Broad Time Scale Research Articles

Estimation of Evolutionary Rates of Mitochondrial DNA in Two Japanese Wood Mouse Species Based on Calibrations with Quaternary Environmental Changes.

Reliable estimates of evolutionary rates of mitochondrial DNA might allow us to build realistic evolutionary scenarios covering broad time scales based on phylogenetic inferences. In the present study, we sought to obtain estimates of evolutionary rates in murine rodents using calibrations against historical biogeographic events. We first assumed that land-bridge-like structures that appeared intermittently at glacial maxima with 100,000-year intervals shaped the divergence patterns of cytochrome b (Cytb) sequences (1140 bp) of the larger Japanese wood mouse Apodemus speciosus. The comparison of sequences from peripheral remote islands that are separated from one another by deep straits allowed us to estimate mitochondrial DNA evolutionary rates (substitutions/site/million years) to be 0.027 to 0.036, with presumed calibrations from 140,000, 250,000, 350,000, and 440,000 years ago. Second, we addressed rapid expansion events inferred from analyses of the Cytb sequences of the lesser Japanese wood mouse A. argenteus. We detected five expansion signals in the dataset and established three categories based on the expansion parameter tau values: 3.9, 5.6-5.7, and 7.8-8.1. Considering that the climate became warmer 15,000, 53,000, and 115,000 years ago after preceding periods of rapid cooling, we calculated evolutionary rates to be 0.114, 0.047, and 0.031, respectively. This preliminary concept of the evolutionary rates on a time scale from 15,000 to 440,000 years ago for the wood mouse should be refined and tested in other species of murine rodents, including mice and rats.

Genome evolution: Shellfish genes

Three new bivalve genomes are resources for comparative genomics over broad timescales, providing a glimpse into the evolution of understudied marine animals and their adaptations to extreme environments.

Identifying critical habitat for freshwater turtles: integrating long-term monitoring tools to enhance conservation and management

The effective conservation and management of threatened species requires comprehensive knowledge about resource utilisation. Here we integrated tissue stable isotope analysis and biotelemetry to identify the predominant dietary resources of two sympatric species of freshwater turtle, and locate where those items were acquired. We deployed an array of underwater acoustic telemetry receivers to autonomously, simultaneously, and continuously, monitor the movements of the threatened Elseya albagula and Elusor macrurus, over a 12-month period. Stable isotope (SI) values (δ13C and δ15N) were measured within the carapace of each species, and compared with SI values within potential food items. The integration of movement information and carapace SI data revealed that whilst these species had overlapping home ranges, there was less than 5% probability of inter-species dietary niche overlap. E. macrurus acquired food items consisting of bivalves, gastropods and aquatic insects within rocky riffles whilst E. albagula fed on filamentous algae and crustaceans foraged from the muddy and vegetated shallow margins of deep water pools. Our findings differ from stomach content analysis and mark-recapture studies, which reported these species to have similar habitat and resource requirements. We argue that the observed disparity is because our methods provided a weighted measure of an individual’s dietary preference and habitat utilisation over a broad time-scale, whilst stomach content analysis and mark-recapture studies offer only a single observation of an individual’s dietary preference. The research demonstrates the utility of integrating passive acoustic telemetry and carapace stable isotope analysis for identifying critical habitat for freshwater turtles.

Multiscale Modeling of Complex Formation and CD80 Depletion during Immune Synapse Development

The mechanisms that discriminate self- and foreign antigen before T cell activation are unresolved. As part of the immune system’s adaptive response to specific infections or neoplasms, antigen-presenting cells (APC) and effector T cells form transcellular molecular complexes. CTLA4 expression on regulatory or effector T cells reduces T cell activation. The CTLA4 transendocytosis hypothesis proposes that CTLA4 depletes CD80 and CD86 proteins from the APC membrane, rendering the APC incapable of activating T cells. We developed a multiscale spatiotemporal model for the interaction of a T cell and APC. Formation of the immune complex between T cell and APC starts with formation of the transmembrane complexes between the major histocompatibility complex and the T cell receptor (Signal 1) and between CD80 or CD86 and CD28 (Signal 2) at the opposing membrane surfaces of the interacting cells. By 0.01 s after contact simulation, an increasing concentration gradient of the free membrane proteins develops between the opposing surfaces and spherical parts of each cell’s membrane, reaching a maximum at ∼30 s. Over several hours, diffusion across the gradient equalizes the free protein concentrations. During this phase, CTLA4 surface expression and its complexation with CD80/CD86 cause internalization and degradation of CD80/CD86. The simulation results show reasonable agreement with reported experimental data and indicate that key molecular processes take place over a very broad timescale, covering five orders of magnitude. Besides the fast complexation reactions, diffusion-limited processes, especially lateral diffusion in cell membranes and geometrical constraints, considerably slow down evolution of the synapse. Our results are consistent with the CTLA4 transendocytosis hypothesis and suggest the importance of lateral diffusion of surface proteins in contributing to a gradual increase in Signal 1 and Signal 2.

The true tempo of evolutionary radiation and decline revealed on the Hawaiian archipelago.

Establishing the relationship between rates of change in species richness and biotic and abiotic environmental change is a major goal of evolutionary biology. Although exquisite fossil and geological records provide insight in rare cases, most groups lack high-quality fossil records. Consequently, biologists typically rely on molecular phylogenies to study the diversity dynamics of clades, usually by correlating changes in diversification rate with environmental or trait shifts. However, inferences drawn from molecular phylogenies can be limited owing to the challenge of accounting for extinct species, making it difficult to accurately determine the underlying diversity dynamics that produce them. Here, using a geologically informed model of the relationship between changing island area and species richness for the Hawaiian archipelago, we infer the rates of species richness change for 14 endemic groups over their entire evolutionary histories without the need for fossil data, or molecular phylogenies. We find that these endemic clades underwent evolutionary radiations characterized by initially increasing rates of species accumulation, followed by slow-downs. In fact, for most groups on most islands, their time of evolutionary expansion has long past, and they are now undergoing previously unrecognized long-term evolutionary decline. Our results show how landscape dynamism can drive evolutionary dynamics over broad timescales, including driving species loss that is not readily detected using molecular phylogenies, or without a rich fossil record. We anticipate that examination of other clades where the relationship between environmental change and species richness change can be quantified will reveal that many other living groups have also experienced similarly complex evolutionary trajectories, including long-term and ongoing evolutionary decline.

Experimental corroboration of the theory of chronoamperometry at high roughness electrode for reversible charge transfer

An asymptotic theory for the single potential step chronoamperometry is validated for ferrocene in 1-Butyl-3-methylimidazolium tetrafluoroborate ([bmim] [BF4]) room temperature ionic liquid (RTIL) at nano-particles deposited mesoporous gold wires. The elegance of asymptotic equation arises due to minimal need of (only two) morphological surface characteristics, viz. roughness factor (R*) and width of roughness of mesoporous layer (h). It also accounts for the contribution from unequal diffusion coefficient of electro-active species and uncompensated solution resistance. Theory is also corrected for electric double layer contribution. Mesoporous electrodes are created (with R* >10) over mechanically roughened gold wires by depositing electrochemically synthesized gold nano-particles. Morphological parameters, R* and h, are determined using cyclic voltammetry (CV) and scanning electron microscopy (SEM), viz. CV and SEM method (see S.Dhillon and R.Kant, 2013). Asymptotic equation shows quantitative agreement with the experimental data over a broad time scale (between 0.2ms and 100s). Finally, this asymptotic equation can be used for the extraction of statistical roughness along with usual electrochemical quantities.

O-Myo! An O-Shaped Myosin Gliding Assay for Characterizing Long-Term Actin-Myosin Behaviors

Nature has evolved molecular machines that are critical in cellular processes occurring over broad timescales, ranging from seconds to days. As an example, myosin in the human heart take ∼10 steps per second and are collectively responsible for ∼10⁵ heart beats per day. Analogous to the engineering of macro-scale machines, the evolution of molecular machines is likely to be constrained by the requirements of high short-term performance and a long lifetime. Here, we developed a circular gliding assay (O-Myo) that utilizes engineered micron-scale DNA nanotube rings with defined geometrical arrangements of dimeric myosin VI, a model system for myosin motor.

Thermo-mechanical properties of white oil and acrylic artist paints

Abstract The mechanical properties of artist paints are affected by strain rate and temperature to varying degrees depending largely on the type of binder used in their formulation. Existing tensile data for these materials are typically given for a single strain rate, and do not fully characterise their time response. In order to expand on past research, the effect of strain rate on the modulus and failure properties of acrylic latex paints was recently reported using a series of uniaxial tensile tests to failure under different conditions of crosshead speed and temperature. The present investigation offers a comparison of the results from acrylics with new findings for traditional and modified oil media. To efficiently summarise mechanical data, the time-temperature superposition (TTS) principle was used to construct master-curves of secant modulus and failure strain as a function of strain rate. Comparisons are given between films tested within this study, and also with individual data points for oil paints obtained from literature. The findings highlight the differences between artist paint media over a broad time-scale, and practical temperature range. A simple estimate of dynamic failure criteria is also presented using a first order approximation.

Communication: Polymer entanglement dynamics: Role of attractive interactions.

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes to the late time diffusive regime, highly coarse grained models with purely repulsive interactions between monomers are widely used since they are computationally the most efficient. Here using large scale molecular dynamics simulations, the effect of including the attractive interaction between monomers on the dynamics of entangled polymer melts is explored for the first time over a wide temperature range. Attractive interactions have little effect on the local packing for all temperatures T and on the chain mobility for T higher than about twice the glass transition Tg. These results, across a broad range of molecular weight, show that to study the dynamics of entangled polymer melts, the interactions can be treated as pure repulsive, confirming a posteriori the validity of previous studies and opening the way to new large scale numerical simulations.

Dynamics in entangled polyethylene melts

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion at the atomic length scale and motion of the entire macromolecule. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using linear polyethylene as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion with λ methylene groups per CG bead (denoted CGλ) with λ = 2,3,4 and 6 from a fully-atomistic polyethylene melt simulation. By rescaling time in the CG models by a factor α, the chain mobility for the atomistic and CG models match. We show that independent of the degree of coarse graining, all measured static and dynamic properties are essentially the same once the dynamic scaling factor α and a non-crossing constraint for the CG6 model are included. The speedup of the CG4 model is about 3 times that of the CG3 model and is comparable to that of the CG6 model. Using these CG models we were able to reach times of over 500 μs, allowing us to measure a number of quantities, including the stress relaxation function, plateau modulus and shear viscosity, and compare directly to experiment.

Engineering Circular Gliding of Actin Filaments Along Myosin-Patterned DNA Nanotube Rings To Study Long-Term Actin-Myosin Behaviors.

Nature has evolved molecular motors that are critical in cellular processes occurring over broad time scales, ranging from seconds to years. Despite the importance of the long-term behavior of molecular machines, topics such as enzymatic lifetime are underexplored due to the lack of a suitable approach for monitoring motor activity over long time periods. Here, we developed an "O"-shaped Myosin Empowered Gliding Assay (OMEGA) that utilizes engineered micron-scale DNA nanotube rings with precise arrangements of myosin VI to trap gliding actin filaments. This circular gliding assay platform allows the same individual actin filament to glide over the same myosin ensemble (50-1000 motors per ring) multiple times. First, we systematically characterized the formation of DNA nanotubes rings with 4, 6, 8, and 10 helix circumferences. Individual actin filaments glide along the nanotube rings with high processivity for up to 12.8 revolutions or 11 min in run time. We then show actin gliding speed is robust to variation in motor number and independent of ring curvature within our sample space (ring diameter of 0.5-4 μm). As a model application of OMEGA, we then analyze motor-based mechanical influence on "stop-and-go" gliding behavior of actin filaments, revealing that the stop-to-go transition probability is dependent on motor flexibility. Our circular gliding assay may provide a closed-loop platform for monitoring long-term behavior of broad classes of molecular motors and enable characterization of motor robustness and long time scale nanomechanical processes.

Quantitative Analysis of Time-Domain Supported Electrochemical Impedance Spectroscopy Data of Li-Ion Batteries: Reliable Activation Energy Determination at Low Frequencies

Physico-chemical processes in batteries are taking place on a broad time scale from fractions of seconds to the order of days [1]. Thus, for an accurate characterization of transport and mobility processes in batteries using electrochemical impedance spectroscopy (EIS), a large frequency range of up to ten decades must be covered. This implies measurement durations on the order of days for low frequency measurements, yielding the risk of distorting electrochemical instabilities in the battery and a considerable change of its state of charge (SOC) due to the probing ac current excitation. It is shown that the SOC change is frequency dependent and with 10-15% of the nominal battery capacity for the sub-millihertz range hardly a small perturbation. Nevertheless, these obstacles can be mitigated by the time domain measurement (TDM) technique [2-4]. TDM is limited to impedance measurements at low frequencies, with a small and frequency-independent SOC change. The combination of TDM and EIS, called time-domain supported electrochemical impedance spectroscopy (TD-EIS), opens up the possibility for a time-efficient implementation of impedance spectroscopy over a large frequency range down to microhertz frequencies [5]. In this work, TD-EIS at varying temperatures in combination with data fitting using an electrical equivalent circuit battery model, is used for the high-accuracy quantification of low-frequency mobility parameters in lithium-ion batteries. It is experimentally demonstrated, for the first time, that the phase of the impedance measurements converges in the sub-millihertz range, which permits a reliable quantification of diffusion kinetics. Moreover, it is shown that with TD-EIS time savings of up to 80% compared to the standard EIS measurement are feasible. From the electrical equivalent circuit battery model fit, an accurate estimate of charge transfer resistance and, in particular, also solid-state diffusion rate are obtained. Both processes follow an Arrhenius law, allowing the determination of activation energies with small variance. The results for the charge transfer process and for the solid-state diffusion process are within the range of literature values measured for similar systems. This work has been published in JECS [6].

Determination of intrinsic ferroelectric polarization in lossy improper ferroelectric systems

We measured the intrinsic hysteretic polarization in lossy improper and nanoferroelectric systems where the nonhysteretic polarization and leakage are large and the relaxation takes place over a broader time scale. We used different measurement protocols such as standard single triangular voltage pulse, a pulse train of Positive Up Negative Down, and an even more complicated pulse train of fourteen voltage pulses and compared the results obtained. We show that a protocol which sends a train of fourteen pulses is more appropriate for extracting relaxed (i.e., time scale independent) and intrinsic remanent polarization for these samples. We also point out that it is possible to select and design an appropriate measurement protocol depending on the magnitude of polarization and leakage of the system.

Human Effects in Holocene Fire Dynamics of Central Western Patagonia (~44° S, Chile)

The forest-steppe ecotone of the eastern slope of the Andes in Central Western Patagonia (43°40'-49°15' S, Chile, South America) provides a unique area for assessing long and short term dynamics between humans and past environments. Central Western Patagonian was a demographically marginal zone inhabited intermittently and with low intensity by hunter-gatherers during the Holocene. This paper adopts a novel approach in order to assess the relationship between trends in the archaeological, pollen and charcoal records. The recognition of temporal and spatial scales in both archaeology and paleoecology is crucial for defining roles in paleofire records. The main goal of the paper is to assess the role of climate and human beings as potential ignitors of wildfires by acknowledging the scales in which they operate and the different roles either one played in paleofire trends. We investigated a case study in the Cisnes River Valley where the frequencies and magnitudes of fire episodes – reconstructed from macro-charcoal particles from the Lake Shaman intermoraine sequence – can be attributed to human action, while acknowledging the driving role of climate over broader time scales. The Lake Shaman charcoal record spanning the last 19000 cal years is compared to the archaeological record starting at 11500 cal years BP. After comparing paleofires, reconstructed from the charcoal record, with peaks and troughs in the radiocarbon record and archaeological evidence at local and site scales, we argue that this approach provides insights for assessing the timing and magnitude of human effects on the environment. We examine collation and correlation scenarios for comparative trends between the archaeological, pollen and charcoal records. The correlation of occupational events at the El Chueco 1 archaeological site and other sites along the Cisnes River Valley with the results obtained at Lake Shaman is suggestive of a combination of human agency and climate drivers in the occurrence of fires during most of the Holocene.

Entropy Production of Nanosystems with Time Scale Separation

Energy flows in biomolecular motors and machines are vital to their function. Yet experimental observations are often limited to a small subset of variables that participate in energy transport and dissipation. Here we show, through a solvable Langevin model, that the seemingly hidden entropy production is measurable through the violation spectrum of the fluctuation-response relation of a slow observable. For general Markov systems with time scale separation, we prove that the violation spectrum exhibits a characteristic plateau in the intermediate frequency region. Despite its vanishing height, the plateau can account for energy dissipation over a broad time scale. Our findings suggest a general possibility to probe hidden entropy production in nanosystems without direct observation of fast variables.

Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies.

For assistance in the design of the next generation of nanomaterials that are functional and have minimal health and safety concerns, it is imperative to establish causality, rather than correlations, in how properties of nanomaterials determine biological and environmental outcomes. Due to the vast design space available and the complexity of nano/bio interfaces, theoretical and computational studies are expected to play a major role in this context. In this minireview, we highlight opportunities and pressing challenges for theoretical and computational chemistry approaches to explore the relevant physicochemical processes that span broad length and time scales. We focus discussions on a bottom-up framework that relies on the determination of correct intermolecular forces, accurate molecular dynamics, and coarse-graining procedures to systematically bridge the scales, although top-down approaches are also effective at providing insights for many problems such as the effects of nanoparticles on biological membranes.

Ultra-slow Li ion jump diffusion in Li2SnO3 studied by two-time 7Li spin-alignment echo NMR and 7Li NMR relaxometry

A deeper understanding of atomic-scale Li+ hopping in solid Li ion conductors requires the study of ion dynamics over a broad time scale and length scale. Here, we report a complementary study, applying 7Li spin-lattice relaxation (SLR) nuclear magnetic resonance (NMR) techniques together with spin-alignment echo (SAE) NMR to study slow Li+ self-diffusion in monoclinic Li2SnO3. The stannate serves as a model substance to quantify both local barriers of the elementary steps of ion diffusion as well as long-range ion transport. From spin-alignment echoes, if recorded at short preparation time of 20μs, activation energies (0.46eV) and Li jump rates were deduced. The same diffusion process is seen via SLR NMR (0.45eV) performed in the rotating frame of reference at a locking frequency of 20kHz. By comparing jump rates extracted from SAE NMR with those recently measured by high-resolution 1D 6Li exchange NMR we attribute the SLR and SAE NMR response to the Li(1,2)–Li(3) exchange process (5s−1) taking place perpendicular to the ab-plane in Li2SnO3. SAE NMR measurements, dedicated to elaborate the influence of dipolar correlations on echo formation at tp>20μs, reveal a strong dependence of the SAE rate constant on preparation time at low temperatures. This finding might points towards heterogeneous dynamics including localized jump processes which are likely to be caused by a slightly disordered structure of the oxide.

Modeling and fundamental aspects of structural relaxation in high-solid hydrocolloid systems

The structural relaxation properties of high-solid gelling polysaccharides, gelatin and whey protein with small-molecule co-solute have been reviewed focusing on the glass transition region and glassy state of the mechanical master curve. Compliance with the principle of thermorheological simplicity is established allowing horizontal superposition of viscoelastic functions in the form of small-deformation stress relaxation or dynamic oscillation modulus. Numerical calculations via the Tikhonov regularization yield smooth stress relaxation spectra over a broad timescale that encompasses the isothermal process of vitrification in these systems. Next, the molecular coupling theory addressed the polymer chain dynamics of the local segmental motions that determine the glass transition temperature (Tg) of condensed matrices. Thus a more complete picture of the physics of intermolecular interactions in the short-time region of the glass dispersion has emerged. It allows estimation of the relaxation time for local segmental motions at Tg, and the extent of cooperativity between adjacent chemical moieties governing kinetics of viscoelastic relaxation in hydrocolloid based systems at the glass transition region.

Detection of the first infra-red quasi-periodic oscillation in a black hole X-ray binary

We present analysis of fast variability of Very Large Telescope/ISAAC (infra-red), \textit{XMM-Newton}/OM (optical) and EPIC-pn (X-ray), and RXTE/PCA (X-ray) observations of the black hole X-ray binary GX 339-4 in a rising hard state of its outburst in 2010. We report the first detection of a Quasi Periodic Oscillation (QPO) in the infra-red band (IR) of a black hole X-ray binary. The QPO is detected at 0.08 Hz in the IR as well as two optical bands (U and V). Interestingly, these QPOs are at half the X-ray QPO frequency at 0.16 Hz, which is classified as the type-C QPO; a weak sub-harmonic close to the IR and optical QPO frequency is also detected in X-rays. The broad band sub-second time scale variability is strongly correlated in IR/X-ray bands, with X-rays leading the IR by over 100 ms. This short time delay, shape of the cross correlation function and spectral energy distribution strongly indicate that this broad band variable IR emission is the synchrotron emission from the jet. A jet origin for the IR QPO is strongly favoured, but cannot be definitively established with the current data. The spectral energy distribution indicates a thermal disc origin for the bulk of the optical emission, but the origin of the optical QPO is unclear. We discuss our findings in the context of the existing models proposed to explain the origin of variability.

Photoluminescence Decay Dynamics in Blue and Green InGaN LED Structures Revealed by the Frequency-Domain Technique

An extended study of charge-carrier localization and delocalization in blue and green InGaN light-emitting diode (LED) test structures has been performed. Using the frequency-domain lifetime measurement (FDLM) technique based on direct harmonic modulation of photoluminescence excitation in the frequency range from 1 Hz to 100 MHz, carrier lifetimes were estimated at scales spanning from milliseconds to nanoseconds. The time resolution was determined using fast Fourier transform analysis. A system comprising a radiative and several nonradiative recombination channels was used to describe the complex photoluminescence decay. Due to the broad timescale, even stretched exponential decays from 2 ns to 4 ns up to 1.5 μs (stretching parameter 0.5 to 0.6) were revealed. A higher degree of carrier delocalization was observed for the blue compared with the green light-emitting structure, providing qualitative insight into disorder, which is tentatively assigned to spatial fluctuations of the indium concentration in the quantum wells. A nanosecond nonradiative recombination channel for the green light-emitting structure was found to be unsaturated throughout the entire photoexcitation power density range and was interpreted as being related to the higher defect density and lower internal quantum efficiency of the sample. To expand the study of lifetimes to much higher photoexcitation power density, time-resolved photoluminescence kinetics were measured.