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We propose a trajectory-based quasi-classical method for approximating dynamics in condensed phase systems. Building upon the previously developed optimized mean trajectory approximation that has been used to compute linear and nonlinear spectra, we borrow some ideas from filtering trajectory methods to obtain a novel semiclassical method for the dynamical propagation of density matrices. This new approximation is tested rigorously against standard multistate electronic models, spin-boson models, and models of the Fenna-Matthews-Olson complex. For dissipative systems, the current method is significantly better or as good as many other semiclassical methods available, especially at low temperatures and for off-diagonal density matrix elements, whereas for scattering models, the current method bears similar limitations as mean-field propagation schemes. All results are tested against the numerically exact hierarchical equations of motion method. The new method shows excellent agreement across various parameter regimes with numerically exact results, highlighting the robustness and accuracy of our approach., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In floating catalyst chemical vapor deposition (FCCVD), high-aspect-ratio carbon nanotubes (CNTs) are produced in the gas phase at high number concentrations and undergo collision and agglomeration, eventually giving rise to a macroscale aerogel, enabling functional material forms such as fibers or mats to be obtained directly from the synthesis process. The self-assembly behavior between high-aspect-ratio CNTs dictates the resulting morphology at the nanoscale and subsequently the bulk properties of the CNT product. Reorientation between CNTs after collision is a critical step that results in bundle formation and precedes aerogel formation. However, it has been challenging to study the phenomenon with existing methods as it spans multiple time and length scales. In this study, a physics-based semi-analytical model was developed to study the gas-phase reorientation dynamics of high-aspect-ratio CNTs and their bundles, with ±10% accuracy compared with mesoscale molecular dynamics simulations, but at <0.1% the computational cost. It was revealed that the reorientation time scale is dictated by the interplay among the van der Waals potential, drag, and the geometric configuration of CNTs upon collision. This then allows the time scale of reorientation (i.e., bundle formation) to be compared with other gas-phase dynamics in a typical FCCVD reactor and offers new insights into the self-assembly behavior of 1D nanoparticles in the gas phase.

Changes in EEG have been reported in both major depressive disorder (MDD) and bipolar disorder (BD). Specifically, power changes in EEG alpha and theta frequency bands during rest and task are known in both disorders. This leaves open whether there are changes in yet another component of the electrophysiological EEG signal, namely phase-related processes that may allow for distinguishing MDD and BD. For that purpose, we investigate EEG-based spontaneous phase in the resting state of MDD, BD and healthy controls. Our main findings show: (i) decreased spontaneous phase variability in frontal theta of both MDD and BD compared to HC; (ii) decreased spontaneous phase variability in central-parietal alpha in MDD compared to both BD and HC; (iii) increased delays or lags of alpha phase cycles in MDD (but not in BD), which (iv) correlate with the decreased phase variability in MDD. Together, we show similar (decreased frontal theta variability) and distinct (decreased central-parietal alpha variability with increased lags or delays) findings in the spontaneous phase dynamics of MDD and BD. This suggests potential relevance of theta and alpha phase dynamics in distinguishing MDD and BD in clinical differential-diagnosis., Competing Interests: Declaration of competing interest None of the authors declare any conflicts of interest., (Copyright © 2024. Published by Elsevier B.V.)

Real-time detection of intermediate species and final products at the surface and near-surface in interfacial solid-gas reactions is critical for an accurate understanding of heterogeneous reaction mechanisms. In this article, an experimental method that can simultaneously monitor the ultrafast dynamics at the surface and above the surface in photoinduced heterogeneous reactions is presented. This method relies on a combination of mass spectrometry and femtosecond pump-probe spectroscopy. As a model system, the photoinduced reaction of methyl iodide on and above a cerium oxide surface is investigated. The species that are simultaneously detected from the surface and gas-phase present distinct features in the mass spectra, such as a sharp peak followed by an adjacent broad shoulder. The sharp peak is attributed to the species detected from the surface, while the broad shoulder is due to the detection of gas-phase species above the surface, as confirmed by multiple experiments. By monitoring the evolution of the sharp peak and broad shoulder as a function of the pump-probe time delay, transient signals are obtained that describe the ultrafast photoinduced reaction dynamics of methyl iodide on the surface and in the gas-phase. Finally, SimION simulations are performed to confirm the origin of the ions produced on the surface and in the gas-phase., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

We propose a method to reconstruct the phase dynamics in rhythmical interacting systems from macroscopic responses to weak inputs by developing linear and nonlinear response theories, which predict the responses in a given system. By solving an inverse problem, the method infers an unknown system: the natural frequency distribution, the coupling function, and the time delay which is inevitable in real systems. In contrast to previous methods, our method requires neither strong invasiveness nor microscopic observations. We demonstrate that the method reconstructs two phase systems from observed responses accurately. The qualitative methodological advantages demonstrated by our quantitative numerical examinations suggest its broad applicability in various fields, including brain systems, which are often observed through macroscopic signals such as electroencephalograms and functional magnetic response imaging.

By means of the dispersive temporal interferometry technique, we carried out a real-time observation of the time separation and relative phase evolutions of two pulses toward harmonic mode-locking. During the separation stage of the buildup process, the time separation increases, while the relative phase decreases synchronously, and the largest change rates are 0.247 fs/r and -0.017 rad/r, respectively. Meanwhile, the two rates show a linear relation with the former 17.4 times larger than the latter. Moreover, a residual phase change rate of -3.89 × 10 -4  rad/r is observed in a steady non-uniform dual-soliton state, while such phase change is absent in a uniform four-soliton state. This study unveils the soliton interaction dynamics in lasers, which not only help to reduce timing jitter in multi-soliton mode-locking, but also bring insight to a temporal tweezing of femtosecond pulse.

We review an approach for reconstructing oscillatory networks' undirected and directed connectivity from data. The technique relies on inferring the phase dynamics model. The central assumption is that we observe the outputs of all network nodes. We distinguish between two cases. In the first one, the observed signals represent smooth oscillations, while in the second one, the data are pulse-like and can be viewed as point processes. For the first case, we discuss estimating the true phase from a scalar signal, exploiting the protophase-to-phase transformation. With the phases at hand, pairwise and triplet synchronization indices can characterize the undirected connectivity. Next, we demonstrate how to infer the general form of the coupling functions for two or three oscillators and how to use these functions to quantify the directional links. We proceed with a different treatment of networks with more than three nodes. We discuss the difference between the structural and effective phase connectivity that emerges due to high-order terms in the coupling functions. For the second case of point-process data, we use the instants of spikes to infer the phase dynamics model in the Winfree form directly. This way, we obtain the network's coupling matrix in the first approximation in the coupling strength., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 Rosenblum and Pikovsky.)

Preparation of neutral non-volatile molecules intact in the gas phase for mass spectrometry or chemical dynamics experiments remains a challenge for many classes of molecules. Here, we report the design and characterization of a fiber-coupled laser-based thermal desorption source capable of preparing intact neutral molecules at high molecular densities in the gas phase for use in velocity-map imaging experiments. Within this source, the sample is deposited onto a thin tantalum foil. Irradiation of the foil from the reverse side by a focused laser beam leads to highly localized heating of the sample, resulting in desorption of a plume of molecules into the gas phase. The fiber-coupled design simplifies the alignment of the desorption laser beam, and the ability to rotate the foil relative to the fixed laser beam allows the sample to be continually refreshed under vacuum. We use 118 nm photoionization of three test molecules-uracil, adenine, and phenylalanine-to characterize the source and to demonstrate various aspects of its performance. These include the dependence of the velocity-map imaging performance on the size of the interaction region and the dependence of the laser-induced desorption source emission on desorption laser power and heating time. Signal levels recorded in these measurements are comparable to those we typically obtain in similar experiments using a pulsed supersonic molecular beam, and we, therefore, believe that the source has considerable potential for use in a wide range of chemical dynamics and other experiments., (© 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

Characterizing the brain's dynamic pattern of response to an input in electroencephalography (EEG) is not a trivial task due to the entanglement of the complex spontaneous brain activity. In this context, the brain's response can be defined as (1) the additional neural activity components generated after the input or (2) the changes in the ongoing spontaneous activities induced by the input. Moreover, the response can be manifested in multiple features. Three commonly studied examples of features are (1) transient temporal waveform, (2) time-frequency representation, and (3) phase dynamics. The most extensively used method of average event-related potentials (ERPs) captures the first one, while the latter two and other more complex features are attracting increasing attention. However, there has not been much work providing a systematic illustration and guidance for how to effectively exploit multifaceted features in neural cognitive research. Based on a visual oddball ERPs dataset with 200 participants, this work demonstrates how the information from the above-mentioned features are complementary to each other and how they can be integrated based on stereotypical neural-network-based machine learning approaches to better exploit neural dynamic information in basic and applied cognitive research.

A comprehensive study of vortex phases and vortex dynamics is presented for a recently discovered high-temperature superconductor YH 6 with T c (onset) of 215 K under a pressure of 200 GPa. The thermal activation energy ( U 0 on magnetic field with a possible crossover at a field around 8-10 T. Furthermore, we have depicted the vortex phase transition from the vortex-glass to vortex-liquid state according to the vortex-glass theory. Finally, vortex phase diagram is constructed for the first time for superhydrides. Very high estimated values of flux flow barriers U 0 ∝ H α on magnetic field with a possible crossover at a field around 8-10 T. Furthermore, we have depicted the vortex phase transition from the vortex-glass to vortex-liquid state according to the vortex-glass theory. Finally, vortex phase diagram is constructed for the first time for superhydrides. Very high estimated values of flux flow barriers U 0 ( H ) = (1.5-7) × 10 4 K together with high crossover fields make YH 6 a rather outstanding superconductor as compared to most cuprates and iron-based systems. The Ginzburg number for YH 6 Gi = (3-7) × 10 -3 indicates that thermal fluctuations are not so strong and cannot broaden superconducting transitions in weak magnetic fields.

We experimentally investigate the stochastic phase dynamics of planar Josephson junctions (JJs) and superconducting quantum interference devices (SQUIDs) defined in epitaxial InAs/Al heterostructures, and characterized by a large ratio of Josephson energy to charging energy. We observe a crossover from a regime of macroscopic quantum tunneling to one of phase diffusion as a function of temperature, where the transition temperature T^{*} is gate-tunable. The switching probability distributions are shown to be consistent with a small shunt capacitance and moderate damping, resulting in a switching current which is a small fraction of the critical current. Phase locking between two JJs leads to a difference in switching current between that of a JJ measured in isolation and that of the same JJ measured in an asymmetric SQUID loop. In the case of the loop, T^{*} is also tuned by a magnetic flux.

Mixer-setters units are widely used in uranium purification processes. For efficient operations of mixer-settler units, it is essential to measure the hydrodynamics parameters of the different phases involved. The residence time distribution (RTD) measurement is commonly used method to estimate the hydrodynamics parameters of process reactors. In the present study, RTD of the aqueous phase was measured in different stages mixer-settler unit (mixers, settlers and mixer-settler units) used for stripping operation using Iodine-131 as a radiotracer. For the RTD measurements, radiotracer was injected as an impulse in aqueous phase feed line and its movement was monitored at different locations in the stripping unit using NaI(Tl) detectors. The mean residence times (MRTs) of the aqueous phase were estimated from measured RTD curves. For quantification of the degree of mixing, suitable flow models were proposed based on design and nature of the measured RTD curves and subsequently used for simulation. Based on the results of the RTD study, the mixing of aqueous phase was characterized and design of the stripping unit and its sub-units were validated. The optimum conditions were identified for efficient for the operation of the stripping unit., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Nonlocally coupled oscillators with a phase lag self-organize into various patterns, such as global synchronization, the twisted state, and the chimera state. In this paper, we consider nonlocally coupled oscillators that move on a ring by randomly exchanging their positions with the neighbors and investigate the combined effects of phase lag and mobility on the collective phase dynamics. Spanning the whole range of phase lag and mobility, we show that mobility promotes synchronization for an attractive coupling, whereas it destroys coherence for a repulsive coupling. The transition behaviors are discussed in terms of the timescales of synchronization and diffusion of the oscillators. We also find a novel spatiotemporal pattern at the border between coherent and incoherent states.

The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two-dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and frequency dimensions in these spectroscopic techniques provide access to rich information on the electronic and vibrational states present, the coupling between them, and the resulting rates at which they exchange energy that are obscured in linear spectroscopy, particularly for condensed phase systems that usually contain many overlapping features. While the exact quantum expression for the third-order response is well established, it is incompatible with the methods that are practical for calculating the atomistic dynamics of large condensed phase systems. These methods, which include both classical mechanics and quantum dynamics methods that retain quantum statistical properties while obeying the symmetries of classical dynamics, such as LSC-IVR, centroid molecular dynamics, and Ring Polymer Molecular Dynamics (RPMD), naturally provide short-time approximations to the multi-time symmetrized Kubo transformed correlation function. Here, we show how the third-order response can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions. We demonstrate the utility and accuracy of our approach by showing how it can be used to obtain the third-order response of a series of model systems using both classical dynamics and RPMD. In particular, we show that this approach captures features such as anharmonically induced vertical splittings and peak shifts while providing a physically transparent framework for understanding multidimensional spectroscopies.

The study was carried out to evaluate the dynamics of monthly numbers of cases, deaths, tests and case fatality ratio worldwide during three phases of the COVID-19 pandemic. Material and methods: Twenty-three sets of databases, dated the 22nd of each month from January 2020 to November 2021, for 213 countries were collected from the Worldometer website. The number of cases, deaths, tests, case fatality ratio, infection fatality ratio, etc. were counted for various periods of time for each of the 213 countries, then the results related to different periods of time were compared. The analysis of main epidemiological parameters resulted in division of three phases of the global pandemic evolution. The first phase (23.01.20-22.07.20), the second phase (23.07.20-22.01.21) and the third phase (23.01.21-22.07.21) were different in terms of the number of tests performed, new cases and mortality due to COVID-19. By the end of second phase, the worldwide statistics indicated end of the pandemic, but the third phase was characterized by sudden rise in number of new cases and deaths. The most dramatic evolution of epidemic curve occurred in the countries where physicians had successfully confronted COVID-19 during the first two phases of the pandemic. Despite the decrease in the overall numbers deaths during the latest months analyzed, additional study is necessary to identify causes of new cases and deaths during the third phase of the pandemic. It can be suggested that preventive and therapeutic protocols should be changed from the 'standard' to 'personalized' types.

The study was carried out to evaluate the dynamics of monthly numbers of cases, deaths, tests and case fatality ratio worldwide during three phases of the COVID-19 pandemic. Material and methods: Twenty-three sets of databases, dated the 22nd of each month from January 2020 to November 2021, for 213 countries were collected from the Worldometer website. The number of cases, deaths, tests, case fatality ratio, infection fatality ratio, etc. were counted for various periods of time for each of the 213 countries, then the results related to different periods of time were compared. The analysis of main epidemiological parameters resulted in division of three phases of the global pandemic evolution. The first phase (23.01.20-22.07.20), the second phase (23.07.20-22.01.21) and the third phase (23.01.21-22.07.21) were different in terms of the number of tests performed, new cases and mortality due to COVID-19. By the end of second phase, the worldwide statistics indicated imminent end of the pandemic, but the third phase was characterized by sudden rise in the number of new cases and deaths that could not be explained rationally. The most dramatic evolution of epidemic curve occurred in the countries where physicians had successfully confronted COVID-19 during the first two phases of the pandemic. Despite the decrease in the overall numbers deaths during the latest months analyzed, additional study is necessary to identify the cause of increasing in the number of new cases and deaths during the third phase of the pandemic. Presumably, there are several causes of negative evolution of the current pandemic, including over-reliance on polymerase chain reaction tests, application of non-specialized premises for quarantine and treatment, non-professional management, following therapeutic protocols applied in countries with high number of deaths, ignoring preventive treatment, and decreasing in mass and individual immunity. It can be suggested that the use of drugs modulating T-cell immunity is necessary, and preventive and therapeutic protocols should be changed from the 'standard' to 'personalized' types.

DNA supercoils are generated in genome regulation processes such as transcription and replication and provide mechanical feedback to such processes. Under tension, a DNA supercoil can present a coexistence state of plectonemic and stretched phases. Experiments have revealed the dynamic behaviors of plectonemes, e.g., diffusion, nucleation, and hopping. To represent these dynamics with conformational changes, we demonstrated first the fast dynamics on the DNA to reach torque equilibrium within the plectonemic and stretched phases, and then identified the two-phase boundaries as collective slow variables to describe the essential dynamics. According to the timescale separation demonstrated here, we developed a two-phase model on the dynamics of DNA supercoiling, which can capture physiologically relevant events across timescales of several orders of magnitudes. In this model, we systematically characterized the slow dynamics between the two phases and compared the numerical results with those from the DNA polymer physics-based worm-like chain model. The supercoiling dynamics, including the nucleation, diffusion, and hopping of plectonemes, have been well represented and reproduced, using the two-phase dynamic model, at trivial computational costs. Our current developments, therefore, can be implemented to explore multiscale physical mechanisms of the DNA supercoiling-dependent physiological processes., (Copyright © 2022 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

DNA replication is a highly regulated process that occurs in the context of chromatin structure and is sensitive to several histone post-translational modifications. In Saccharomyces cerevisiae, the histone methylase Set1 is responsible for the transcription-dependent deposition of H3K4 methylation (H3K4me) throughout the genome. Here we show that a combination of a hypomorphic replication mutation (orc5-1) with the absence of Set1 (set1Δ) compromises the progression through S-phase, and this is associated with a large increase in DNA damage. The ensuing DNA damage checkpoint activation, in addition to that of the spindle assembly checkpoint, restricts the growth of orc5-1 set1Δ. The opposite effects of the lack of RNase H activity and the reduction of histone levels on orc5-1 set1Δ viability are in agreement with their expected effects on replication fork progression. We propose that the role of H3K4 methylation during DNA replication becomes critical when the replication forks acceleration due to decreased origin firing in the orc5-1 background increases the risk for transcription replication conflicts. Furthermore, we show that an increase of reactive oxygen species levels, likely a consequence of the elevated DNA damage, is partly responsible for the lethality in orc5-1 set1Δ., (Copyright © 2021 The Author(s). Published by Elsevier B.V. All rights reserved.)

Through its ability to image liquid-phase dynamics at nano/atomic-scale resolution, liquid-cell electron microscopy is essential for a wide range of applications, including wet-chemical synthesis, catalysis, and nanoparticle tracking, for which involved structural features are critical. However, statistical investigations by usual techniques remain challenging because of the difficulty in fabricating substantial liquid cells with appreciable efficiency. Here, we report a general approach for efficiently printing huge numbers of ready-to-use liquid cells (∼9000) within 30 s by electrospinning, with the unique feature of statistical liquid-phase studies requiring only one experimental time slot. Our solution efficiently resolves a complete transition picture of bubble evolution and also the induced nanoparticle motion. We statistically quantify the effect of the electron dose rate on the bubble variation and conclude that the bubble-driven nanoparticle motion is a ballistic-like behavior insignificant to morphological asymmetries. The versatile approach here is critical for statistical research, offering great opportunities in liquid-phase-associated dynamic studies.

Understanding the pathways and time scales underlying electrically driven insulator-metal transitions is crucial for uncovering the fundamental limits of device operation. Using stroboscopic electron diffraction, we perform synchronized time-resolved measurements of atomic motions and electronic transport in operating vanadium dioxide (VO 2 ) switches. We discover an electrically triggered, isostructural state that forms transiently on microsecond time scales, which is shown by phase-field simulations to be stabilized by local heterogeneities and interfacial interactions between the equilibrium phases. This metastable phase is similar to that formed under photoexcitation within picoseconds, suggesting a universal transformation pathway. Our results establish electrical excitation as a route for uncovering nonequilibrium and metastable phases in correlated materials, opening avenues for engineering dynamical behavior in nanoelectronics., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Intrinsic optical signal (IOS) imaging promises a noninvasive method for objective assessment of retinal function. This study demonstrates concurrent optical coherence tomography (OCT) of amplitude-IOS and phase-IOS changes in human photoreceptors. A new procedure for differential-phase-mapping (DPM) is validated to enable depth-resolved phase-IOS imaging. Dynamic OCT revealed rapid amplitude-IOS and phase-IOS changes, which occur almost right away after the stimulus onset. These IOS changes were predominantly observed within the photoreceptor outer segment (OS), particularly two boundaries connecting to the inner segment and retinal pigment epithelium. The comparative analysis supports that both amplitude-IOS and phase-IOS attribute to transient OS morphological change associated with phototransduction activation in retinal photoreceptors. A simulation modeling is proposed to discuss the relationship between the photoreceptor OS length and phase-IOS changes., Competing Interests: The authors declare that there are no conflicts of interest related to this article., (© 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement.)

Batch production of continuous and uniform graphene films is critical for the application of graphene. Chemical vapor deposition (CVD) has shown great promise for mass producing high-quality graphene films. However, the critical factors affected the uniformity of graphene films during the batch production need to be further studied. Herein, we propose a method for batch production of uniform graphene films by controlling the gaseous carbon source to be uniformly distributed near the substrate surface. By designing the growth space of graphene into a rectangular channel structure, we adjusted the velocity of feedstock gas flow to be uniformly distributed in the channel, which is critical for uniform graphene growth. The monolayer graphene film grown inside the rectangular channel structure shows high uniformity with average sheet resistance of 345 Ω sq -1 without doping. The experimental and simulation results show that the placement of the substrates during batch growth of graphene films will greatly affect the distribution of gas-phase dynamics near the substrate surface and the growth process of graphene. Uniform graphene films with large-scale can be prepared in batches by adjusting the distribution of gas-phase dynamics.

By characterizing the phase dynamics in coupled oscillators, we gain insights into the fundamental phenomena of complex systems. The collective dynamics in oscillatory systems are often described by order parameters, which are insufficient for identifying more specific behaviors. To improve this situation, we propose a topological approach that constructs the quantitative features describing the phase evolution of oscillators. Here, the phase data are mapped into a high-dimensional space at each time, and the topological features describing the shape of the data are subsequently extracted from the mapped points. These features are extended to time-variant topological features by adding the evolution time as an extra dimension in the topological feature space. The time-variant features provide crucial insights into the evolution of phase dynamics. Combining these features with the kernel method, we characterize the multiclustered synchronized dynamics during the early evolution stages. Finally, we demonstrate that our method can qualitatively explain chimera states. The experimental results confirmed the superiority of our method over those based on order parameters, especially when the available data are limited to the early-stage dynamics.

Aneurysmal subarachnoid haemorrhage (SAH) is a devastating subset of stroke. One of the major determinates of morbidity is the development of delayed cerebral ischemia (DCI). Disruption of the nitric oxide (NO) pathway and consequently the control of cerebral blood flow (CBF), known as cerebral autoregulation, is believed to play a role in its pathophysiology. Through the pharmacological manipulation of in vivo NO levels using an exogenous NO donor we sought to explore this relationship. Phase synchronisation index (PSI), an expression of the interdependence between CBF and arterial blood pressure (ABP) and thus cerebral autoregulation, was calculated before and during sodium nitrite administration in 10 high-grade SAH patients acutely post-rupture. In patients that did not develop DCI, there was a significant increase in PSI around 0.1 Hz during the administration of sodium nitrite (33%; p-value 0.006). In patients that developed DCI, PSI did not change significantly. Synchronisation between ABP and CBF at 0.1 Hz has been proposed as a mechanism by which organ perfusion is maintained, during periods of physiological stress. These findings suggest that functional NO depletion plays a role in impaired cerebral autoregulation following SAH, but the development of DCI may have a distinct pathophysiological aetiology., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

When a solute molecule is placed in solution, is it acceptable to presume that its electronic structure is essentially the same as that in the gas phase? In this paper, we address this question from a simulation perspective for the case of the sodium dimer cation (Na 2 ) molecule in both liquid Ar and liquid tetrahydrofuran (THF). In previous work, we showed that, when local specific interactions between a solute and solvent are energetically on the order of a hydrogen bond, the solvent can become part of the chemical identity of the solute. Here, using mixed quantum/classical molecular dynamics simulations, we see that, for the Na + ) molecule in both liquid Ar and liquid tetrahydrofuran (THF). In previous work, we showed that, when local specific interactions between a solute and solvent are energetically on the order of a hydrogen bond, the solvent can become part of the chemical identity of the solute. Here, using mixed quantum/classical molecular dynamics simulations, we see that, for the Na 2 + molecule, solute-solvent interactions lead to two stable, chemically distinct coordination states (Na(THF) 4 -Na(THF) 5 ) that are not only stable themselves as gas-phase molecules but that also have a completely new electronic structure with important implications for the excited-state photodissociation of this molecule in the condensed phase. Furthermore, we show through a set of comparative classical simulations that treating the solute's bonding electron explicitly quantum mechanically is necessary to understand both the ground-state dynamics and chemical identity of this simple diatomic molecule; even use of the quantum-derived potential of mean force is insufficient to describe the behavior of the molecule classically. Finally, we calculate the results of a proposed transient hole-burning experiment that could be used to spectroscopically disentangle the presence of the different coordination states.+ and Na(THF) 5 -Na(THF) 5 + ) that are not only stable themselves as gas-phase molecules but that also have a completely new electronic structure with important implications for the excited-state photodissociation of this molecule in the condensed phase. Furthermore, we show through a set of comparative classical simulations that treating the solute's bonding electron explicitly quantum mechanically is necessary to understand both the ground-state dynamics and chemical identity of this simple diatomic molecule; even use of the quantum-derived potential of mean force is insufficient to describe the behavior of the molecule classically. Finally, we calculate the results of a proposed transient hole-burning experiment that could be used to spectroscopically disentangle the presence of the different coordination states.

Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.

The complicated chemical vapour deposition (CVD) is currently the most viable method of producing graphene. Most studies have extensively focused on chemical aspects either through experiments or computational studies. However, gas-phase dynamics in CVD reportedly plays an important role in improving graphene quality. Given that mass transport is the rate-limiting step for graphene deposition in atmospheric-pressure CVD (APCVD), the interfacial phenomena at the gas-solid interface (i.e., the boundary layer) are a crucial controlling factor. Accordingly, only by understanding and controlling the boundary-layer thickness can uniform full-coverage graphene deposition be achieved. In this study, a simplified computational fluid dynamics analysis of APCVD was performed to investigate gas-phase dynamics during deposition. Boundary-layer thickness was also estimated through the development of a customised homogeneous gas model. Interfacial phenomena, particularly the boundary layer and mass transport within it, were studied. The effects of Reynolds number on these factors were explored and compared with experimentally obtained results of the characterised graphene deposit. We then discussed and elucidated the important relation of fluid dynamics to graphene growth through APCVD.

Cell viability and cytotoxicity assays are highly important for drug screening and cytotoxicity tests of antineoplastic or other therapeutic drugs. Even though biochemical-based tests are very helpful to obtain preliminary preview, their results should be confirmed by methods based on direct cell death assessment. In this study, time-dependent changes in quantitative phase-based parameters during cell death were determined and methodology useable for rapid and label-free assessment of direct cell death was introduced. The goal of our study was distinction between apoptosis and primary lytic cell death based on morphologic features. We have distinguished the lytic and non-lytic type of cell death according to their end-point features (Dance of Death typical for apoptosis versus swelling and membrane rupture typical for all kinds of necrosis common for necroptosis, pyroptosis, ferroptosis and accidental cell death). Our method utilizes Quantitative Phase Imaging (QPI) which enables the time-lapse observation of subtle changes in cell mass distribution. According to our results, morphological and dynamical features extracted from QPI micrographs are suitable for cell death detection (76% accuracy in comparison with manual annotation). Furthermore, based on QPI data alone and machine learning, we were able to classify typical dynamical changes of cell morphology during both caspase 3,7-dependent and -independent cell death subroutines. The main parameters used for label-free detection of these cell death modalities were cell density (pg/pixel) and average intensity change of cell pixels further designated as Cell Dynamic Score (CDS). To the best of our knowledge, this is the first study introducing CDS and cell density as a parameter typical for individual cell death subroutines with prediction accuracy 75.4% for caspase 3,7-dependent and -independent cell death.

The phase of low-frequency, rhythmic cortical activity is essential for organizing brain processes because it provides a recurrent temporal frame for information coding. However, the low-frequency cortical phase exhibits great flexibility in response to external influences. Given that brain rhythms have been found to track respiratory inputs, we hypothesized that slow breathing, commonly associated with mental regulation, could reorganize the relationship between these two rhythmic systems through the adjustment of the cortical phase to such a slow train of inputs. Based on simultaneous magnetoencephalography and respiratory measurements, we report that while participants performed paced breathing, slow relative to normal breathing modulated cortical phase activity in the alpha range across widespread brain areas. Such modulation effects were specifically locked to the middle of the inspiration stage and exhibited a well-structured pattern. At the single-subject level, the phase angles underlying the effects became more likely to be diametrically opposed across breaths, indicating unique and consistent phase adjustment to slow inspiratory inputs. Neither cardiac fluctuations nor breathing-unrelated task effects could account for the findings. We suggest that slow-paced inspiration could organize the cortical phase in a regularized phase pattern, revealing a rhythmic but dynamic neural network integrated with different neurophysiological systems through volitional control. NEW & NOTEWORTHY Breathing is more complicated than a simple gas exchange, as it is integrated with numerous cognitive and emotional functions. Controlled slow breathing has often been used to regulate mental processes. This magnetoencephalography study demonstrates that slow-paced relative to normal-paced inspiration could organize the timing of alpha rhythmic activities across breathing cycles in a structured manner over widespread brain areas. Our results reveal how a volitionally controlled change in respiratory behavior could systematically modulate cortical activity.

We report the exact phase dynamics of Manakov bright and dark vector solitons in an inhomogeneous optical system by means of a variable coefficient coupled nonlinear Schrödinger equation. To investigate the phase dynamics, we have modified the Manakov system with a relation between two modes of propagation, that are obtained by the Hirota bilinear method. The importance of the phase study in soliton interaction is revealed by asymptotic analysis of two-soliton solutions. In contrast with the Manakov bright soliton, the time-dependent dark vector soliton exhibits a gradual phase shift due to the blackness factor. The various inhomogeneous effects on the soliton phase are investigated, with a particular emphasis on nonlinear tunneling. The intensity and corresponding phase of the tunneling soliton either forms a peak or valley and retains its shape after tunneling. Unlike the bright counterpart, the gain or loss term significantly affects the phase of the dark soliton. Apart from the study of soliton intensity, the phase profile of bright and dark vector solitons and its dynamical features are also explored. As the study is not limited to intensity description, the present study could serve as a reference for the future studies on multisolitons phase dynamics in photonics and related fields.

Background Growth differentiation factor 15 (GDF-15) in ST-elevation myocardial infarction (STEMI) is prognostic in first-generation radioimmunoassays. We examined GDF-15 temporal dynamics in STEMI and its predictive value using a first fully automated GDF-15 electrochemiluminescence assay. Methods In this prospective study, circulating GDF-15 concentration was measured at admission (0 h), 12 h and 24 h in 1026 consecutive STEMI patients treated between February 2011 and May 2016 with primary percutaneous coronary intervention. GDF-15 dynamics (0 h, 12 h, 24 h) and predictive value (30 days and 3 years) were examined. Results Median GDF-15 concentration was 1443 pg/mL at 0 h, 1731 pg/mL at 12 h and 1510 pg/mL at 24 h (p<0.001). During follow-up, 94 patients died (9.2%) and 154 (15.0%) were hospitalized. GDF-15 was a strong predictor of 30-day mortality (hazard ratio [HR] 1.76, 95% confidence interval [CI], 1.33-2.34 at 0 h; HR 2.99 [95% CI, 2.18-4.09] at 12 h, and HR 1.97 [95% CI, 1.47-2.63] at 24 h) in multivariable Cox proportional hazards models. GDF-15 improved discrimination and reclassification of a clinical risk model. GDF-15 was also associated with 3-year mortality (HR 1.31 [95% CI, 1.04-1.65] at 0 h, HR 1.42 [95% CI, 1.10-1.84] at 12 h, and HR 1.51 [95% CI, 1.16-1.96] at 24 h) and 3-year composite of mortality and cardiovascular hospitalization (HR 1.17 [95% CI, 1.01-1.37] at 0 h, HR 1.20 [95% CI, 1.02-1.42] at 12 h, and HR 1.27 [95% CI, 1.08-1.50] at 24 h). Conclusions GDF-15 peaked at 12 h and remained elevated at 24 h in STEMI. GDF-15 measurement during the first 24 h in STEMI is valuable for predicting especially short- but also long-term outcomes, and may be a useful addition to risk stratification.

The conventional view of conversion reaction is based on the reversibility, returning to an initial material structure through reverse reaction at each cycle in cycle life, which impedes the complete understanding on a working mechanism upon a progression of cycles in conversion-reaction-based battery electrodes. Herein, a series of tin-doped ferrites (Fe 3- x Sn x O 4 , x = 0-0.36) are prepared and applied to a lithium-ion battery anode. By achieving the ideal reoxidation into SnO 2 , the Fe 2.76 Sn 0.24 O 4 composite anchored on reduced graphene oxide shows a high reversible capacity of 1428 mAh g -1 at 200 mA g -1 after 100 cycles, which is the best performance of Sn-based anode materials so far. Significantly, a newly formed γ-FeOOH phase after 100 cycles is identified from topological features through synchrotron X-ray absorption spectroscopy with electronic and atomic structural information, suggesting the phase transformation from magnetite to lepidocrocite upon cycling. Contrary to the conventional view, our work suggests a variable working mechanism in an iron-based composite with the dynamic phases from iron oxide to iron oxyhydroxide in the battery cycle life, based on the reactivity of metal nanoparticles formed during reaction toward the solid electrolyte interface layer.

Human color vision is achieved by mixing neural signals from cone photoreceptors sensitive to different wavelengths of light. The spatial arrangement and proportion of these spectral types in the retina set fundamental limits on color perception, and abnormal or missing types are responsible for color vision loss. Imaging provides the most direct and quantitative means to study these photoreceptor properties at the cellular scale in the living human retina, but remains challenging. Current methods rely on retinal densitometry to distinguish cone types, a prohibitively slow process. Here, we show that photostimulation-induced optical phase changes occur in cone cells and carry substantial information about spectral type, enabling cones to be differentiated with unprecedented accuracy and efficiency. Moreover, these phase dynamics arise from physiological activity occurring on dramatically different timescales (from milliseconds to seconds) inside the cone outer segment, thus exposing the phototransduction cascade and subsequent downstream effects. We captured these dynamics in cones of subjects with normal color vision and a deuteranope, and at different macular locations by: ( i ) marrying adaptive optics to phase-sensitive optical coherence tomography to avoid optical blurring of the eye, ( ii ) acquiring images at high speed that samples phase dynamics at up to 3 KHz, and ( iii ) localizing phase changes to the cone outer segment, where photoactivation occurs. Our method should have broad appeal for color vision applications in which the underlying neural processing of photoreceptors is sought and for investigations of retinal diseases that affect cone function., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Polymer characterizations are often performed using mass spectrometry (MS). Aside from MS and different tandem MS (MS/MS) techniques, ion mobility-mass spectrometry (IM-MS) has been recently added to the inventory of characterization technique. However, only few studies have focused on the reproducibility and robustness of polymer IM-MS analyses. Here, we perform collisional and electron-mediated activation of polymer ions before measuring IM drift times, collision cross-sections (CCS), or reduced ion mobilities (K 0 ). The resulting IM behavior of different activated product ions is then compared to non-activated native intact polymer ions. First, we analyzed collision induced unfolding (CIU) of precursor ions to test the robustness of polymer ion shapes. Then, we focused on fragmentation product ions to test for shape retentions from the precursor ions: cation ejection species (CES) and product ions with m/z and charge state values identical to native intact polymer ions. The CES species are formed using both collision induced dissociation (CID) and electron transfer dissociation (ETD, formally ETnoD) experiments. Only small drift time, CCS, or K 0 deviations between the activated/formed ions are observed compared to the native intact polymer ions. The polymer ion shapes seem to depend solely on their mass and charge state. The experiments were performed on three synthetic homopolymers: poly(ethoxy phosphate) (PEtP), poly(2-n-propyl-2-oxazoline) (Pn-PrOx), and poly(ethylene oxide) (PEO). These results confirm the robustness of polymer ion CCSs for IM calibration, especially singly charged polymer ions. The results are also discussed in the context of polymer analyses, CCS predictions, and probing ion-drift gas interaction potentials. Graphical Abstract.

Domain walls (DWs) in strongly correlated materials have provided fertile ground for the discovery of exotic phenomena, and controlling the formation of DWs is still a challenge. Here, it is demonstrated that a new type of structural DW can be induced in a series of manganite thin films, which are engineered to achieve a robust charge-ordering insulating (COI) ground state by selecting various films and substrates. The monoclinic domains are somewhat irregular in shape, and the corresponding DWs, taking the shape of closed loops, are ferromagnetic and metallic (FMM) at low temperatures. Remarkably, the DWs exhibit little dependence on temperature or magnetic field, due to the structural origins of the domains. Additionally, using magnetic force microscopy, the role played by DWs in the dynamics of the COI and FMM phases at the mesoscopic scale is revealed. They function as barriers, strictly confining the phase dynamics within each domain, reflecting the strong coupling of electronic phases with the lattice. Each domain exhibits binary occupation by a single pure phase, resulting in a quasi-periodic phase separation. The universal behaviors of the multiple engineered films elucidate the possibility of controlling the formation of DWs and tuning phase dynamics through DW design., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Groundwater contamination from ethanol (e.g., alternative fuels) can support vigorous biodegradation, with many possible reactions producing dissolved gases. The objective of this study was to improve the understanding of the development and evolution of trapped gas phase changes occurring within an ethanol plume undergoing biodegradation. The experiment performed involved highly detailed spatial and temporal monitoring of gas phase saturations using Time Domain Reflectometry probes embedded in a 2-dimensional (175 cm high × 525 cm long) synthetic aquifer (homogeneous sand tank with horizontal groundwater flow). Ethanol injection immediately promoted gas-producing reactions, including: fermentation, denitrification, sulphate-reduction and iron(III)-reduction, with methanogenesis developing between 69 and 109 days. Substantial in situ increases in trapped gas were observed over ~330 days, with maximum gas saturations reaching 27% of the pore volume. Despite sustained gas production, this maximum was never exceeded, likely due to the onset of gas phase mobilization (i.e., ebullition) upon reaching a buoyancy-capillarity threshold. Reductions in the quasi-saturated hydraulic conductivity, resulting from the gas phase accumulation, were restricted by ebullition to a factor of ≤2; but still appeared to alter the groundwater flow field. Overall, trapped gas saturations exhibited high spatial and temporal variability, including declines within the plume and increases outside of the plume. Influential factors included vertically-shifting ethanol inputs and resultant secondary redox reactions, microbial controls on redox zonation, ebullition, and altered groundwater flows. These observations have implications for the transport of gases and volatile compounds within plumes and above the water table at sites with groundwater contamination from ethanol or other highly degradable organics., (Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.)

This study proposes a two-dimensional (2D) oscillator model of p53 network, which is derived via reducing the multidimensional two-phase dynamics model into a model of ataxia telangiectasia mutated (ATM) and Wip1 variables, and studies the impact of p53-regulators on cell fate decision. First, the authors identify a 6D core oscillator module, then reduce this module into a 2D oscillator model while preserving the qualitative behaviours. The introduced 2D model is shown to be an excitable relaxation oscillator. This oscillator provides a mechanism that leads diverse modes underpinning cell fate, each corresponding to a cell state. To investigate the effects of p53 inhibitors and the intrinsic time delay of Wip1 on the characteristics of oscillations, they introduce also a delay differential equation version of the 2D oscillator. They observe that the suppression of p53 inhibitors decreases the amplitudes of p53 oscillation, though the suppression increases the sustained level of p53. They identify Wip1 and P53DINP1 as possible targets for cancer therapies considering their impact on the oscillator, supported by biological findings. They model some mutations as critical changes of the phase space characteristics. Possible cancer therapeutic strategies are then proposed for preventing these mutations' effects using the phase space approach.

A dynamic system showing stable rhythmic activity can be represented by the dynamics of phase oscillators. This would provide a useful mathematical framework through which one can understand the system's dynamic properties. A recent study proposed a Bayesian approach capable of extracting the underlying phase dynamics directly from time-series data of a system showing rhythmic activity. Here we extended this method to spike data that otherwise provide only limited phase information. To determine how this method performs with spike data, we applied it to simulated spike data generated by a realistic neuronal network model. We then compared the estimated dynamics obtained based on the spike data with the dynamics theoretically derived from the model. The method successfully extracted the modeled phase dynamics, particularly the interaction function, when the amount of available data was sufficiently large. Furthermore, the method was able to infer synaptic connections based on the estimated interaction function. Thus, the method was found to be applicable to spike data and practical for understanding the dynamic properties of rhythmic neural systems.

We attempted to elucidate early-phase dynamics of HIV-1 infection using replication-competent, red-fluorescent-protein (mCherry)-labeled HIV-1 JR-FL (HIV JR-FL mC ) and NOD/SCID/Jak3 -/- mice transplanted with Individual-A's human peripheral blood mononuclear cells (hPBMC)(hNOJ mice). On day 7 following HIV JR-FL mC inoculation, mCherry-signal-emitting infection foci were readily identified in the subserosa of 10 of 10 HIV JR-FL mC -inoculated hNOJ mice, although infection foci were not located without the mCherry signal in unlabeled HIV-1 JR-FL -inoculated mice (n = 6). Even on day 14, infection foci were hardly located in the unlabeled HIV-1 JR-FL -inoculated mice, while in all of 7 HIV JR-FL mC -inoculated hNOJ mice examined, mCherry-signal-emitting lymph nodes were easily identified, in which active viral replication was present. On day 14, a significantly larger number of mesenteric lymph nodes were seen in HIV JR-FL mC -exposed hNOJ mice than in HIV JR-FL mC -unexposed mice (P = 0.0025). The weights of mesenteric lymph nodes of those HIV JR-FL mC -exposed hNOJ mice were also greater than those of HIV JR-FL mC -unexposed mice (P = 0.0005). When hNOJ mice were inoculated with HIV JR-FL mC -exposed hPBMC from Individual-B, significantly greater viremia was seen than in cell-free HIV JR-FL mC -inoculated hNOJ mice as examined on day 7. In the lymph nodes of those mice inoculated with HIV JR-FL mC -exposed hPBMC from Individual-B, a substantial number of Individual-B's HIV JR-FL mC -infected cells were identified together with Individual-A's cells as examined on day 14. The present HIV JR-FL mC -infected mouse model represents the first system reported using traceable HIV JR-FL mC and human target cells, not using SIV or simian cells, which should be of utility in studies of early-phases of HIV-1 transmission and in evaluating the effects of potential agents for post-exposure and pre-exposure prophylaxis., (Copyright © 2017. Published by Elsevier B.V.)

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

Purpose: Circulating tumor cells (CTCs) can provide a potentially minimal invasive source for monitoring chemotherapeutic effects. However, detailed in vivo dynamics of CTC after chemotherapy remain largely unknown., Methods: We monitored CTC number and morphology early after chemotherapy using a newly developed cytology-based CTC detection device and triple-negative breast cancer mouse CTC models with spontaneous lung metastatic potential., Results: Paclitaxel inhibited cell growth of breast cancer cells by mainly G2/M cell cycle arrest and partly apoptosis, whereas doxorubicin inhibited cell growth mainly by apoptosis and partly G2 cell cycle arrest in vitro. The number of CTCs was significantly increased 3-10 days after paclitaxel and doxorubicin chemotherapy and decreased thereafter in two mouse CTC models. The transiently increased CTCs early post-chemotherapy consisted of not only G2/M arrested cells (apoptotic cells), but also morphologically near-intact live cells. This heterogeneous cell population of CTCs was similar to that of primary tumor tissue after chemotherapy., Conclusions: These results indicate that CTCs can be mobilized from the primary tumor in rapid response to chemotherapy and suggest the possibility that CTC monitoring from both numerical and morphological viewpoints early after chemotherapy using a cytology-based CTC detection device would be a useful diagnostic tool for predicting drug sensitivity/resistance in preclinical and clinical setting.

We show that coupled mode-locked semiconductor lasers can operate in a subharmonic regime in which the two lasers pulsate in an anti-phase manner at one-half the fundamental mode-locking frequency of the solitary lasers. In the subharmonic mode, each pulse has almost twice the energy carried by the isolated lasers in the fundamental mode-locked regime and is also significantly shorter in duration. Depending on the unsaturated gain and coupling strength, the lasers can also exhibit bistability, perfect synchronization, and delayed synchronization, as well as three-halves and five-halves harmonic mode locking. The observed behaviors are robust and persist in the presence of noise.

The processes governing multilayer nucleation in the chemical vapour deposition (CVD) of graphene are important for obtaining high-quality monolayer sheets, but remain poorly understood. Here we show that higher-order carbon species in the gas-phase play a major role in multilayer nucleation, through the use of in-situ ultraviolet (UV) absorption spectroscopy. These species are the volatilized products of reactions between hydrogen and carbon contaminants that have backstreamed into the reaction chamber from downstream system components. Consequently, we observe a dramatic suppression of multilayer nucleation when backstreaming is suppressed. These results point to an important and previously undescribed mechanism for multilayer nucleation, wherein higher-order gas-phase carbon species play an integral role. Our work highlights the importance of gas-phase dynamics in understanding the overall mechanism of graphene growth.

Objective: To assess factors that might contribute to a delayed sleep schedule in young adults with sub-clinical features of delayed sleep phase disorder., Methods: Two groups of 14 young adults (eight women) were compared: one group complaining of a delayed sleep schedule and a control group with an earlier bedtime and no complaint. For one week, each subject maintained a target bedtime reflecting their habitual sleep schedule. Subjects were then admitted to the laboratory for the assessment of circadian phase (dim light melatonin onset), subjective sleepiness, and non-visual light sensitivity. All measures were timed relative to each participant's target bedtime. Non-visual light sensitivity was evaluated using subjective sleepiness and salivary melatonin during 1.5-h exposure to blue light, starting one hour after target bedtime., Results: Compared to control subjects, delayed subjects had a later circadian phase and a slower increase of subjective sleepiness in the late evening. There was no group difference in non-visual sensitivity to blue light, but we found a positive correlation between melatonin suppression and circadian phase within the delayed group., Conclusions: Our results suggest that a late circadian phase, a slow build-up of sleep need, and an increased circadian sensitivity to blue light contribute to the complaint of a delayed sleep schedule. These findings provide targets for strategies aiming to decreasing the severity of a sleep delay and the negative consequences on daytime functioning and health., (Copyright © 2017 Elsevier B.V. All rights reserved.)

While Boolean logic has been the backbone of digital information processing, there exist classes of computationally hard problems wherein this paradigm is fundamentally inefficient. Vertex coloring of graphs, belonging to the class of combinatorial optimization, represents one such problem. It is well studied for its applications in data sciences, life sciences, social sciences and technology, and hence, motivates alternate, more efficient non-Boolean pathways towards its solution. Here we demonstrate a coupled relaxation oscillator based dynamical system that exploits insulator-metal transition in Vanadium Dioxide (VO 2 ) to efficiently solve vertex coloring of graphs. Pairwise coupled VO 2 oscillator circuits have been analyzed before for basic computing operations, but using complex networks of VO 2 oscillators, or any other oscillators, for more complex tasks have been challenging in theory as well as in experiments. The proposed VO 2 oscillator network harnesses the natural analogue between optimization problems and energy minimization processes in highly parallel, interconnected dynamical systems to approximate optimal coloring of graphs. We further indicate a fundamental connection between spectral properties of linear dynamical systems and spectral algorithms for graph coloring. Our work not only elucidates a physics-based computing approach but also presents tantalizing opportunities for building customized analog co-processors for solving hard problems efficiently.

Light is the primary signal that calibrates circadian neural circuits and thus coordinates daily physiological and behavioral rhythms with solar entrainment cues. Drosophila and mammalian circadian circuits consist of diverse populations of cellular oscillators that exhibit a wide range of dynamic light responses, periods, phases, and degrees of synchrony. How heterogeneous circadian circuits can generate robust physiological rhythms while remaining flexible enough to respond to synchronizing stimuli has long remained enigmatic. Cryptochrome is a short-wavelength photoreceptor that is endogenously expressed in approximately half of Drosophila circadian neurons. In a previous study, physiological light response was measured using real-time bioluminescence recordings in Drosophila whole-brain explants, which remain intrinsically light-sensitive. Here we apply analysis of real-time bioluminescence experimental data to show detailed dynamic ensemble representations of whole circadian circuit light entrainment at single neuron resolution. Organotypic whole-brain explants were either maintained in constant darkness (DD) for 6 days or exposed to a phase-advancing light pulse on the second day. We find that stronger circadian oscillators support robust overall circuit rhythmicity in DD, whereas weaker oscillators can be pushed toward transient desynchrony and damped amplitude to facilitate a new state of phase-shifted network synchrony. Additionally, we use mathematical modeling to examine how a network composed of distinct oscillator types can give rise to complex dynamic signatures in DD conditions and in response to simulated light pulses. Simulations suggest that complementary coupling mechanisms and a combination of strong and weak oscillators may enable a robust yet flexible circadian network that promotes both synchrony and entrainment. A more complete understanding of how the properties of oscillators and their signaling mechanisms facilitate their distinct roles in light entrainment may allow us to direct and augment the circadian system to speed recovery from jet lag, shift work, and seasonal affective disorder., (© 2016 The Author(s).)

Alpha oscillations (7-14Hz) are modulated in response to visual temporal and spatial cues. However, the neural response to alerting cues is less explored, as is how this response is affected by healthy aging. Using scalp EEG, we examined how visual cortical alpha activity relates to working memory performance. Younger (20-30 years) and older (60-70 years) participants were presented with a visual alerting cue uninformative of the position or size of a lateralized working memory array. Older adults showed longer response times overall and reduced accuracy when memory load was high. Older adults had less consistent cue-evoked alpha phase resetting than younger adults, which predicted worse performance. Alpha phase prior to memory array presentation predicted response time, but the relationship between phase and response time was weaker in older adults. These results suggest that changes in alpha phase dynamics, especially prior to presentation of task-relevant stimuli, potentially contribute to age-related cognitive decline., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Characterizing the complicated flow behaviors arising from high water cut and low velocity oil-water flows is an important problem of significant challenge. We design a high-speed cycle motivation conductance sensor and carry out experiments for measuring the local flow information from different oil-in-water flow patterns. We first use multivariate time-frequency analysis to probe the typical features of three flow patterns from the perspective of energy and frequency. Then we infer complex networks from multi-channel measurements in terms of phase lag index, aiming to uncovering the phase dynamics governing the transition and evolution of different oil-in-water flow patterns. In particular, we employ spectral radius and weighted clustering coefficient entropy to characterize the derived unweighted and weighted networks and the results indicate that our approach yields quantitative insights into the phase dynamics underlying the high water cut and low velocity oil-water flows.