Non-equilibrium Transport Model Research Articles

Enhancing herbicide adsorption in low-fertility soil using sugarcane biochar: Insights from Imazapic dynamics

Biochar amendment has emerged as a potential solution for preventing, remediating, and mitigating agricultural compound pollution. This groundbreaking technique not only improves crucial soil properties like porosity, water retention capacity, cation exchange capacity, and pH, but also intricately impacts the interaction and retention mechanisms of polluting molecules. In this study, we investigate the dynamic of the herbicide Imazapic when subjected to applying pyrolyzed biochars, specifically at temperatures of 300 and 500 °C, within the context of a low-fertility soil characterized as dystrophic Yellow Ultisol (YUd) in a sugarcane cultivation area in Igarassu-PE, Brazil. The biochars were produced from sugarcane bagasse by pyrolysis process in a muffle furnace. In laboratory conditions, with saturated soil columns under steady-state, analyses of the mechanisms involved in interaction and transport and determining hydrodispersive parameters for Imazapic were performed by the two-site nonequilibrium transport model using the CXTFIT 2.0 program. Samples of YUd soil amended with biochar pyrolyzed at 300 °C presented a negligible interaction with Imazapic. However, adding biochar pyrolyzed at 500 °C (BC500) to the soil samples enhanced the adsorption coefficient and improved the interaction with Imazapic. This research points out that biochar produced from agricultural waste biomass, such as sugarcane bagasse specifically pyrolyzed at 500 °C, offers a potential means to adsorb herbicides, reducing their leaching to deeper layers of the amended soils and the risk of groundwater contamination and potential environmental negative impacts.

Sediment transport and bed erosion during storm surge using a coupled hydrodynamic and morphodynamic model considering wave and current interaction

Storm surge, a major disaster in coastal areas, is generated by tropical cyclones. Strong currents and waves during storm surges often cause sediment transport and beach erosion, significantly damaging the coastal ecosystem. This paper presents a flow-wave-sediment-morphodynamic coupled model to predict morphodynamic changes caused by overwash during storm surges. In the model, the flow field is calculated using the generalized shallow water equations coupled with the Simulating Waves Nearshore (SWAN) model, while sediment transport and bed changes are computed using a non-equilibrium total-load sediment transport model. The model solves the governing equations by employing the explicit finite-volume approach based on a rectangular mesh. The Godunov-type central upwind scheme is adopted to calculate the interface fluxes, thereby solving the complex Riemann problem. A series of numerical experiments considering wave-induced longshore current and short-term bed erosion are conducted to validate the established model and demonstrate its ability to simulate waves, flow fields, and bed changes during storm surge. Specifically, we used the model to simulate the morphological evolution of the Santa Rosa barrier island caused by Hurricane Ivan's storm surge, and the results indicate that the model accurately predicts the real-case erosion process caused by storm surge and overwash during the hurricane. The simulated results clearly explain overwash development, including washover fans, foredune erosion, and back-barrier deposition. It demonstrates that the front dune significantly eroded with the Santa Rosa barrier island coastline retreating by a maximum of about 80 m during the storm surge. More than three breaches with a width of up to 135 m were formed on the sandy barrier due to wave overwash, while the topography at the breach changed significantly.

Signatures of hot carriers and hot phonons in the re-entrant metallic and semiconducting states of Moiré-gapped graphene

Stacking of graphene with hexagonal boron nitride (h-BN) can dramatically modify its bands from their usual linear form, opening a series of narrow minigaps that are separated by wider minibands. While the resulting spectrum offers strong potential for use in functional (opto)electronic devices, a proper understanding of the dynamics of hot carriers in these bands is a prerequisite for such applications. In this work, we therefore apply a strategy of rapid electrical pulsing to drive carriers in graphene/h-BN heterostructures deep into the dissipative limit of strong electron-phonon coupling. By using electrical gating to move the chemical potential through the “Moiré bands”, we demonstrate a cyclical evolution between metallic and semiconducting states. This behavior is captured in a self-consistent model of non-equilibrium transport that considers the competition of electrically driven inter-band tunneling and hot-carrier scattering by strongly non-equilibrium phonons. Overall, our results demonstrate how a treatment of the dynamics of both hot carriers and hot phonons is essential to understanding the properties of functional graphene superlattices.

Theoretical Analysis of a Nonequilibrium Transport Model of Two-Dimensional Nonisothermal Reactive Chromatography Accounting for Bi-Langmuir Isotherm.

The current study investigates a nonequilibrium and nonlinear two-dimensional lumped kinetic transport model of nonisothermal reactive liquid chromatography, considering the Bi-Langmuir adsorption isotherm, heterogeneous reaction rates, radial and axial concentration variations, and the adsorption and reaction enthalpies. The mathematical models of packed bed chromatographic processes are expressed by a highly nonlinear system of coupled partial differential algebraic equations connecting the phenomena of convection, diffusion, and reaction, for mass and energy balance, the differential algebraic equations for mass balance in the solid phase, and the algebraical expressions for the adsorption isotherms and for the reaction rates. The nonlinearity of the reaction term and the adsorption isotherm preclude the derivation of an analytical solution for the model equations. For this reason, a semidiscrete, high-resolution, finite-volume technique is extended and employed in this study to obtain the numerical solution. Several consistency checks are performed to evaluate the model predictions and analyze the precision of the proposed numerical scheme. A number of heterogeneously catalyzed stoichiometric reactions are numerically simulated to examine reactor performance under the influence of temperature and Bi-Langmuir adsorption dynamics, the level of coupling between mass and energy fronts, and to study the effects of various critical parameters. The numerical results obtained are beneficial for optimal predictive control and process optimization during production and the development of methods for systematic design and fault detection of nonisothermal liquid chromatographic reactors, and hence constitute the first step to provide deeper insight into the overall evaluation of integrated reaction and separation processes.

Driven Tracer in the Symmetric Exclusion Process: Linear Response and Beyond.

Tracer dynamics in the symmetric exclusion process (SEP), where hard-core particles diffuse on an infinite one-dimensional lattice, is a paradigmatic model of anomalous diffusion. While the equilibrium situation has received a lot of attention, the case where the tracer is driven by an external force, which provides a minimal model of nonequilibrium transport in confined crowded environments, remains largely unexplored. Indeed, the only available analytical results concern the means of both the position of the tracer and the lattice occupation numbers in its frame of reference and higher-order moments but only in the high-density limit. Here, we provide a general hydrodynamic framework that allows us to determine the first cumulants of the bath-tracer correlations and of the tracer's position in function of the driving force, up to quadratic order (beyond linear response). This result constitutes the first determination of the bias dependence of the variance of a driven tracer in the SEP for an arbitrary density. The framework presented here can be applied, beyond the SEP, to more general configurations of a driven tracer in interaction with obstacles in one dimension.

Highly inhibited transport of dissolved thallium(I) in manganese oxide-coated sand: Chemical condition effects and retention mechanisms

Thallium contamination in water can cause great danger to the environment. In this study, we synthesized manganese oxide-coated sand (MOCS) and investigated the transport and retention behaviors of Tl(I) in MOCS under different conditions. Characterization methods combined with a two-site nonequilibrium transport model were applied to explore the retention mechanisms. The results showed that Tl(I) mobility was strongly inhibited in MOCS media, and the retention capacity calculated from the fitted model was 510.41 mg/g under neutral conditions. The retention process included adsorption and oxidative precipitation by the manganese oxides coated on the sand surface. Cotransport with the same concentration of Mn(II) led to halving Tl(I) retention due to competition for reactive sites. Enhanced Tl(I) retention was observed under alkaline conditions, as increasing pH promoted electronegativity on the media surface. Moreover, the competitive cation Ca2+ significantly weakened Tl(I) retention by occupying adsorption sites. These findings provide new insights into understanding Tl(I) transport behavior in water-saturated porous media and suggest that manganese oxide-coated sand can be a cost-effective filter media for treating Tl-contaminated water.

Study on Tritium and Iodine Species Transport through Porous Granite: A Non-Sorption Effect by Anion Exclusion.

The safety of deep geological repositories is important in the disposal of high-level radioactive waste (HLW). In this study, advection–dispersion experiments were designed to build a transport model through a calibration/validation process, and the transport behavior of tritiated water (HTO) and various iodine species (iodide: I− and iodate: IO3−) was studied on a dynamic compacted granite column. Breakthrough curves (BTCs) were plotted under various flow rates (1–5 mL/min). BTCs showed that the non-sorption effect by anion exclusion was observed only in I− transport because the retardation factor (R) of I− was lower than that of HTO (R = 1). Moreover, equilibrium and nonequilibrium transport models were used and compared to identify the mobile/immobile zones in the compacted granite column. The anion exclusion effect was influenced by the immobile zones in the column. The non-sorption effect by anion exclusion (R < 1) was only observed for I− at 5.0 ± 0.2 mL/min flow rate, and a relatively higher Coulomb’s repulsive force may be caused by the smaller hydration radius of I−(3.31 Å) than that of IO3−(3.74 Å).

Generalized non-equilibrium suspended sediment transport model with hindered settling effect for open channel flows

The present paper formulates a generalized model for non-equilibrium suspended sediment transport through an open channel turbulent flow that contains all the existing models in literature as special cases. The two-dimensional (2D) unsteady model for suspended concentration distribution contains the effect of hindered settling and the bottom boundary condition considers deposition velocity together with equilibrium bottom concentration. OpenFOAM, an open-source Finite Volume (FV) method based framework, has been used for the numerical approximation of the model. The proposed model addresses the non-linearity in the governing equation as well as the non-linearity in boundary conditions. Picard iteration approach has been utilized to ensure the convergence of the numerical solution. With different physical parameters and conditions, concentration profiles of suspended sediment particles have been analysed theoretically and graphically. It greatly extends the domain of the numerical solutions for determining sediment distribution in suspension through an open channel turbulent flow in a non-equilibrium state.

Effects of biochar on transport and retention of phosphorus in porous media: Laboratory test and modeling

Given the complexity of soil components, a detailed understanding of the effects of single factors on phosphorus transport and retention will play a key role in understanding the environmental effects of phosphorus. In this work, quartz sand columns (considering five factors: doping rate, pH, particle size, ionic strength and cation type), combined with a two-site nonequilibrium transport model (TSM), were used to investigate phosphate (P) transport behavior. The results show that changes in doping ratio (0.4%–1.6%) and pH (5–9) have a notable effect on the transport of P, while, particle size of quartz sand hardly impacts the transport. When biochar was added at 1.6%, the surface of biochar increased the P fixation rate by about 37% through direct interaction with phosphate and bridging action with metal ions. As the morphology of P changed under different pH conditions, a part of P was immobilized in the form of precipitation. The immobilization of P was further enhanced with the increase of ionic strength. Compared with the direct interaction of P with biochar in Na+ solution, Ca2+ and Mg2+ solutions are more likely to adsorb P. Meanwhile, the TSM model also fits the transport behavior well. This study provides a perspective for evaluating the environmental behavior of P in the porous media interaction with biochar.

Modeling and visualizing the transport and retention of cationic and oxyanionic metals (Cd and Cr) in saturated soil under various hydrochemical and hydrodynamic conditions

Cationic and oxyanionic metals are widely existed in the aquatic and soil environment with the process of industrialization and they may behave different transport properties in aquifer systems due to the opposite charges. In this study, the comparative transport behaviors of Cd2+ and CrO42− in water-saturated soil columns were investigated under a variety of hydrochemical and hydraulic conditions such as pH, ionic strength (IS), and flow rate. The transport mechanisms of Cd(II) and Cr(VI) were explored by fitting the breakthrough curves with a two-site non-equilibrium transport model. Results indicated that high solution pH inhibited the transport of Cd(II) due to the enhanced electrostatic interaction. In contrast, the migration of Cr(VI) was promoted with the least amount of Cr(VI) (1.23 mg) being retained in soil at high pH, ascribing to the stronger electrostatic repulsion between anions and soil surface. Meanwhile, high pH conditions were not favorable for the participation of reduced iron in the reduction process of Cr(VI), resulting in the least amount of Cr(III) detected (22%). The increase in ionic strength decreased the negativity of the potential at the adsorption plane, which enhanced the transport of cationic Cd(II) and the retardation of anionic Cr(VI). In addition, the increase in flow rate facilitated the transport of Cd(II) and Cr(VI), mainly due to the decreasing contacting with porous media and enhanced dispersion effect. These findings demonstrated that the fate and environmental behavior of metal cations and anions differed with the change of hydrochemical and hydrodynamic properties, which should be considered for the risk assessment and remediation of metal contaminated sites.

Impact of Atmospheric Pressure Fluctuations on Nonequilibrium Transport of Volatile Organic Contaminants in the Vadose Zone: Experimental and Numerical Modeling

AbstractAtmospheric pressure fluctuations can induce subsurface airflow, affecting Volatile Organic Compound (VOC) contaminant migration in the vadose zone. When modeling this process, traditional vapor intrusion models have relied on the assumption of local equilibrium conditions and neglected kinetic mass transfer processes among different phases. In this study, a nonequilibrium multiphase flow and transport model was developed to investigate the impact of atmospheric pressure fluctuations on VOC release from groundwater to the atmosphere. Kinetic mass transfer processes between vapor &amp; liquid phases, and between liquid &amp; solid phases were taken into consideration. A series of soil column experiments with downward/upward pumped gas flow were conducted to validate the model. The experimental results imply the necessity to use nonequilibrium models for quantifying the impact of atmospheric pressure fluctuation. The validated model was used to investigate the role of atmospheric pressure fluctuations for various practical hydrogeologic settings under daily pressure fluctuations. It was found that when the soil organic carbon content is relatively large, the nonequilibrium model more accurately represents VOC migration than a traditional equilibrium model. Therefore, this study suggests the need to apply nonequilibrium vapor intrusion models at sites with high soil organic matter content.

Thermal non-equilibrium natural convection in a trapezoidal porous cavity with heated cylindrical obstacles

Thermal and flow analysis is performed for natural convection in a porous trapezoidal cavity considering a non-equilibrium thermal energy transport model. The model study comprises a partially and fully heated bottom wall while obstacles are placed inside the cavity to examine the thermal behavior. However, governing energy and momentum equations exhibit an unsteady state, but the numerical outcomes are obtained after employing the steady-state condition. The physical problem is expressed in a mathematical model and numerically simulated using the finite difference scheme. The results are presented in graphical sets, while a comparative tabular analysis with existing literature is also reported. It is demonstrated that the parameters γ and H affect thermal non-equilibrium and that the isotherms and streamlines are symmetrically distributed around the obstacles. The local Nusselt number and average Nusselt numbers show a dominant enhancement for both fluids and solid phases assisted by Rayleigh numbers while decreased with an increase in the heating domains. The reported study will be useful in analyzing the natural convection thermal non-equilibrium models in curvilinear geometries.

Development and Verification of Nonequilibrium Reacting Airflow Modeling in ANSYS Fluent

High-speed flow problems of practical interest require a solution of nonequilibrium aerothermochemistry to accurately predict important flow phenomena, including surface heat transfer and stresses. The complex coupling of nonequilibrium effects on the aerothermal load remains a challenging aspect of hypersonic flow modeling. As a majority of these flow problems are in the continuum regime, computational fluid dynamics (CFD) is a useful tool for modeling nonequilibrium flows. However, there are a limited number of CFD solvers with nonequilibrium flow modeling capabilities that are highly scalable on parallel architectures and can handle complex geometries. This work demonstrates that a commercial general purpose CFD solver can be effectively modified to include high-fidelity nonequilibrium aerothermochemistry and transport models. The paper presents modifications of a general purpose CFD solver, ANSYS Fluent, using the user defined functions to model salient aspects of nonequilibrium flow in air with a five-species reacting mixture: , , NO, N, and O. The modifications to the solver include Gupta–Yos high temperature mixing laws and Park’s two-temperature nonequilibrium chemistry models. The developed solver was verified for several benchmark nonequilibrium flow problems and compared with the available experimental data and other nonequilibrium flow simulations. The work establishes future possibilities for coupled aerothermal and electromagnetic simulations in thermochemical nonequilibrium.

Review of non-equilibrium flow and transport models in saturated porous media

This study deals with review of different improvements done in the formulation of the governing equations to simulate accurate solute transport in saturated porous media over the years. The traditional advection-dispersion equation (ADE) model is the simplest lumped model founded on the assumptions of Fick’s law of diffusion. But it typically underestimates the breakthrough concentration in leading and/or tailing region due to non-fickian transport. It is modified into mobile-immobile model (MIM) considering the medium having micropores with stagnant water pockets but allowing solute exchange by diffusion between mobile and immobile zone which is quantified by mass transfer coefficient. Multi-process non-equilibrium (MPNE) model further simulates for a system with both physical and chemical non-equilibrium by assuming instantaneous and rate-limited sorption in advective and non-advective domains. Using the concept of dual permeability, slow fast transport (SFT) model divides the liquid phase in the domain into three zones i.e. fast, slow and immobile. Here chemical interaction between the fluid and soil matrix takes place only in slow and immobile zones. Non-fickian solute transport does not follow Brownian motion rules so a random variable is required to explain it. Hence continuous time random walk (CTRW) model is used where solute transport is characterized by joint probability variable. Special case of CTRW with solute having considerable probability of moving long distances and follow power law gives Fractional advection-dispersion equation (FADE) model. These models varying from relatively simple to more complex formulations and assumptions are discussed here highlighting the merits and demerits of each.

Different transport behaviors and mechanisms of perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS) in saturated porous media

Perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS) in soil aroused increasing concern, however there is little information about their transport in porous media, which is urgently needed to better control their environmental risks. In this study, saturated sand columns (considering the coupled effect of solution cation type and pH) and a two-site nonequilibrium transport model (TSM) were used to investigate the transport behaviors and mechanisms of PFOA and PFOS. Breakthrough data and the TSM parameters showed PFOA had higher mobility than PFOS, and divalent cation could inhibit their transport by increasing the nonequilibrium interactions between them and the sand. pH had little influence on PFOA migration when there was only monovalent cation in the solution since PFOA had limited affinity with the sand, however, polyvalent cation could provide additional adsorption sites for it through cation bridging and enhance the effect of pH. Differently, decreasing pH inhibited the transport of PFOS more significantly, and the effect was stronger than that of changing cation type. That proved mechanisms like hydrogen-bonding which were sensitive to solution pH played an important role in PFOS migration. These results provide important scientific basis to the remediation strategy and the migration prediction model development of PFOA and PFOS.

Bayesian Optimization of Terahertz Quantum Cascade Lasers

We use Bayesian optimization algorithms in combination with a nonequilibrium Green's function transport model to increase the maximum operating temperature of terahertz quantum cascade lasers. This procedure lead to the recent temperature record of 210 K in terahertz quantum cascade lasers, and here we provide even-further-improved structures. The Bayesian optimization algorithm, which takes into account all the available history of the optimization, converges much faster and more securely than the commonly used genetic algorithm. Designs based on two and three wells per period are considered, and using the large amount of data generated, we systematically evaluate the studied schemes in terms of optimal extraction energy and relevance of electron-electron correlations. This analysis shows that the two-well scheme is superior for reaching high operating temperatures, while the three-well scheme is more robust to variations in layer thicknesses. Furthermore, we study the sensitivity to flux-rate fluctuations during growth and simulation-model inaccuracies, showing the period thickness needs to be controlled to within a few percent, which is challenging but achievable with present-day molecular-beam epitaxy. These limits to the growth accuracy can be a guiding principle for experimentalists, along with the suggestion to fabricate devices across the wafer radius so as to find the optimal period thickness.

Numerical simulation of sediment-laden flow on the Yarlung Zangbo River incorporating the climate change

The Yarlung Zangbo River originates from the Qinghai-Tibet Plateau, and runoff consists of the rainfall, melting of snow and glaciers in the upper high-altitude areas. The flow and sediment transport induced by flow in the Yarlung Zangbo River is highly sensitive to changes in climatic conditions. Changes in flow and sediment transport will also have an impact on the downstream wetland ecosystem. In order to study the changes of flow and sediment transport in the Yarlung Zangbo River, Niyang River wetlands under the changes of climatic conditions is used as the considered case. The two-dimensional shallow water equation and the non-equilibrium bedload sediment transport model are proposed in the Yarlung Zangbo-Niyang River. The model is discretized using the unstructured grid finite volume method (FVM). The model includes approximately 355 km length and covers an area of approximately 673 km2. According to the measured time series of flow data at Nuxia hydrology station and the simulated data under the climate change conditions by the climate change model, the water level, flow velocity, erosion and siltation, and sediment gradation change in the river channel are calculated. The calculation results show that by the year 2025, the water level of Niyang River wetlands will increase by 2m under RCP8.5 (Representative Concentration Pathway), and accordingly the total area of the wetlands will decrease by 5%. The results show that climate change has a significant impact on the flow and sediment transport and downstream ecological environment of the Yarlung Zangbo River.

Apparent respiratory quotient observed in headspace of static respirometers underestimates cellular respiratory quotient of pear fruit

Abstract A three-compartment non-equilibrium gas transport model of ‘Conference’ pear fruit under controlled atmosphere (CA) storage was developed. The model fruit tissue consists of cells, in which the concentrations of respiratory gasses can show gradients, and intercellular space, in which gasses are uniformly distributed. Non-equilibrium of gas concentrations in the cell compartment and intercellular space is assumed. A respiration model based on Michaelis-Menten respiration kinetics without inhibition of respiration by CO2 and incorporating down-regulation of the maximal O2 consumption rate in response to O2 was developed. Conversion of CO2 dissolved in the cell compartment to hydrogen carbonate at a constant pH of 5.0 was included. The model was validated based on experimental data of ‘Conference’ pear fruit during a complete depletion experiment starting from 3.58 mol m−3 O2 and 0.00 mol m−3 CO2. Model predictions match experimental observations well. Gas concentrations in the cell compartment were found to be in equilibrium with the gas concentrations in the intercellular space. The model was used to calculate apparent respiration rates and RQ as if measured in the storage headspace. Apparent values were compared to actual values in the fruit cells and it was found that apparent respiration rates and RQ, calculated based on headspace measurements, underestimated the actual respiration rate and respiratory quotient in the fruit cells. Relative differences of 4 %, 41 % and 41 % were found for the apparent O2 consumption rate, CO2 production rate and RQ, respectively. This affects the design of commercial RQ based DCA systems.

Transport of Cd2+ through saturated porous media: Insight into the effects of low-molecular-weight organic acids

Low-molecular-weight organic acids (LMWOAs) are ubiquitous in the aquatic environment and consequently may affect the heavy metal transport in aquifer systems. In this study, the influences of LMWOAs on the transport of Cd2+ under different pH conditions in saturated porous media were evaluated. For this, three LMWOAs such as acetic acid, tartaric acid, and citric acid were employed. A two-site nonequilibrium transport model was applied to simulate the transport data. Under acidic conditions (pH 5.0), the results indicated that LMWOAs inhibited the transport of Cd2+ even at the low concentrations of organic acids (i.e., 0.05 and 0.1 mM). The inhibition effects might be attributed to the complexation role of the sand surface-bound organic acids and also electrostatic interaction. Meanwhile, the inhibition effects of LMWOAs on Cd2+ transport in the following order of citric acid > tartaric acid > acetic acid, which was also in agreement with the decreasing complex stability constants between Cd2+ and LMWOAs. This order may be dependent on their molecular structures (i.e., amount and type of functional groups) and complexing strength. Interestingly, when the LMWOA concentrations 0.5 mM, tartaric acid and citric acid still inhibited Cd2+ transport, while acetic acid slightly enhanced the Cd2+ mobility due to its weaker complexing strength. However, under neutral conditions (pH 7.0), LMWOAs generally enhanced the transport of Cd2+. The transport-enhancement of LMWOAs was ascribed to the formation of stable aqueous non-adsorbing Cd–organic acid complexes. In addition, citric acid could obviously inhibit the transport of Cd2+ under competitive transport conditions (i.e., with competing cations), which is mainly due to different complex affinities of citric acid to Pb2+ and Cd2+. These findings demonstrate that LMWOAs may inhibit or facilitate Cd2+ transport under different environmental conditions. Thus, environmental assessment concerning the transport of heavy metals should consider the roles of organic acids.

Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic

Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here, we integrate quantitative, multidimensional experimental analysis and mathematical modeling to indicate that MeCP2 is a global transcriptional regulator whose binding to DNA creates "slow sites" in gene bodies. We hypothesize that waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shockwaves in nonequilibrium physics transport models. This mechanism differs from conventional gene-regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene-expression patterns are choreographed.