Project description:Magnetic reconnection is a fundamental plasma process, by which magnetic energy is explosively released in the current sheet to energize charged particles and to create bi-directional Alfvénic plasma jets. Numerical simulations predicted that evolution of the reconnecting current sheet is dominated by formation and interaction of magnetic flux ropes, which finally leads to turbulence. Accordingly, most volume of the reconnecting current sheet is occupied by the ropes, and energy dissipation occurs via multiple relevant mechanisms, e.g., the parallel electric field, the rope coalescence and the rope contraction. As an essential element of the reconnecting current sheet, however, how these ropes evolve has been elusive. Here, we present direct evidence of secondary reconnection in the filamentary currents within the ropes. The observations indicate that secondary reconnection can make a significant contribution to energy conversion in the kinetic scale during turbulent reconnection.
Project description:Non-equilibrium kinetics techniques like pressure-jump nuclear magnetic resonance (NMR) are powerful in tracking changes in oligomeric populations and are not limited by relaxation rates for the time scales of exchange that can be probed. However, these techniques are less sensitive to minor, transient populations than are Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments. We integrated non-equilibrium pressure-jump and equilibrium CPMG relaxation dispersion data to fully map the kinetic landscape of melittin tetramerization. While monomeric peptides weakly form dimers (Kd,D/M ≈ 26 mM) whose population never exceeds 1.6% at 288 K, dimers associate tightly to form stable tetrameric species (Kd,T/D ≈ 740 nM). Exchange between the monomer and dimer, along with exchange between the dimer and tetramer, occurs on the millisecond time scale. The NMR approach developed herein can be readily applied to studying the folding and misfolding of a wide range of oligomeric assemblies.
Project description:Molecular association plays a ubiquitous role in biochemistry and is often accompanied by conformational exchange in one or both binding partners. Traditionally, two limiting mechanisms are considered for the association of two molecules. In a conformational selection (CS) mechanism, a ligand preferentially binds to a subset of conformations in its binding partner. In contrast, an induced fit (IF) mechanism describes the ligand-dependent isomerization of the binding partner in which binding occurs prior to conformational exchange. Measurements of the ligand concentration dependence of observed rates of relaxation are commonly used to probe whether CS or IF is taking place. Here we consider a four-state thermodynamic cycle subject to detailed balance and demonstrate the existence of a relatively unexplored class of kinetic signatures where an initial decrease in the observed rate is followed by a subsequent increase under pseudo-first-order conditions. We elucidate regions of rate space necessary to generate a nonmonotonic observed rate and show that, under certain conditions, the position of the minimum of the observed rate correlates with a transition in equilibrium flux between CS and IF pathways. Furthermore, we demonstrate that monotonic trends in the observed rate can occur when both CS and IF mechanisms are taking place, suggesting that caution must be taken not to overinterpret monotonic trends as evidence of the absence of either CS or IF. Lastly, we conclude that a nonmonotonic kinetic signature is uniquely unambiguous in the sense that when this trend is observed, one may conclude that both CS and IF mechanistic paths are utilized.
Project description:A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly varying collective variables, where subsequent analyses are made, such as clustering or estimation of free energy profiles or Markov state models. However, existing "dynamical" dimension reduction methods, such as the time-lagged independent component analysis (TICA), are only valid if the dynamics obeys detailed balance (microscopic reversibility) and typically require long, equilibrated simulation trajectories. Here, we develop a dimension reduction method for non-equilibrium dynamics based on the recently developed Variational Approach for Markov Processes (VAMP) by Wu and Noé. VAMP is illustrated by obtaining a low-dimensional description of a single file ion diffusion model and by identifying long-lived states from molecular dynamics simulations of the KcsA channel protein in an external electrochemical potential. This analysis provides detailed insights into the coupling of conformational dynamics, the configuration of the selectivity filter, and the conductance of the channel. We recommend VAMP as a replacement for the less general TICA method.
Project description:Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
Project description:In the study of non-equilibrium polariton condensates it is usually assumed that the dispersion relation of polaritons is parabolic in nature. We show that considering the true non-parabolic kinetic energy of polaritons leads to significant changes in the behaviour of the condensate due to the curvature of the dispersion relation and the possibility of transfer of energy to high wavenumber components in the condensate spatial profile. We present explicit solutions for plane waves and linear excitations, and identify the differences in the theoretical predictions between the parabolic and non-parabolic mean-field models, showing the possibility of symmetry breaking in the latter. We then consider the evolution of wavepackets and show that self-localisation effects may be observed due to the curvature of the dispersion relation. Finally, we revisit the dynamics of dark soliton trains and show that additional localized density excitations may emerge in the dynamics due to the excitation of high frequency components, mimicking the appearance of near-bright solitary waves over short timescales.
Project description:New Magnetospheric Multiscale (MMS) observations of small-scale (~7 ion inertial length radius) flux transfer events (FTEs) at the dayside magnetopause are reported. The 10 km MMS tetrahedron size enables their structure and properties to be calculated using a variety of multispacecraft techniques, allowing them to be identified as flux ropes, whose flux content is small (~22 kWb). The current density, calculated using plasma and magnetic field measurements independently, is found to be filamentary. Intercomparison of the plasma moments with electric and magnetic field measurements reveals structured non-frozen-in ion behavior. The data are further compared with a particle-in-cell simulation. It is concluded that these small-scale flux ropes, which are not seen to be growing, represent a distinct class of FTE which is generated on the magnetopause by secondary reconnection.
Project description:Forecasting the geomagnetic effects of solar storms, known as coronal mass ejections (CMEs), is currently severely limited by our inability to predict the magnetic field configuration in the CME magnetic core and by observational effects of a single spacecraft trajectory through its 3-D structure. CME magnetic flux ropes can lead to continuous forcing of the energy input to the Earth's magnetosphere by strong and steady southward-pointing magnetic fields. Here we demonstrate in a proof-of-concept way a new approach to predict the southward field B z in a CME flux rope. It combines a novel semiempirical model of CME flux rope magnetic fields (Three-Dimensional Coronal ROpe Ejection) with solar observations and in situ magnetic field data from along the Sun-Earth line. These are provided here by the MESSENGER spacecraft for a CME event on 9-13 July 2013. Three-Dimensional Coronal ROpe Ejection is the first such model that contains the interplanetary propagation and evolution of a 3-D flux rope magnetic field, the observation by a synthetic spacecraft, and the prediction of an index of geomagnetic activity. A counterclockwise rotation of the left-handed erupting CME flux rope in the corona of 30° and a deflection angle of 20° is evident from comparison of solar and coronal observations. The calculated Dst matches reasonably the observed Dst minimum and its time evolution, but the results are highly sensitive to the CME axis orientation. We discuss assumptions and limitations of the method prototype and its potential for real time space weather forecasting and heliospheric data interpretation.
Project description:Non-normalizable states are difficult to interpret in the orthodox quantum formalism but often occur as solutions to physical constraints in quantum gravity. We argue that pilot-wave theory gives a straightforward physical interpretation of non-normalizable quantum states, as the theory requires only a normalized density of configurations to generate statistical predictions. In order to better understand such states, we conduct the first study of non-normalizable solutions of the harmonic oscillator from a pilot-wave perspective. We show that, contrary to intuitions from orthodox quantum mechanics, the non-normalizable eigenstates and their superpositions are bound states in the sense that the velocity field [Formula: see text] at large [Formula: see text]. We argue that defining a physically meaningful equilibrium density for such states requires a new notion of equilibrium, named pilot-wave equilibrium, which is a generalisation of the notion of quantum equilibrium. We define a new H-function [Formula: see text], and prove that a density in pilot-wave equilibrium minimises [Formula: see text], is equivariant, and remains in equilibrium with time. We prove an H-theorem for the coarse-grained [Formula: see text], under assumptions similar to those for relaxation to quantum equilibrium. We give an explanation of the emergence of quantization in pilot-wave theory in terms of instability of non-normalizable states due to perturbations and environmental interactions. Lastly, we discuss applications in quantum field theory and quantum gravity, and implications for pilot-wave theory and quantum foundations in general.
Project description:Uncovering the underlying biophysical principles of emergent collective computational abilities, such as working memory, in neural circuits is one of the most essential concerns in modern neuroscience. Working memory system is often desired to be robust against noises. Such systems can be highly flexible for adapting environmental demands. How neural circuits reconfigure themselves according to the cognitive task requirement remains unclear. Previous studies explored the robustness and the flexibility in working memory by tracing individual dynamical trajectories in a limited time scale, where the accuracy of the results depends on the volume of the collected statistical data. Inspired by thermodynamics and statistical mechanics in physical systems, we developed a non-equilibrium landscape and flux framework for studying the neural network dynamics. Applying this approach to a biophysically based working memory model, we investigated how changes in the recurrent excitation mediated by slow NMDA receptors within a selective population and mutual inhibition mediated by GABAergic interneurons between populations affect the robustness against noises. This is realized through quantifying the underlying non-equilibrium potential landscape topography and the kinetics of state switching. We found that an optimal compromise for a working memory circuit between the robustness and the flexibility can be achieved through the emergence of an intermediate state between the working memory states. An optimal combination of both increased self-excitation and inhibition can enhance the flexibility to external signals without significantly reducing the robustness to the random fluctuations. Furthermore, we found that the enhanced performance in working memory is supported by larger energy consumption. Our approach can facilitate the design of new network structure for cognitive functions with the optimal balance between performance and cost. Our work also provides a new paradigm for exploring the underlying mechanisms of many cognitive functions based on non-equilibrium physics.