Detection of Mixing Dynamics During Pumping of a Flooded Coal Mine

In complex hydrogeological environments the effective management of groundwater quality problems by pump-and-treat operations can be most confidently achieved if the mixing dynamics induced within the aquifer by pumping are well understood. The utility of isotopic environmental tracers (C-, H-, O-, S-stable isotopic analyses and age indicators—14C, 3H) for this purpose is illustrated by the analysis of a pumping test in an abstraction borehole drilled into flooded, abandoned coal mineworkings at Deerplay (Lancashire, UK). Interpretation of the isotope data was undertaken conjunctively with that of major ion hydrochemistry, and interpreted in the context of the particular hydraulic setting of flooded mineworkings to identify the sources and mixing of water qualities in the groundwater system. Initial pumping showed breakdown of initial water quality stratification in the borehole, and gave evidence for distinctive isotopic signatures (d34S(SO4) ~= -1.6‰, d18O(SO4) ~= +15‰) associated with primary oxidation of pyrite in the zone of water table fluctuation—the first time this phenomenon has been successfully characterized by these isotopes in a flooded mine system. The overall aim of the test pumping—to replace an uncontrolled outflow from a mine entrance in an inconvenient location with a pumped discharge on a site where treatment could be provided—was swiftly achieved. Environmental tracing data illustrated the benefits of pumping as little as possible to attain this aim, as higher rates of pumping induced in-mixing of poorer quality waters from more distant old workings, and/or renewed pyrite oxidation in the shallow subsurface.

A tripartite microbial reporter gene system for real-time assays of soil nutrient status

Plant-derived carbon is the substrate which drives the rate of microbial assimilation and turnover of nutrients, in particular N and P, within the rhizosphere. To develop a better understanding of rhizosphere dynamics, a tripartite reporter gene system has been developed. We used three lux-marked Pseudomonas fluorescens strains to report on soil (1) assimilable carbon, (2) N-status, and (3) P-status. In vivo studies using soil water, spiked with C, N and P to simulate rhizosphere conditions, showed that the tripartite reporter system can provide real-time assessment of carbon and nutrient status. Good quantitative agreement for bioluminescence output between reference material and soil water samples was found for the C and P reporters. With regard to soil nitrate, the minimum bioavailable concentration was found to be greater than that analytically detectable in soil water. This is the first time that bioavailable soil C, N and P have been quantified using a tripartite reporter gene system.

Current-induced atomic dynamics, instabilities, and Raman signals: Quasiclassical Langevin equation approach

We derive and employ a semiclassical Langevin equation obtained from path integrals to describe the ionic dynamics of a molecular junction in the presence of electrical current. The electronic environment serves as an effective nonequilibrium bath. The bath results in random forces describing Joule heating, current-induced forces including the nonconservative wind force, dissipative frictional forces, and an effective Lorentz-type force due to the Berry phase of the nonequilibrium electrons. Using a generic two-level molecular model, we highlight the importance of both current-induced forces and Joule heating for the stability of the system. We compare the impact of the different forces, and the wide-band approximation for the electronic structure on our result. We examine the current-induced instabilities (excitation of runaway "waterwheel" modes) and investigate the signature of these in the Raman signals.

Fragility of the spin-glass-like collective state to a magnetic field in an interacting Fe-C nanoparticle system

The effect of applied magnetic fields on the collective nonequilibrium dynamics of a strongly interacting Fe-C nanoparticle system has been investigated. It is experimentally shown that the magnetic aging diminishes to finally disappear for fields of moderate strength. The field needed to remove the observable aging behavior increases with decreasing temperature. The same qualitative behavior is observed in an amorphous metallic spin glass (Fe0.15Ni0.85)(75)P16B6Al3.

Emergent thermodynamics in a quenched quantum many-body system

We study the statistics of the work done, the fluctuation relations and the irreversible entropy production in a quantum many-body system subject to the sudden quench of a control parameter. By treating the quench as a thermodynamic transformation we show that the emergence of irreversibility in the nonequilibrium dynamics of closed many-body quantum systems can be accurately characterized. We demonstrate our ideas by considering a transverse quantum Ising model that is taken out of equilibrium by the instantaneous switching of the transverse field.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Nonlinear dynamics of multidimensional electrostatic excitations in nonthermal plasmas

Electrostatic solitary waves in plasmas are the focus of many current studies of localized electrostatic disturbances in both laboratory and astrophysical plasmas. Motivated by recent experimental observations, in which electrostatic solitary structures were detected in laser-plasma experiments, we have undertaken an investigation of the nonlinear dynamics of plasma evolving in two dimensions, in the presence of excess superthermal background electrons. We investigate the effect of a magnetic field on weakly nonlinear ion-acoustic waves. Deviation from the Maxwellian distribution is effectively modelled by the kappa model. A linear dispersion relation is derived, and a decrease in frequency and phase speed in both parallel and perpendicular modes can be seen, which is due to excess superthermal electrons, and which is stronger in the upper mode, and hardly noticeable in the lower (acoustic) mode. We show that ion-acoustic solitary waves can be generated during the nonlinear evolution of a plasma fluid, and their nonlinear propagation is governed by a Zakharov-Kuznetsov (ZK) type equation. A multiple scales perturbation technique is used to derive the ZK equation. Shock excitations can be produced if we allow for dissipation in the model, resulting in a Zakharov-Kuznetsov Burgers type equation. Different types of shock solutions and solitary waves are obtained, depending on the relation between the system parameters, and the effect of these on electrostatic shock structures is investigated numerically. A parametric investigation is conducted into the role of plasma nonthermality and magnetic field strength. © 2013 IOP Publishing Ltd.

Tuning non-Markovianity by spin-dynamics control

We study the interplay between forgetful and memory-keeping evolution enforced on a two-level system by a multi-spin environment whose elements are coupled to local bosonic baths. Contrarily to the expectation that any non-Markovian effect would be buried by the forgetful mechanism induced by the spin-bath coupling, one can actually induce a full Markovian-to-non-Markovian transition of the two-level system's dynamics, controllable by parameters such as the mismatch between the energy of the two-level system and of the spin environment. For a symmetric coupling, the amount of non-Markovianity surprisingly grows with the number of decoherence channels. DOI: 10.1103/PhysRevA.87.022317

Linear Optics Simulation of Quantum Non-Markovian Dynamics

The simulation of open quantum dynamics has recently allowed the direct investigation of the features of system-environment interaction and of their consequences on the evolution of a quantum system. Such interaction threatens the quantum properties of the system, spoiling them and causing the phenomenon of decoherence. Sometimes however a coherent exchange of information takes place between system and environment, memory effects arise and the dynamics of the system becomes non-Markovian. Here we report the experimental realisation of a non-Markovian process where system and environment are coupled through a simulated transverse Ising model. By engineering the evolution in a photonic quantum simulator, we demonstrate the role played by system-environment correlations in the emergence of memory effects.

PTEN Phosphatase-Independent Maintenance of Glandular Morphology in a Predictive Colorectal Cancer Model System

Organotypic models may provide mechanistic insight into colorectal cancer (CRC) morphology. Three-dimensional (3D) colorectal gland formation is regulated by phosphatase and tensin homologue deleted on chromosome 10 (PTEN) coupling of cell division cycle 42 (cdc42) to atypical protein kinase C (aPKC). This study investigated PTEN phosphatase-dependent and phosphatase-independent morphogenic functions in 3D models and assessed translational relevance in human studies. Isogenic PTEN-expressing or PTEN-deficient 3D colorectal cultures were used. In translational studies, apical aPKC activity readout was assessed against apical membrane (AM) orientation and gland morphology in 3D models and human CRC. We found that catalytically active or inactive PTEN constructs containing an intact C2 domain enhanced cdc42 activity, whereas mutants of the C2 domain calcium binding region 3 membrane-binding loop (M-CBR3) were ineffective. The isolated PTEN C2 domain (C2) accumulated in membrane fractions, but C2 M-CBR3 remained in cytosol. Transfection of C2 but not C2 M-CBR3 rescued defective AM orientation and 3D morphogenesis of PTEN-deficient Caco-2 cultures. The signal intensity of apical phospho-aPKC correlated with that of Na/H exchanger regulatory factor-1 (NHERF-1) in the 3D model. Apical NHERF-1 intensity thus provided readout of apical aPKC activity and associated with glandular morphology in the model system and human colon. Low apical NHERF-1 intensity in CRC associated with disruption of glandular architecture, high cancer grade, and metastatic dissemination. We conclude that the membrane-binding function of the catalytically inert PTEN C2 domain influences cdc42/aPKC-dependent AM dynamics and gland formation in a highly relevant 3D CRC morphogenesis model system.

Geographies of Communality, Colonialism, and Capitalism: Ecology and the World-System

Drawing upon recent reworkings of world systems theory and Marx’s concept of metabolic rift, this paper attempts to ground early nineteenth-century Ireland more clearly within these metanarratives, which take the historical-ecological dynamics of the development of capitalism as their point of departure. In order to unravel the socio-spatial complexities of Irish agricultural production throughout this time, attention must be given to the prevalence of customary legal tenure, institutions of communal governance, and their interaction with the colonial apparatus, as an essential feature of Ireland’s historical geography often neglected by famine scholars. This spatially differentiated legacy of communality, embedded within a country-wide system of colonial rent, and burgeoning capitalist system of global trade, gave rise to profound regional differentiations and ecological contradictions, which became central to the distribution of distress during the Great Famine (1845-1852). Contrary to accounts which depict it as a case of discrete transition from feudalism to capitalism, Ireland’s pre-famine ecology must be understood through an analysis which emphasises these socio-spatial complexities. Consequently, this structure must be conceptualised as one in which communality, colonialism, and capitalism interact dynamically, and in varying stages of development and devolution, according to space and time.

Malthusian Dynamics in a Diverging Europe: Northern Italy, 1650–1881

Recent empirical research questions the validity of using Malthusian theory in preindustrial England. Using real wage and vital rate data for the years 1650–1881, I provide empirical estimates for a different region: Northern Italy. The empirical methodology is theoretically underpinned by a simple Malthusian model, in which population, real wages, and vital rates are determined endogenously. My findings strongly support the existence of a Malthusian economy wherein population growth decreased living standards, which in turn influenced vital rates. However, these results also demonstrate how the system is best characterized as one of weak homeostasis. Furthermore, there is no evidence of Boserupian effects given that increases in population failed to spur any sustained technological progress.

A drive-by inspection system via vehicle moving force identification

This paper presents a novel method to carry out monitoring of transport infrastructure such as pavements and bridges through the analysis of vehicle accelerations. An algorithm is developed for the identification of dynamic vehicle-bridge interaction forces using the vehicle response. Moving force identification theory is applied to a vehicle model in order to identify these dynamic forces between the vehicle and the road and/or bridge. A coupled half-car vehicle-bridge interaction model is used in theoretical simulations to test the effectiveness of the approach in identifying the forces. The potential of the method to identify the global bending stiffness of the bridge and to predict the pavement roughness is presented. The method is tested for a range of bridge spans using theoretical simulations and the influences of road roughness and signal noise on the accuracy of the results are investigated.

Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e. g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

Robust nonadiabatic molecular dynamics for metals and insulators

We present a new formulation of the correlated electron-ion dynamics (CEID) scheme, which systematically improves Ehrenfest dynamics by including quantum fluctuations around the mean-field atomic trajectories. We show that the method can simulate models of nonadiabatic electronic transitions and test it against exact integration of the time-dependent Schrodinger equation. Unlike previous formulations of CEID, the accuracy of this scheme depends on a single tunable parameter which sets the level of atomic fluctuations included. The convergence to the exact dynamics by increasing the tunable parameter is demonstrated for a model two level system. This algorithm provides a smooth description of the nonadiabatic electronic transitions which satisfies the kinematic constraints (energy and momentum conservation) and preserves quantum coherence. The applicability of this algorithm to more complex atomic systems is discussed.