassembly process. This is consistent with but challenges common interpretations of previous observations at the PHO5 promoter and suggests chromatin opening by binding competition.
| S-EPMC8004102 | biostudies-literature
Project description:Microbial exponential growth is expected to occur infrequently in environments that have long periods of nutrient starvation punctuated by short periods of high nutrient flux. These conditions likely impose nongrowth states for microbes. However, nongrowth states are uncharacterized for the majority of environmental bacteria, especially in regard to exometabolite production. We compared exometabolites produced over stationary phase across three environmental bacteria: Burkholderia thailandensis E264 (ATCC 700388), Chromobacterium violaceum ATCC 31532, and Pseudomonas syringae pv. tomato DC3000 (ATCC BAA-871). We grew each strain in monoculture and investigated exometabolite dynamics from mid-exponential to stationary phases. We focused on exometabolites that were released into the medium and accumulated over 45?h, including approximately 20?h of stationary phase. We also analyzed transcripts (transcriptome sequencing [RNA-seq]) to interpret exometabolite output. We found that the majority of exometabolites released were strain specific, with a subset of identified exometabolites involved in both central and secondary metabolism. Transcript analysis supported that exometabolites were released from intact cells, as various transporters had either increased or consistent transcripts through time. Interestingly, we found that succinate was one of the most abundant identifiable exometabolites for all strains and that each strain rerouted their metabolic pathways involved in succinate production during stationary phase. These results show that nongrowth states can be metabolically dynamic and that environmental bacteria can enrich a minimal environment with diverse chemical compounds as a consequence of growth and postgrowth maintenance in stationary phase. This work provides insights into microbial community interactions via exometabolites under conditions of growth cessation or limitation.IMPORTANCE Nongrowth states are common for bacteria that live in environments that are densely populated and predominantly nutrient exhausted, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary-phase exometabolites and RNA transcripts for each of three environmental bacterial strains. We observed that diverse exometabolites were produced and provide evidence that these exometabolites accumulate over time through release by intact cells. Additionally, each bacterial strain had a characteristic exometabolite profile and exhibited dynamics in exometabolite composition. This work affirms that stationary phase is metabolically dynamic, with each strain tested creating a unique chemical signature in the extracellular space and altering metabolism in stationary phase. These findings set the stage for understanding how bacterial populations can support surrounding neighbors in environments with prolonged nutrient exhaustion through exometabolite-mediated interspecies interactions.
| S-EPMC7762789 | biostudies-literature
Project description:The assumption that quantum systems relax to a stationary state in the long-time limit underpins statistical physics and much of our intuitive understanding of scientific phenomena. For isolated systems this follows from the eigenstate thermalization hypothesis. When an environment is present the expectation is that all of phase space is explored, eventually leading to stationarity. Notable exceptions are decoherence-free subspaces that have important implications for quantum technologies and have so far only been studied for systems with a few degrees of freedom. Here we identify simple and generic conditions for dissipation to prevent a quantum many-body system from ever reaching a stationary state. We go beyond dissipative quantum state engineering approaches towards controllable long-time non-stationarity typically associated with macroscopic complex systems. This coherent and oscillatory evolution constitutes a dissipative version of a quantum time crystal. We discuss the possibility of engineering such complex dynamics with fermionic ultracold atoms in optical lattices.
| S-EPMC6465298 | biostudies-literature
Project description:The three-dimensional (3D) organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state-accessibility and amount of gene expression-of the chromatin. Recent advances in chromosome conformation capture experiments provide partial information on the chromatin organization in a cell population, namely the contact count between any segment pairs, but not on the interaction strength that leads to these contact counts. However, given the contact matrix, determining the complete 3D organization of the whole chromatin polymer is an inverse problem. In this work, a novel inverse Brownian dynamics method based on a coarse-grained bead-spring chain model has been proposed to compute the optimal interaction strengths between different segments of chromatin such that the experimentally measured contact count probability constraints are satisfied. Applying this method to the α-globin gene locus in two different cell types, we predict the 3D organizations corresponding to active and repressed states of chromatin at the locus. We show that the average distance between any two segments of the region has a broad distribution and cannot be computed as a simple inverse relation based on the contact probability alone. The results presented for multiple normalization methods suggest that all measurable quantities may crucially depend on the nature of normalization. We argue that by experimentally measuring predicted quantities, one may infer the appropriate form of normalization.
| S-EPMC7203009 | biostudies-literature
Project description:We present numerical simulations of metastable states in heterogeneous neural fields that are connected along heteroclinic orbits. Such trajectories are possible representations of transient neural activity as observed, for example, in the electroencephalogram. Based on previous theoretical findings on learning algorithms for neural fields, we directly construct synaptic weight kernels from Lotka-Volterra neural population dynamics without supervised training approaches. We deliver a MATLAB neural field toolbox validated by two examples of one- and two-dimensional neural fields. We demonstrate trial-to-trial variability and distributed representations in our simulations which might therefore be regarded as a proof-of-concept for more advanced neural field models of metastable dynamics in neurophysiological data.
| S-EPMC4485166 | biostudies-literature
Project description:What will be the growth of the Gross Domestic Product (GDP) or the competitiveness of China, United States, and Vietnam in the next 3, 5 or 10 years? Despite this kind of questions has a large societal impact and an extreme value for economic policy making, providing a scientific basis for economic predictability is still a very challenging problem. Recent results of a new branch--Economic Complexity--have set the basis for a framework to approach such a challenge and to provide new perspectives to cast economic prediction into the conceptual scheme of forecasting the evolution of a dynamical system as in the case of weather dynamics. We argue that a recently introduced non-monetary metrics for country competitiveness (fitness) allows for quantifying the hidden growth potential of countries by the means of the comparison of this measure for intangible assets with monetary figures, such as GDP per capita. This comparison defines the fitness-income plane where we observe that country dynamics presents strongly heterogeneous patterns of evolution. The flow in some zones is found to be laminar while in others a chaotic behavior is instead observed. These two regimes correspond to very different predictability features for the evolution of countries: in the former regime, we find strong predictable pattern while the latter scenario exhibits a very low predictability. In such a framework, regressions, the usual tool used in economics, are no more the appropriate strategy to deal with such a heterogeneous scenario and new concepts, borrowed from dynamical systems theory, are mandatory. We therefore propose a data-driven method--the selective predictability scheme--in which we adopt a strategy similar to the methods of analogues, firstly introduced by Lorenz, to assess future evolution of countries.
| S-EPMC4325004 | biostudies-literature
Project description:BackgroundTemperature and humidity strongly affect the physiology, longevity, fecundity and dispersal behavior of Aedes aegypti, vector of dengue fever. Contrastingly, the statistical associations measured between time series of mosquito abundance and meteorological variables are often weak and contradictory. Here, we investigated the significance of these relationships at different time scales.Methods and findingsA time series of the adult mosquito abundance from a medium-sized city in Brazil, lasting 109 weeks was analyzed. Meteorological variables included temperature, precipitation, wind velocity and humidity. As analytical tools, generalized linear models (GLM) with time lags and interaction terms were used to identify average effects while the wavelet analysis was complementarily used to identify transient associations. The fitted GLM showed that mosquito abundance is significantly affected by the interaction between lagged temperature and humidity, and also by the mosquito abundance a week earlier. Extreme meteorological variables were the best predictors, and the mosquito population tended to increase at values above [Formula: see text] and 54% humidity. The wavelet analysis identified non-stationary local effects of these meteorological variables on abundance throughout the study period, with peaks in the spring-summer period. The wavelet detected weak but significant effects for precipitation and wind velocity.ConclusionOur results support the presence of transient relationships between meteorological variables and mosquito abundance. Such transient association may be explained by the ability of Ae. aegypti to buffer part of its response to climate, for example, by choosing sites with proper microclimate. We also observed enough coupling between the abundance and meteorological variables to develop a model with good predictive power. Extreme values of meteorological variables with time lags, interaction terms and previous mosquito abundance are strong predictors and should be considered when understanding the climate effect on mosquito abundance and population growth.
| S-EPMC3748059 | biostudies-literature
Project description:Evolution is often conceived as changes in the properties of a population over generations. Does this notion exhaust the possible dynamics of evolution? Life is hierarchically organized, and evolution can operate at multiple levels with conflicting tendencies. Using a minimal model of such conflicting multilevel evolution, we demonstrate the possibility of a novel mode of evolution that challenges the above notion: individuals ceaselessly modify their genetically inherited phenotype and fitness along their lines of descent, without involving apparent changes in the properties of the population. The model assumes a population of primitive cells (protocells, for short), each containing a population of replicating catalytic molecules. Protocells are selected towards maximizing the catalytic activity of internal molecules, whereas molecules tend to evolve towards minimizing it in order to maximize their relative fitness within a protocell. These conflicting evolutionary tendencies at different levels and genetic drift drive the lineages of protocells to oscillate endlessly between high and low intracellular catalytic activity, i.e. high and low fitness, along their lines of descent. This oscillation, however, occurs independently in different lineages, so that the population as a whole appears stationary. Therefore, ongoing evolution can be hidden behind an apparently stationary population owing to conflicting multilevel evolution.
| S-EPMC4874703 | biostudies-literature