19 results on '"Phase dynamics"'
Search Results
2. Two-phase dynamics of DNA supercoiling based on DNA polymer physics
- Author
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Wan, Biao and Yu, Jin
- Subjects
Biological Sciences ,Macromolecular and Materials Chemistry ,Chemical Sciences ,Genetics ,1.1 Normal biological development and functioning ,DNA ,DNA ,Superhelical ,Nucleic Acid Conformation ,Physics ,Polymers ,Physical Sciences ,Biophysics ,Biological sciences ,Chemical sciences ,Physical sciences - Abstract
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.
- Published
- 2022
3. Phase dynamics of noise-induced coherent oscillations in excitable systems
- Author
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Jinjie Zhu, Yuzuru Kato, and Hiroya Nakao
- Subjects
Physics ,QC1-999 - Abstract
Noise can induce coherent oscillations in excitable systems without periodic orbits. Here, we establish a method to derive a hybrid system approximating the noise-induced coherent oscillations in excitable systems and further perform phase reduction of the hybrid system to derive an effective, dimensionality-reduced phase equation. We apply the reduced phase model to a periodically forced excitable system and two-coupled excitable systems, both undergoing noise-induced oscillations. The reduced phase model can quantitatively predict the entrainment of a single system to the periodic force and the mutual synchronization of two coupled systems, including the phase slipping behavior due to noise, as verified by Monte Carlo simulations. The derived phase model gives a simple and efficient description of noise-induced oscillations and can be applied to the analysis of more general cases.
- Published
- 2022
- Full Text
- View/download PDF
4. Phase Dynamics in Human Visuomotor Control - Health & Disease
- Author
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Engel, David
- Subjects
Visuomotor control ,Physics ,Parkinson's disease ,Human postural control ,Balancekontrolle ,Gleichgewichtskontrolle ,Body sway ,Motion tracking ,Virtual reality ,Physik ,Bewegungsmessung ,Visuomotorisches System ,Balance control ,Visuomotorik ,COM ,COP - Abstract
In this thesis, comprised of four publications, I investigated phase dynamics of visuomotor control in humans during upright stance in response to an oscillatory visual drive. For this purpose, I applied different versions of a ���moving room��� paradigm in virtual reality while stimulating human participants with anterior-posterior motion of their visual surround and analyzed their bodily responses. Human balance control constitutes a complex interplay of interdependent processes. The main sensory contributors include vision, vestibular input, and proprioception, with a dominant role attributed to vision. The purpose of the balance control system is to keep the body���s center of mass (COM) within a certain spatial range around the current base of support. Ever-changing environmental circumstances along with sensory noise cause the body to permanently sway around its point of equilibrium. Considering this sway, the human body can be modelled as a (multi-link) inverted pendulum. To maintain balance while being exposed to perturbations of the visual environment, humans adjust their sway to counteract the perceived motion of their bodies. Neurodegenerative diseases like Parkinson���s impair balance control and thus are likely to affect these mechanisms. Hence, investigation of bodily responses to a visual drive gives insight into visuomotor control in health and disease. In my first study, I introduced inter-trial phase coherence (ITPC) as a novel method to investigate postural responses to periodical visual stimulation. I found that human participants phase-locked the motion of their center of pressure (COP) to a 3-D dot cloud which oscillated in the anterior-posterior direction. This effect was equally strong for a low frequency of visual stimulation at 0.2 Hz and a high frequency of 1.5 Hz, the latter exceeding the previously assumed frequency range associated with coherent postural sway responses to periodical oscillations of the visual environment (moving room). Moreover, I was able to show that ITPC reliably captured responses in almost all participants, thereby addressing the common problem of inter-subject variability in body sway research. Based on the results of my first study, I concluded phase locking to be an essential feature in human postural control. For the second study, I introduced a mobile and cost-effective setup to apply a visual paradigm consisting of a virtual tunnel which stretched in the anterior-posterior direction and oscillated back and forth at three distinct frequencies (0.2 Hz, 0.8 Hz, and 1.2 Hz). Because tracking of the COP alone neglects crucial information about how COM shifts are arranged across the body, I included additional full-body motion tracking here to evaluate sway of individual body segments. Using a modified measure of phase locking, the phase locking value (PLV), allowed me to find participants phase-locking not only their COP, but also additional segments of their body to the visual drive. While their COP exhibited a strong phase locking to all frequencies of visual stimulation, distribution of phase locking across the body underwent a shift as the frequency of the visual stimulation increased. For the lowest frequency of 0.2 Hz, participants phase-locked almost their entire body to the stimulus. At higher frequencies, this phase locking shifted towards the lower torso and hip, with subjects almost exclusively phase-locking their hip to the visual drive at the highest frequency of 1.2 Hz. Having introduced a novel and reliable measurement along with a mobile setup, these results allowed me to empirically confirm shifts in postural strategies previously proposed in the literature. In the third study, a collaboration with the neurology department of the Universit��tsklinikum Gie��en und Marburg (UKGM), I used the same setup and paradigm as in the previous study and additionally derived the trajectory of the COM from a weighted combination of certain body segments. The aim was to investigate phase locking of body sway in a group of patients suffering from Parkinson���s disease (PD) to find potential means for an early diagnosis of the illness. For this purpose, I recruited a group of PD patients, an age-matched control group, and a group of young healthy adults. Even though the sway amplitude of PD patients was significantly larger than that of both other groups, they phase-locked their COP and COM in a similar manner as the control groups. However, considering individual body segments, the shift in PLV distribution differed between groups. While young healthy adults, analogous to the participants in the second study, exhibited a shift towards exclusive phase locking of their hips as frequency of the stimulation increased, both PD patients and age-matched controls maintained a rather homogeneous phase locking across their body. This suggested increased body stiffness, although being an effect of age rather than disease. Overall, I concluded that patients of early-to-mid stage PD exhibit impaired motor control, reflected in their increased sway amplitude, but intact visuomotor processing, indicated by their ability to phase-lock the motion of their body to a visual drive. The fourth study, to which I contributed as second author, used experimental data collected from an additional visual condition in the course of the third study. This condition consisted of unpredictable back and forward motion of the simulated tunnel. Here, we investigated the velocity profiles of the COP and COM in response to the unpredictable visual motion and a baseline condition at which the tunnel remained static. We found PD patients to exhibit larger velocities of their COP and COM under both conditions when compared to the control groups. When examining the net increase that unpredictable motion had on the velocity of both parameters, we found a significantly higher increase in COP velocity for both PD patients and age-matched controls, but no increase in COM velocity in any of the groups. These results suggested that all groups successfully maintained their balance under unpredictable visual perturbations, but that PD patients and older adults required more effort to accomplish this task, as reflected by the increased velocity of their COP. Again, these results indicated an effect of age rather than disease on the observed postural responses. In summary, using innovative phase-locking techniques and simultaneously tracking multiple body sway parameters, I was able to provide novel insight into visuomotor control in humans. First, I overcame previous issues of inconsistent sway parameters in groups of participants; Second, I found phase-locking to be an essential feature of visuomotor processing, which also allowed me to empirically confirm previously established theories of postural control; Third, through studies in collaboration with the neurology department of the UKGM, I was able to uncover new aspects of visuomotor processing in Parkinson���s, contributing to a better understanding of the sensorimotor aspects of the disease., Im Rahmen dieser Arbeit, welche sich aus vier experimentellen Studien zusammensetzt, habe ich das Phasenverhalten des menschlichen visuomotorischen Systems w��hrend des aufrechten Stands in Antwort auf visuelle Bewegungsreize untersucht. Hierf��r verwendete ich verschiedene Varianten des ���Moving Room���-Paradigmas, welches ich in virtueller Realit��t (VR) simulierte. W��hrend sich das visuelle Umfeld meiner Proband:innen in unterschiedlicher Weise in anterior-posteriorer (a-p) Richtung bewegte, zeichnete ich die K��rperbewegungen auf, mit denen sie darauf reagierten. Das Halten unseres Gleichgewichts w��hrend des aufrechten Stands bedarf eines komplexen Zusammenspiels vieler voneinander abh��ngiger Prozesse. Die wichtigsten Sinne, welche uns hierf��r zur Verf��gung stehen, sind unser Sehsinn, die Signale unseres Vestibularorgans (Gleichgewichtssinn) sowie unsere Propriozeption. Hierbei wird unserem Sehsinn eine dominante Rolle zugeschrieben. Die Aufgabe unseres sensomotorischen Systems ist es, unseren K��rperschwerpunkt (engl.: Center Of Mass, COM) in eine situationsabh��ngige Gleichgewichtsposition zu bringen und dort zu halten. Da sich unsere Umwelt fortlaufend ver��ndert und unsere Sinneseindr��cke mit einem Grundrauschen versehen sind, schwankt unser K��rper typischerweise kontinuierlich um diesen Gleichgewichtspunkt. In Bezug auf diese Bewegung kann der menschliche K��rper als umgedrehtes (mehrgliedriges) Pendel aufgefasst werden. Nehmen wir durch St��rungen unseres visuellen Umfelds eine Bewegung unseres K��rpers wahr, so regulieren wir besagtes Schwanken, um der wahrgenommenen Bewegung entgegenzuwirken. Neurodegenerative Krankheiten wie Morbus Parkinson beeintr��chtigen diese Mechanismen und somit einen stabilen aufrechten Stand. Aus diesem Grund erm��glichen Untersuchungen von K��rperbewegungen in Antwort auf visuelle Bewegungsreize Einblicke in die visuomotorische Verarbeitung in gesunden und neuropathologischen Populationen. In meiner ersten Studie f��hrte ich eine neue Methode der Datenanalyse ein, mit welcher ich die Phasenkoh��renz der k��rperlichen Antworten auf oszillatorische visuelle Bewegungsreize zwischen einzelnen Versuchsdurchl��ufen (engl.: Trials) untersuchte (engl.: Inter-trial Phase Coherence, ITPC). Ich fand heraus, dass menschliche Proband:innen die Phase der Bewegung ihres Druckschwerpunktes auf dem Boden (engl.: Center Of Pressure, COP) an den periodischen visuellen Reiz koppelten. Der Stimulus bestand aus einer 3-D Punktewolke, welche in a-p Richtung oszillierte. Diese Kopplung trat sowohl bei einer niedrigen Frequenz der visuellen Oszillation von 0,2 Hz als auch bei einer hohen Frequenz von 1,5 Hz auf. Dabei ��berstiegen die von mir gefundenen Kopplungen an die Frequenz von 1,5 Hz das bisher angenommene Spektrum koh��renter Antworten auf eine periodische Schwingung der Umwelt (���moving room���) bei menschlichen K��rperschwankungen. Ich konnte zeigen, dass ITPC als neue Analysemethode im Kontext von K��rperbewegungen erlaubt, verl��ssliche Antworten bei fast allen Proband:innen nachzuweisen, wodurch es mir zus��tzlich gelang, das in diesem Forschungsfeld g��ngige Problem einer hohen Varianz der Antworten ��ber Proband:innen hinweg zu adressieren. Meine Ergebnisse legen nahe, dass Phasenkopplung einen wichtigen Bestandteil der menschlichen Gleichgewichtskontrolle darstellt. Im Rahmen der zweiten Studie entwickelte ich einen neuen, mobilen und kosteng��nstigen Versuchsaufbau, um visuelle Bewegungsreize in virtueller Realit��t zu pr��sentieren und dabei K��rperbewegungen aufzuzeichnen. Das neue Versuchs-Paradigma bestand hier aus einem virtuellen Tunnel, welcher sich in die a-p Richtung erstreckte. Im Experiment oszillierte der Tunnel mit einer von drei verschiedenen Frequenzen (0,2 Hz; 0,8 Hz; 1,2 Hz) vor und zur��ck. Da ein alleiniges Aufzeichnen des COP unzureichende Informationen dazu liefert, wie Bewegungen des COM realisiert werden, implementierte ich zus��tzlich ein mit dem VR-Setup synchronisiertes video-basiertes Bewegungsmesssystem, welches mir erlaubte, die Bewegungsantworten des gesamten K��rpers aufzuzeichnen. In dieser Studie verwendete ich eine leicht modifizierte Analyse zu Phasenkopplungen, den sogenannten ���Phase-Coupling Value��� (PLV). Mithilfe dieser Analyse fand ich heraus, dass Proband:innen nicht nur die Bewegung ihres COP, sondern auch die Bewegung einzelner K��rpersegmente an die Phase des visuellen Reizes koppelten. W��hrend diese Kopplung im Falle des COP bei allen pr��sentierten Frequenzen deutlich vorhanden war, zeigten die Antworten bestimmter K��rperteile mit steigender Frequenz unterschiedlich starke Kopplungen. Bei der niedrigsten Frequenz von 0,2 Hz koppelten die Proband:innen die Phase der Bewegung ihres nahezu ganzen K��rpers an den visuellen Reiz. Mit steigender Frequenz konzentrierte sich die Phasenkopplung auf den unteren Torso und die H��fte, w��hrend die Proband:innen bei der h��chsten Frequenz von 1,2 Hz beinahe nur noch ausschlie��lich ihre H��ftbewegung an die Phase des Reizes koppelten. Mein neuartiger Versuchsaufbau und die Analysemethode der Phasenkopplung erm��glichten es mir somit, frequenzabh��ngige Bewegungsmuster als Antworten auf die visuellen Reize nachzuweisen, wodurch ich bestehende Theorien empirisch belegen konnte. In der dritten Studie, welche als Kollaboration mit der Klinik f��r Neurologie des Unversit��tsklinikums Gie��en und Marburg (UKGM) durchgef��hrt wurde, verwendete ich denselben Versuchsaufbau und das gleiche Paradigma wie in der vorherigen Studie. Zus��tzlich errechnete ich in dieser Studie die Trajektorie des COM als gewichtete Kombination bestimmter K��rpersegmente. Ziel dieser Studie war es, die Phasenkopplung von K��rperschwingungen in einer Gruppe von Parkinson-Patient:innen zu untersuchen, um langfristig dabei mitzuwirken, Methoden f��r eine m��gliche Fr��herkennung der Krankheit zu entwickeln. Zu diesem Zweck untersuchte ich eine Gruppe von Patient:innen, eine Gruppe von gleichaltrigen, gesunden Kontrollproband:innen sowie eine Gruppe von jungen, gesunden Erwachsenen. Patient:innen zeigten eine deutlich erh��hte Amplitude ihrer K��rperbewegungen, koppelten jedoch die Phase ihres COP und auch ihres COM in gleicher Weise an den Stimulus wie beide Kontrollgruppen. Eine Untersuchung der Bewegung einzelner K��rperteile ergab hier jedoch, dass die in der zweiten Studie beschriebenen Bewegungsmuster in Antwort auf h��here Frequenzen in den einzelnen Gruppen unterschiedlich waren. W��hrend die junge Kontrollgruppe, analog zu den Proband:innen meiner zweiten Studie, ihr Bewegungsmuster an die h��heren Frequenzen anpasste bzw. wechselte, behielten sowohl die Patient:innen als auch die gleichaltrige Kontrollgruppe ein eher homogenes Bewegungsmuster bei, auch bei den beiden h��heren Frequenzen des visuellen Reizes. Dies lie�� mich auf eine erh��hte k��rperliche Steifigkeit schlie��en, welche jedoch ein Effekt des Alters und nicht der Krankheit zu sein scheint. Generell folgerte ich aus den Ergebnissen dieser Studie, dass Parkinson-Patient:innen in fr��hen Stadien der Krankheit zwar eine beeintr��chtigte Motorik zeigen, was sich in ihrer erh��hten Bewegungsamplitude widerspiegelt, sie jedoch keine Beeintr��chtigung in ihrer visuomotorischen Verarbeitung aufweisen, da sie prinzipiell noch immer in der Lage sind, die Phase ihrer K��rperbewegung an den visuellen Reiz zu koppeln. In der vierten Studie, in welcher ich als Zweitautor mitwirkte, nutzten wir Daten, welche wir in einem in der dritten Studie zus��tzlich verwendeten Paradigma erhoben hatten. Dieses Paradigma bestand aus einer kontinuierlichen, aber unvorhersehbaren a-p Bewegung des virtuellen Tunnels. Anhand dieser Daten untersuchten wir die Geschwindigkeitsprofile des COP und COM in Antwort auf die unvorhersehbare Bewegung sowie auf eine Kontrollbedingung, w��hrend welcher der Tunnel stillstand. Patient:innen zeigten im Vergleich zu den Kontrollgruppen erh��hte Geschwindigkeiten beider Parameter (COP und COM) unter beiden visuellen Bedingungen. Untersuchungen der Geschwindigkeitserh��hung beider Parameter als Effekt der unvorhersehbaren Bewegung des Tunnels ergaben einen Anstieg der mittleren Geschwindigkeit des COP bei Patient:innen und der gleichaltrigen Kontrollgruppe, jedoch keine Ver��nderung bei der jungen Kontrollgruppe. Die mittlere Geschwindigkeit des COM ��nderte sich bei keiner der Gruppen. Dies lie�� uns schlussfolgern, dass alle Gruppen bei unvorhersehbaren St��rungen ihres visuellen Umfelds in der Lage waren, ihr Gleichgewicht zu halten. Jedoch mussten Patient:innen und ��ltere Kontrollproband:innen hierf��r einen gesteigerten Aufwand betreiben, was sich in der erh��hten mittleren Geschwindigkeit ihres COP zeigte. Die Ergebnisse dieser Studie zeigten erneut einen Alters-, jedoch keinen Krankheits-Effekt. Zusammenfassend kann gesagt werden, dass meine neu in der Forschung zu Stand- und Gangverhalten eingef��hrte Analysemethode der Phasenkopplung sowie das gleichzeitige Aufzeichnen mehrerer Bewegungsparameter es mir erlaubten, neue Erkenntnisse ��ber die visuomotorische Verarbeitung beim Menschen zu gewinnen. Zum einen konnte ich g��ngige Probleme von inkonsistenten Bewegungsantworten innerhalb von untersuchten Personengruppen ��berwinden. Zum anderen konnte ich zeigen, dass Phasenkopplung ein essenzieller Bestandteil der visuomotorischen Verarbeitung zu sein scheint, was mir zus��tzlich erm��glichte, bestehende Theorien der posturalen Kontrolle beim Menschen empirisch zu best��tigen. Zus��tzlich konnte ich durch Studien in Kollaboration mit der Klinik f��r Neurologie des UKGM neue Aspekte der visuomotorischen Verarbeitung bei Morbus Parkinson untersuchen, wodurch ich zu einem besseren Verst��ndnis von sensomotorischen Aspekten der Krankheit beitragen konnte.
- Published
- 2022
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5. Phase Dynamics and Andreev Bound State Spectroscopy in Planar Josephson Junctions
- Author
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Haxell, Daniel
- Subjects
- Josephson junctions, Physics
- Abstract
Josephson junctions (JJs) are an integral component in quantum computing, low temperature electronics, and fundamental physics research. Hybrid superconductor-semiconductor JJs in two-dimensional materials have recently emerged as a paradigm for novel applications, harnessing gate-tunable supercurrents and strong spin-orbit coupling in a scalable platform. In this thesis, we present a detailed study of planar JJs in an InAs/Al heterostructure, when subjected to bias currents, microwave irradiation and in-plane magnetic fields. First, we investigate the stochastic dynamics of the superconducting-to-resistive transition of planar JJs and superconducting quantum interference devices (SQUIDs). We find that dynamics at low temperature are dominated by quantum fluctuations in the superconducting phase, which suppress the switching current to values less than half of the critical current. Phase dynamics are altered in a SQUID, such that the switching current of a JJ is more than doubled in a SQUID relative to being in isolation. Moderate damping leads to phase diffusion at higher temperatures, with a transition temperature that is tunable with gate voltages, magnetic fields and fluxes threading the SQUID. In a second experiment, we perform tunnelling spectroscopy measurements on a planar JJ irradiated by a microwave signal. Replicas in the conductance spectrum are shown to be consistent with photon assisted tunnelling (PAT) between the spectroscopic probe and Andreev bound states (ABSs) in the junction, rather than due to novel light-matter coupling in the form of Floquet-Andreev states. By tuning the tunnel-barrier transparency and Fermi energy with gate voltages, in addition to complementary current-phase relation (CPR) measurements, signatures unique to PAT are identified. Further, microwave-induced distortions to the CPR are shown to be consistent with a non-equilibrium occupation of ABSs, without invoking Floquet states. Finally, supercurrent and tunnelling spectroscopy measurements are performed on planar JJs in an in-plane magnetic field. Phase shifts in the CPR are reported relative to a phase reference, in devices with different superconducting lead sizes to investigate orbital effects. At low fields, we observe gate-dependent phase shifts of up to φ=0.5π, consistent with a Zeeman field coupling to highly-transmissive ABSs via Rashba spin-orbit interaction. A distinct phase shift at larger fields is concomitant with a switching current minimum and a closing and reopening of the superconducting gap. These signatures of a phase transition, which might resemble a topological transition, scale with the superconducting lead size indicating the crucial role of orbital effects in planar JJs. Our results give a new baseline understanding of planar JJs in InAs/Al heterostructures, and elucidate the interplay of Zeeman, spin-orbit and orbital effects in magnetic fields. This guides towards improved realisations of gate-tunable qubits, superconducting electronic.
- Published
- 2023
6. Strong coupling yields abrupt synchronization transitions in coupled oscillators
- Author
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Jorge L. Ocampo-Espindola, István Z. Kiss, Christian Bick, and Kyle C. A. Wedgwood
- Subjects
Physics ,QC1-999 - Abstract
Coupled oscillator networks often display transitions between qualitatively different phase-locked solutions—such as synchrony and rotating wave solutions—following perturbation or parameter variation. In the limit of weak coupling, these transitions can be understood in terms of commonly studied phase approximations. As the coupling strength increases, however, predicting the location and criticality of transition, whether continuous or discontinuous, from the phase dynamics may depend on the order of the phase approximation—or a phase description of the network dynamics that neglects amplitudes may become impossible altogether. Here we analyze synchronization transitions and their criticality systematically for varying coupling strength in theory and experiments with coupled electrochemical oscillators. First, we analyze bifurcations analysis of synchrony and splay states in an abstract phase model and discuss conditions under which synchronization transitions with different criticalities are possible. In particular, we show that such conditions can be understood by considering the relative contributions of higher harmonics to the phase dynamics. Second, we illustrate that transitions with different criticality indeed occur in experimental systems. Third, we highlight that the amplitude dynamics observed in the experiments can be captured in a numerical bifurcation analysis of delay-coupled oscillators. Our results showcase that reduced order phase models may miss important features that one would expect in the dynamics of the full system.
- Published
- 2024
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7. Self-heating effects and switching dynamics in graphene multiterminal Josephson junctions
- Author
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Máté Kedves, Tamás Pápai, Gergő Fülöp, Kenji Watanabe, Takashi Taniguchi, Péter Makk, and Szabolcs Csonka
- Subjects
Physics ,QC1-999 - Abstract
We experimentally investigate the electronic transport properties of a three-terminal graphene Josephson junction. We find that self-heating effects strongly influence the behavior of this multiterminal Josephson junction (MTJJ) system. We show that existing simulation methods based on resistively and capacitively shunted Josephson junction networks can be significantly improved by taking into account these heating effects. We also investigate the phase dynamics in our MTJJ by measuring its switching current distribution and find correlated switching events in different junctions. We show that the switching dynamics is governed by phase diffusion at low temperatures. Furthermore, we find that self-heating introduces additional damping that results in overdamped I−V characteristics when normal and supercurrents coexist in the device.
- Published
- 2024
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8. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.
- Author
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Junier, Ivan, Ghobadpour, Elham, Espeli, Olivier, and Everaers, Ralf
- Subjects
BACTERIAL DNA ,BASE pairs ,PHYSICS ,BIOLOGISTS ,CHROMOSOMES ,DNA replication - Abstract
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first Physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to aminimum and we provide some explanatory background material for the two communities. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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9. Cathodes pinpoints for the next generation of energy storage devices: the LiFePO4 case study
- Author
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Beatriz Arouca Maia, Beatriz Moura Gomes, Antonio Nuno Guerreiro, Raquel Miriam Santos, and Maria Helena Braga
- Subjects
cathodes ,energy ,batteries ,LFP ,LPSCl ,solid electrolyte ,Materials of engineering and construction. Mechanics of materials ,TA401-492 ,Physics ,QC1-999 - Abstract
There are still essential aspects regarding cathodes requiring a comprehensive understanding. These include identifying the underlying phenomena that prevent reaching the theoretical capacity, explaining irreversible losses, and determining the cut-off potentials at which batteries should be cycled. We address these inquiries by investigating the cell’s capacity and phase dynamics by looking into the transport properties of electrons. This approach underlines the crucial role of electrons in influencing battery performance, similar to their significance in other materials and devices such as transistors, thermoelectrics, or superconductors. We use lithium iron phosphate LFP as a case study to demonstrate that understanding the electrochemical cycling behavior of a battery cell, particularly a Li//LFP configuration, hinges on factors like the total local potentials used to calculate chemical potentials, electronic density of states (DOS), and charge carrier densities. Our findings reveal that the stable plateau potential difference is 3.42 V, with maximum charge and minimum discharge potentials at 4.12 V and 2.80 V, respectively. The study illustrates the dynamic formation of metastable phases at a plateau voltage exceeding 3.52 V. Moreover, we establish that determining the working chemical potentials of elements like Li and Al can be achieved by combining their workfunction and DOS analysis. Additionally, we shed light on the role of carbon black beyond conductivity enhancement. Through Density functional theory (DFT) calculations and experimental methods involving scanning Kelvin probe (SKP) and electrochemical analysis, we comprehensively examine various materials, including Li, C, Al, Cu, LFP, FePO _4 , Li _0.25 FePO _4 , polyvinylidene fluoride, and Li _6 PS _5 Cl. The insights derived from this study, which solely rely on electrical properties, have broad applicability to all cathodes and batteries. They provide valuable information for efficiently selecting optimal formulations and conditions for cycling batteries.
- Published
- 2024
- Full Text
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10. Phase diagram of one-dimensional driven-dissipative exciton-polariton condensates
- Author
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Francesco Vercesi, Quentin Fontaine, Sylvain Ravets, Jacqueline Bloch, Maxime Richard, Léonie Canet, and Anna Minguzzi
- Subjects
Physics ,QC1-999 - Abstract
We consider a one-dimensional driven-dissipative exciton-polariton condensate under incoherent pump, described by the stochastic generalized Gross-Pitaevskii equation. It was shown that the condensate phase dynamics maps under some assumptions to the Kardar-Parisi-Zhang (KPZ) equation, and the temporal coherence of the condensate follows a stretched exponential decay characterized by KPZ universal exponents. In this paper, we determine the main mechanisms, which lead to the departure from the KPZ phase, and identify three possible other regimes: (i) a soliton-patterned regime at large interactions and weak noise, populated by localized structures analog to dark solitons; (ii) a vortex-disordered regime at high noise and weak interactions, dominated by point-like phase defects in space-time; and (iii) a defect-free reservoir-textured regime where the adiabatic approximation breaks down. We characterize each regime by the space-time maps, the first-order correlations, the momentum distribution and the density of topological defects. We thus obtain the phase diagram at varying noise, pump intensity and interaction strength. Our predictions are amenable to observation in state-of-art experiments with exciton-polaritons.
- Published
- 2023
- Full Text
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11. Excitation polarization-independent photo-induced restoration of inversion symmetry in Td-WTe2
- Author
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Ryota Aoki, Kento Uchida, and Koichiro Tanaka
- Subjects
Physics ,QC1-999 - Abstract
Td-WTe2 is a topologically nontrivial material and exhibits a variety of physical properties, such as giant unsaturated magnetoresistance and the unconventional thermoelectric effect, due to its topological nature. It is also known to exhibit ultrafast topological phase transitions that restore its inversion symmetry by intense terahertz and mid-infrared pulses, and these properties demonstrate the possibility of ultrafast control of devices based on topological properties. Recently, a novel photo-induced topological phase transition by using polarization-controlled infrared excitation has been proposed, which is expected to control the material topology by rearranging the atomic orbitals near the Weyl point. To examine this topological phase transition, we experimentally studied the excitation-polarization dependence of the infrared-induced phase dynamics in a thin-layer of Td-WTe2. Time-resolved second harmonic generation (SHG) measurements showed that SHG intensity decreases after the infrared pump regardless of the polarization. Polarization-resolved infrared pump–probe measurements indicated that the polarization-selected excited state relaxes quite rapidly (i.e., within 10–40 fs). Considering these experimental results, we conclude that it is difficult to control the photo-induced phase transition through orbital-selective excitation owing to the rapid loss of carrier distribution created by polarization-selective excitation in thin-layer Td-WTe2 under our experimental condition. These results indicate that the suppression of the electron scattering process is crucial for experimentally realizing the photo-induced phase transition based on the polarization selection rule of the materials.
- Published
- 2022
- Full Text
- View/download PDF
12. Kardar-Parisi-Zhang universality in discrete two-dimensional driven-dissipative exciton polariton condensates
- Author
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Konstantinos Deligiannis, Quentin Fontaine, Davide Squizzato, Maxime Richard, Sylvain Ravets, Jacqueline Bloch, Anna Minguzzi, and Léonie Canet
- Subjects
Physics ,QC1-999 - Abstract
The statistics of the fluctuations of quantum many-body systems are highly revealing of their nature. In driven-dissipative systems displaying macroscopic quantum coherence, as exciton polariton condensates under incoherent pumping, the phase dynamics can be mapped to the stochastic Kardar-Parisi-Zhang (KPZ) equation. However, it was argued theoretically that in two dimensions the KPZ regime may be hindered by the presence of vortices, and a nonequilibrium Berezinskii-Kosterlitz-Thouless behavior was reported close to the condensation threshold. We demonstrate here that, when a discretized two-dimensional (2D) polariton system is considered, universal KPZ properties can emerge. We support our analysis by extensive numerical simulations of the discrete stochastic generalized Gross-Pitaevskii equation. We show that the first-order correlation function of the condensate exhibits stretched exponential behaviors in space and time with critical exponents characteristic of the 2D KPZ universality class and find that the related scaling function accurately matches the KPZ theoretical one, stemming from functional renormalization group. We also obtain the distribution of the phase fluctuations and find that it is non-Gaussian, as expected for a KPZ stochastic process.
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- 2022
- Full Text
- View/download PDF
13. Integrated Autopilot Guidance Based on Zero-Effort-Miss Formulation for Tail-Controlled Missiles
- Author
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Hyeong-Geun Kim and Jongho Shin
- Subjects
integrated guidance and control ,tail-controlled missile ,non-minimum phase ,zero-effort-miss ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
This paper presents a control structure integrating guidance and control loops for tail-controlled missile systems. Motivated by the fact that common tail-controlled missiles involve non-minimum phase dynamics, the proposed controller is designed to prevent the internal dynamics from diverging, as well as achieving homing against the intended target. To minimize the miss distance at the end of homing, we derive a formulation of a zero-effort-miss using engagement kinematics that contain the rotating dynamics of the missile, which is different from existing approaches. Subsequently, to nullify the zero-effort-miss, a nonlinear controller is designed based on the Lyapunov stability theory. Since the derived controller has a similar structure to the conventional three-loop topology that has been utilized for various tail-controlled flight systems, it is expected that the proposed method can be applied to the actual system from a practical point of view. Numerical simulation results also show that the proposed method achieves target interception while possessing stable internal dynamics.
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- 2022
- Full Text
- View/download PDF
14. Reports Summarize Fluids Physics Findings from Tsinghua University (Numerical Study of Double Emulsion Generation In a Flow-focusing Microchannel By Multiple-relaxation-time Lattice Boltzmann Method).
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LATTICE Boltzmann methods ,PHYSICS ,EMULSIONS ,FLUIDS - Abstract
A recent study conducted by researchers at Tsinghua University in Beijing, China, explores the formation mechanism of double emulsions in microchannels using microfluidic technology. The researchers developed a lattice Boltzmann model to simulate the complex multiphase flow behavior in microchannels and investigated the influence of various factors such as flow rate, viscosity ratio, interfacial tension ratio, and orifice section size on the formation of double emulsions. The study identified two distinct droplet formation mechanisms and assessed the effect of interfacial tension combinations and orifice width on the emulsion mechanics. The findings contribute to a deeper understanding of double emulsion mechanics and provide a versatile platform for future research in this field. [Extracted from the article]
- Published
- 2024
15. Delta- and theta-band cortical tracking and phase-amplitude coupling to sung speech by infants
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Helen Olawole-Scott, Áine Ní Choisdealbha, Sheila Flanagan, Natasha Mead, Christina Grey, Adam Attaheri, Samuel Gibbon, Giovanni M. Di Liberto, Sinead Rocha, Isabel Williams, Usha Goswami, Panagiotis Boutris, Perrine Brusini, Attaheri, Adam [0000-0002-5158-7329], Mead, Natasha [0000-0003-0737-8738], Flanagan, Sheila [0000-0003-0119-4196], Goswami, Usha [0000-0001-7858-2336], and Apollo - University of Cambridge Repository
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Cognitive Neuroscience ,Speech recognition ,Neurosciences. Biological psychiatry. Neuropsychiatry ,Electroencephalography ,Tracking (particle physics) ,050105 experimental psychology ,03 medical and health sciences ,0302 clinical medicine ,Modulation (music) ,medicine ,Humans ,0501 psychology and cognitive sciences ,Neural oscillations ,Longitudinal Studies ,EEG ,Theta Rhythm ,030304 developmental biology ,Language ,Physics ,Auditory Cortex ,0303 health sciences ,medicine.diagnostic_test ,Quantitative Biology::Neurons and Cognition ,05 social sciences ,Brain ,Infant ,Neurophysiology ,Speech processing ,United Kingdom ,Coupling (electronics) ,Amplitude ,Neurology ,Acoustic Stimulation ,Delta Rhythm ,Speech Perception ,TRF ,030217 neurology & neurosurgery ,Decoding methods ,Energy (signal processing) ,Envelope (motion) ,RC321-571 - Abstract
The amplitude envelope of speech carries crucial low-frequency acoustic information that assists linguistic decoding at multiple time scales. Neurophysiological signals are known to track the amplitude envelope of adult-directed speech (ADS), particularly in the theta-band. Acoustic analysis of infant-directed speech (IDS) has revealed significantly greater modulation energy than ADS in an amplitude-modulation (AM) band centered on ∼2 Hz. Accordingly, cortical tracking of IDS by delta-band neural signals may be key to language acquisition. Speech also contains acoustic information within its higher-frequency bands (beta, gamma). Adult EEG and MEG studies reveal an oscillatory hierarchy, whereby low-frequency (delta, theta) neural phase dynamics temporally organize the amplitude of high-frequency signals (phase amplitude coupling, PAC). Whilst consensus is growing around the role of PAC in the matured adult brain, its role in the development of speech processing is unexplored.Here, we examined the presence and maturation of low-frequency (Graphical abstractHighlightsLongitudinal EEG study in which 4, 7- & 11-month infants listened to nursery rhymesWe demonstrate cortical speech tracking via delta & theta neural signals (mTRF)Periodogram (PSD) analysis revealed stimulus related delta & theta PSD peaksDelta and theta driven phase amplitude coupling (PAC) was found at all agesGamma frequency amplitudes displayed stronger PAC to low frequency phases than beta
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- 2022
16. Handbook of Radio and Optical Networks Convergence
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Tetsuya Kawanishi and Tetsuya Kawanishi
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- Physics, Optics, Telecommunication
- Abstract
This handbook provides comprehensive knowledge on device and system technologies for seamlessly integrated networks of various types of transmission media such as optical fibers and millimeter and THz waves to offer super high-speed data link service everywhere. The seamless integration of the knowledge of radio and optical technologies is needed to construct wired and wireless seamless networks. High-frequency bands such as millimeter-wave and THz-wave bands where super wideband spectra are available can offer high-speed data transmission and high-resolution sensing. However, the expected coverage is limited due to large wave propagation loss. Thus, convergence of radio and optical links is indispensable to construct worldwide networks. The radio and optical technologies share the same physics and are closely related to each other but have been developed independently. Therefore, there is a big gap between these two fields. Bridging the two fields, this handbook is also intended as a common platform to design integrated networks consisting of wireless and wired links. Full coverage of wireless and wired convergence fields ranging from basics of device and transmission media to applications allows the reader to efficiently access all the important references in this single handbook. Further, it also showcases state-of-the-art technology and cases of its use.
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- 2024
17. Handbook of Multiphase Flow Science and Technology
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Guan Heng Yeoh, Jyeshtharaj B. Joshi, Guan Heng Yeoh, and Jyeshtharaj B. Joshi
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- Fluid mechanics, Physics, Thermodynamics, Heat engineering, Heat transfer, Mass transfer, Engineering mathematics, Engineering—Data processing, Soft condensed matter, Mechanics
- Abstract
This Handbook provides readers with the current cutting edge of multiphase flow technology. It reviews the rapid development of multiphase flow technology, demonstrates the latest development of the technology and showcase the very latest applications. It provides readers with comprehensive updated reference information covering theory, modelling and numerical methods, design and measurement, and new applications in multiphase flow systems.The Handbook consists of three parts or volumes:1. Theory: describes the fundamentals including the concepts and definitions of multiphase flows. Classifications of multiphase flows. Basic understanding of different length scales involved – micro/nano, meso and macro. Treatment of such flows by different solution frameworks.2. Modelling and Measurement: covers both classical and state-of the-art measurement and modelling approaches to resolve different classifications of multiphase flows. 3. Applications: highlights the very latest applications of measurement and modelling approaches in tackling different classification of multiphase flows in a variety of natural, biological and industrial systems and different length scales.
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- 2023
18. Encyclopedia of Chemical Physics and Physical Chemistry : Volume 2: Methods
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John H. Moore, Nicholas D. Spencer, John H. Moore, and Nicholas D. Spencer
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- Physics, Chemistry, Physical and theoretical--Encyclopedias, Physics--Encyclopedias, Chemistry, Physical and theoretical
- Abstract
The Encyclopedia of Physical Chemistry and Chemical Physics introduces possibly unfamiliar areas, explains important experimental and computational techniques, and describes modern endeavors. The encyclopedia quickly provides the basics, defines the scope of each subdiscipline, and indicates where to go for a more complete and detailed explanation. Particular attention has been paid to symbols and abbreviations to make this a user-friendly encyclopedia. Care has been taken to ensure that the reading level is suitable for the trained chemist or physicist. The encyclopedia is divided in three major sections: FUNDAMENTALS: the mechanics of atoms and molecules and their interactions, the macroscopic and statistical description of systems at equilibrium, and the basic ways of treating reacting systems. The contributions in this section assume a somewhat less sophisticated audience than the two subsequent sections. At least a portion of each article inevitably covers material that might also be found in a modern, undergraduate physical chemistry text. METHODS: the instrumentation and fundamental theory employed in the major spectroscopic techniques, the experimental means for characterizing materials, the instrumentation and basic theory employed in the study of chemical kinetics, and the computational techniques used to predict the static and dynamic properties of materials. APPLICATIONS: specific topics of current interest and intensive research.For the practicing physicist or chemist, this encyclopedia is the place to start when confronted with a new problem or when the techniques of an unfamiliar area might be exploited. For a graduate student in chemistry or physics, the encyclopedia gives a synopsis of the basics and an overview of the range of activities in which physical principles are applied to chemical problems. It will lead any of these groups to the salient points of a new field as rapidly as possible and gives pointers as to where to read about the topic in more detail.
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- 2023
19. Patterns and Interfaces in Dissipative Dynamics : Revised and Extended, Now Also Covering Patterns of Active Matter
- Author
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Len Pismen and Len Pismen
- Subjects
- System theory, Pattern formation (Biology), Biophysics, Physics, Chemometrics, Dynamical systems
- Abstract
Spontaneous pattern formation in nonlinear dissipative systems far from equilibrium is a paradigmatic case of emergent behaviour associated with complex systems. It is encountered in a great variety of settings, both in nature and technology, and has numerous applications ranging from nonlinear optics through solid and fluid mechanics, physical chemistry and chemical engineering to biology.This book is a first-hand account by one of the leading players in this field, which gives in-depth descriptions of analytical methods elucidating the complex evolution of nonlinear dissipative systems, and brings the reader to the forefront of current research.Since the publication of the first edition, applications of the theory of nonlinear dynamics have been substantially extended to the novel area of active systems, largely motivated by problems of biophysics and biomorphic technology. These problems typically involve media with internal orientation. This new edition incorporates a chapter discussing dynamics of liquids and soft solids with internal orientation, including special features of their instabilities and motion of topological defects, which form the background for various applications to the motion of cells, tissues, and activated soft materials. The contents of the first edition have also been substantially reworked, improving graphics, emphasizing more complex secondary instabilities, and dropping some material pertaining to dynamical systems.This book caters for graduate students and young researchers from many pertinent areas including applied mathematics, physical chemistry, chemical engineering and biophysics, as well as the seasoned scientist in search of a modern source of reference.
- Published
- 2023
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