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1
Kitazawa, Soichiro, Maho Yagi-Utsumi, Koichi Kato, and Ryo Kitahara. "Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin." Molecules 22, no. 9 (August 28, 2017): 1414. http://dx.doi.org/10.3390/molecules22091414.
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Ashwin, S. S., Tadasu Nozaki, Kazuhiro Maeshima, and Masaki Sasai. "Organization of fast and slow chromatin revealed by single-nucleosome dynamics." Proceedings of the National Academy of Sciences 116, no. 40 (September 16, 2019): 19939–44. http://dx.doi.org/10.1073/pnas.1907342116.
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Understanding chromatin organization and dynamics is important, since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bimodal nature of the mean square displacement distribution of nucleosomes allows for a natural categorization of the nucleosomes as fast and slow. Analyses of the nucleosome–nucleosome correlation functions within these categories along with the density of vibrational modes show that the nucleosomes form dynamically correlated fluid regions (i.e., dynamic domains of fast and slow nucleosomes). Perturbed nucleosome dynamics by global histone acetylation or cohesin inactivation indicate that nucleosome–nucleosome interactions along with tethering of chromatin chains organize nucleosomes into fast and slow dynamic domains. A simple polymer model is introduced, which shows the consistency of this dynamic domain picture. Statistical analyses of single-nucleosome movement provide rich information on how chromatin is dynamically organized in a fluid manner in living cells.
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Williams, R. E., and S. M. Horvath. "Recovery from dynamic exercise." American Journal of Physiology-Heart and Circulatory Physiology 268, no. 6 (June 1, 1995): H2311—H2320. http://dx.doi.org/10.1152/ajpheart.1995.268.6.h2311.
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Minimal information is available on the basic interactions within the metabolic and cardiovascular systems during recovery from exercise. Nine men participated in three experiments: one control and two cost-equivalent (52 liters O2) exercise tests of 30 (EX30) and 45 (EX45) min. Exercise intensities were adjusted accordingly. During recovery, all parameters reestablished baseline levels within 10 min, except for heart rate (30 min). Correlations for each parameter for EX30 and EX45 were obtained by evaluating each subject's exercise cost and recovery "payback." A split, two-factor analysis of variance was run separately on the "fast" (minutes 1-7) and "slow" (minutes 10-60) phases of recovery to determine if the time course of recovery was related to exercise intensity. It was concluded that for a work cost of approximately 300 kcal, 1) the slow phase of recovery was unaffected by the exercise intensity, 2) the fast phase of cardiovascular recovery was unaffected by exercise intensity while minute ventilation and O2 and CO2 uptake were affected, and 3) cardiac output and the ventilatory equivalents for O2 and CO2 correlated well between work cost and recovery payback.
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Garbett, Damien, and Anthony Bretscher. "PDZ interactions regulate rapid turnover of the scaffolding protein EBP50 in microvilli." Journal of Cell Biology 198, no. 2 (July 16, 2012): 195–203. http://dx.doi.org/10.1083/jcb.201204008.
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Scaffolding proteins containing PDZ (postsynaptic density 95/discs large/zonula occludens-1) domains are believed to provide relatively stable linkages between components of macromolecular complexes and in some cases to bridge to the actin cytoskeleton. The microvillar scaffolding protein EBP50 (ERM-binding phosphoprotein of 50 kD), consisting of two PDZ domains and an ezrin-binding site, retains specific proteins in microvilli and is necessary for microvillar biogenesis. Our analysis of the dynamics of microvillar proteins in vivo indicated that ezrin and microvillar membrane proteins had dynamics consistent with actin treadmilling and microvillar lifetimes. However, EBP50 was highly dynamic, turning over within seconds. EBP50 turnover was reduced by mutations that inactivate its PDZ domains and was enhanced by protein kinase C phosphorylation. Using a novel in vitro photoactivation fluorescence assay, the EBP50–ezrin interaction was shown to have a slow off-rate that was dramatically enhanced in a PDZ-regulated manner by addition of cell extract to near in vivo levels. Thus, the linking of relatively stable microvillar components can be mediated by surprisingly dynamic EBP50, a finding that may have important ramifications for other scaffolding proteins.
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Jitapunkul, Kulpavee, Pisanu Toochinda, and Luckhana Lawtrakul. "Molecular Dynamic Simulation Analysis on the Inclusion Complexation of Plumbagin with β-Cyclodextrin Derivatives in Aqueous Solution." Molecules 26, no. 22 (November 10, 2021): 6784. http://dx.doi.org/10.3390/molecules26226784.
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Stable encapsulation of medically active compounds can lead to longer storage life and facilitate the slow-release mechanism. In this work, the dynamic and molecular interactions between plumbagin molecule with β-cyclodextrin (BCD) and its two derivatives, which are dimethyl-β-cyclodextrin (MBCD), and 2-O-monohydroxypropyl-β-cyclodextrin (HPBCD) were investigated. Molecular dynamics simulations (MD) with GLYCAM-06 and AMBER force fields were used to simulate the inclusion complex systems under storage temperature (4 °C) in an aqueous solution. The simulation results suggested that HPBCD is the best encapsulation agent to produce stable host–guest binding with plumbagin. Moreover, the observation of the plumbagin dynamic inside the binding cavity revealed that it tends to orient the methyl group toward the wider rim of HPBCD. Therefore, HPBCD is a decent candidate for the preservation of plumbagin with a promising longer storage life and presents the opportunity to facilitate the slow-release mechanism.
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Chen, Xue-Qing, and Lei Tong. "Multiscale flow characteristics of droplet spreading with microgravity conditions." Canadian Journal of Physics 97, no. 8 (August 2019): 869–74. http://dx.doi.org/10.1139/cjp-2018-0474.
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In this paper, mesoscopic lattice–Boltzmann method (LBM) and microscopic molecular dynamics simulation method were used to simulate droplet dynamic wetting under microgravity. In terms of LBM, the wetting process of a droplet on a solid wall surface was simulated by introducing the fluid–fluid and solid–fluid interactions. In terms of molecular dynamics simulation, the spreading process of water on gold surface was simulated. Calculation results showed that two kinds of calculation methods were based on the microscopic molecular theory or mesoscopic kinetics theory, and such models could effectively overcome the contact line paradox issue, which results from the macro-continuum assumption and non-slip boundary condition assumption. The spreading exhibits two-stage behavior: fast spreading and slow spreading stages. For the two simulation methods, the ratio of fast spreading stage duration to slow spreading duration, spreading capacity (equilibrium contact radius/initial radius), and the spreading exponent of the rapid stage were very close. However, the predictive spreading index of the slow spreading stage was different, owing to the different spreading mechanisms between meso- and nanoscales.
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Yin, Chunyue, and Lilianna Solnica-Krezel. "Convergence and extension movements affect dynamic notochord-somite interactions essential for zebrafish slow muscle morphogenesis." Developmental Dynamics 236, no. 10 (2007): 2742–56. http://dx.doi.org/10.1002/dvdy.21295.
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Grossman-Haham, Iris, Gabriel Rosenblum, Trishool Namani, and Hagen Hofmann. "Slow domain reconfiguration causes power-law kinetics in a two-state enzyme." Proceedings of the National Academy of Sciences 115, no. 3 (January 3, 2018): 513–18. http://dx.doi.org/10.1073/pnas.1714401115.
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Protein dynamics are typically captured well by rate equations that predict exponential decays for two-state reactions. Here, we describe a remarkable exception. The electron-transfer enzyme quiescin sulfhydryl oxidase (QSOX), a natural fusion of two functionally distinct domains, switches between open- and closed-domain arrangements with apparent power-law kinetics. Using single-molecule FRET experiments on time scales from nanoseconds to milliseconds, we show that the unusual open-close kinetics results from slow sampling of an ensemble of disordered domain orientations. While substrate accelerates the kinetics, thus suggesting a substrate-induced switch to an alternative free energy landscape of the enzyme, the power-law behavior is also preserved upon electron load. Our results show that the slow sampling of open conformers is caused by a variety of interdomain interactions that imply a rugged free energy landscape, thus providing a generic mechanism for dynamic disorder in multidomain enzymes.
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PEIRSON, WILLIAM L., and ANDREW W. GARCIA. "On the wind-induced growth of slow water waves of finite steepness." Journal of Fluid Mechanics 608 (July 11, 2008): 243–74. http://dx.doi.org/10.1017/s002211200800205x.
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Determining characteristic growth rates for water waves travelling more slowly than the wind has continued to be a key unresolved problem of air–sea interaction for over half a century. Analysis of previously reported and recently acquired laboratory wave data shows a systematic decline in normalized wave growth with increasing mean wave steepness that has not previously been identified. The normalized growth dynamic range is comparable with previously observed scatter amongst other laboratory data gathered in the slow wave range. Strong normalized growth rates are observed at low wave steepnesses, implying an efficient wave-coherent tangential stress contribution. Data obtained during this study show quantitative agreement with the predictions of others of the interactions between short wind waves and the longer lower-frequency waves. Measured normalized wave growth rates are consistent with numerically predicted growth due to wave drag augmented by significant wave-coherent tangential stress.
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Yen, Shih-Hsiang, Pei-Chong Tang, Yuan-Chiu Lin, and Chyi-Yeu Lin. "A Sensorless and Low-Gain Brushless DC Motor Controller Using a Simplified Dynamic Force Compensator for Robot Arm Application." Sensors 19, no. 14 (July 18, 2019): 3171. http://dx.doi.org/10.3390/s19143171.
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Robot arms used for service applications require safe human–machine interactions; therefore, the control gain of such robot arms must be minimized to limit the force output during operation, which slows the response of the control system. To improve cost efficiency, low-resolution sensors can be used to reduce cost because the robot arms do not require high precision of position sensing. However, low-resolution sensors slow the response of closed-loop control systems, leading to low accuracy. Focusing on safety and cost reduction, this study proposed a low-gain, sensorless Brushless DC motor control architecture, which performed position and torque control using only Hall-effect sensors and a current sensor. Low-pass filters were added in servo controllers to solve the sensing problems of undersampling and noise. To improve the control system’s excessively slow response, we added a dynamic force compensator in the current controllers, simplified the system model, and conducted tuning experiments to expedite the calculation of dynamic force. These approaches achieved real-time current compensation, and accelerated control response and accuracy. Finally, a seven-axis robot arm was used in our experiments and analyses to verify the effectiveness of the simplified dynamic force compensators. Specifically, these experiments examined whether the sensorless drivers and compensators could achieve the required response and accuracy while reducing the control system’s cost.
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Aebischer, Kathrin, Lea Marie Becker, Paul Schanda, and Matthias Ernst. "Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR." Magnetic Resonance 5, no. 1 (June 11, 2024): 69–86. http://dx.doi.org/10.5194/mr-5-69-2024.
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Abstract. Dynamic processes in molecules can occur on a wide range of timescales, and it is important to understand which timescales of motion contribute to different parameters used in dynamics measurements. For spin relaxation, this can easily be understood from the sampling frequencies of the spectral-density function by different relaxation-rate constants. In addition to data from relaxation measurements, determining dynamically averaged anisotropic interactions in magic-angle spinning (MAS) solid-state NMR allows for better quantification of the amplitude of molecular motion. For partially averaged anisotropic interactions, the relevant timescales of motion are not so clearly defined. Whether the averaging depends on the experimental methods (e.g., pulse sequences) or conditions (e.g., MAS frequency, magnitude of anisotropic interaction, radio-frequency field amplitudes) is not fully understood. To investigate these questions, we performed numerical simulations of dynamic systems based on the stochastic Liouville equation using several experiments for recoupling the dipolar coupling, chemical-shift anisotropy or quadrupolar coupling. As described in the literature, the transition between slow motion, where parameters characterizing the anisotropic interaction are not averaged, and fast motion, where the tensors are averaged leading to a scaled anisotropic quantity, occurs over a window of motional rate constants that depends mainly on the strength of the interaction. This transition region can span 2 orders of magnitude in exchange-rate constants (typically in the microsecond range) but depends only marginally on the employed recoupling scheme or sample spinning frequency. The transition region often coincides with a fast relaxation of coherences, making precise quantitative measurements difficult. Residual couplings in off-magic-angle experiments, however, average over longer timescales of motion. While in principle one may gain information on the timescales of motion from the transition area, extracting such information is hampered by low signal-to-noise ratio in experimental spectra due to fast relaxation that occurs in the same region.
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Abdelghafor, Z., G. Taimuri, P. Kujala, Y. Wang, and S. Hirdaris. "Numerical studies on tugboat performance during pushing operations." IOP Conference Series: Materials Science and Engineering 1288, no. 1 (August 1, 2023): 012003. http://dx.doi.org/10.1088/1757-899x/1288/1/012003.
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Abstract This paper introduces a RANS CFD methodology for the evaluation of tugboat dynamics during pushing operations. Two- and three- dimensional methods that respectively utilize “Dynamic Fluid Body Interactions - (DFBI)” and “Tug Force Equilibrium kinematics-(TFE)” are assessed and compared with the aim to better understand the influence of fluid modelling on ship dynamics. For the DFBI method, an unsteady RANS solver comprising of a dynamic fluid body interaction module and a contact mechanics coupling algorithm are used to predict the forces between a tugboat and an assisted ship. For the TFE method, a steady RANS method is applied and contact actions are calculated as a sum of the hydrodynamic forces on the hull and the propeller. Whereas DFBI accounts for the time variation of the contact forces, the TFE is more rapid and could be used to derive operational decision support criteria. To demonstrate the latter the TFE method is used to derive the pushing forces based on a set of 16 numerical simulations. It is concluded that irrespective of the model used the tugboat speed and orientation may amplify the pushing forces. This effect could be prominent, especially at slow speeds for which the sway force acts in opposite direction to the tug.
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Dell'Orco, Daniele, and Karl-Wilhelm Koch. "A dynamic scaffolding mechanism for rhodopsin and transducin interaction in vertebrate vision." Biochemical Journal 440, no. 2 (November 14, 2011): 263–71. http://dx.doi.org/10.1042/bj20110871.
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The early steps in vertebrate vision require fast interactions between Rh (rhodopsin) and Gt (transducin), which are classically described by a collisional coupling mechanism driven by the free diffusion of monomeric proteins on the disc membranes of rod and cone cells. Recent findings, however, point to a very low mobility for Rh and support a substantially different supramolecular organization. Moreover, Rh–Gt interactions seem to possibly occur even prior to light stimuli, which is also difficult to reconcile with the classical scenario. We investigated the kinetics of interaction between native Rh and Gt in different conditions by surface plasmon resonance and analysed the results in the general physiological context by employing a holistic systems modelling approach. The results from the present study point to a mechanism that is intermediate between pure collisional coupling and physical scaffolding. Such a ‘dynamic scaffolding’, in which prevalently dimeric Rh and Gt interact in the dark by forming transient complexes (~25% of Gt is precoupled to Rh), does not slow down the phototransduction cascade, but is compatible with the observed photoresponses on a broad scale of light stimuli. We conclude that Rh molecules and Rh–Gt complexes can both absorb photons and trigger the visual cascade.
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Shahravi, Morteza, and Milad Azimi. "A Hybrid Scheme of Synthesized Sliding Mode/Strain Rate Feedback Control Design for Flexible Spacecraft Attitude Maneuver Using Time Scale Decomposition." International Journal of Structural Stability and Dynamics 16, no. 02 (February 25, 2016): 1450101. http://dx.doi.org/10.1142/s0219455414501016.
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Presented herein is a new control approach for large angle attitude maneuver of flexible spacecraft. The singular perturbation theory (SPT) provides a useful tool for two time rate scale separation (mapping) of rigid and flexible body dynamics. The resulting slow and fast subsystems, enabling the use of two control approach for attitude (Modified Sliding Mode) and vibration Strain Rate Feedback (SRF) control of flexible spacecraft, respectively. An attractive feature of the present control approach is that the global stability of the entire system has been guaranteed while the controllers accomplished their tasks in coupled rigid/flexible dynamic domain without parasitic parameter interactions. Numerical simulations show the effectiveness of the present approach.
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Manna, Balaram, Pramodh Bharati, Subrata Paul, Animesh Mahata, Subhabrata Mondal, Supriya Mukherjee, Amit Kumar Dutta, and Banamali Roy. "Results and Discussion of Dengue Model with Temperature Effects in Interval Environment." SciNexuses 1 (September 3, 2024): 75–81. http://dx.doi.org/10.61356/j.scin.2024.1372.
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We have investigated a dengue model with temperature effects under interval uncertainty in this work. This study observed the Aedes aegypti temperature-dependent entomological parameters that affect dengue illness transmission dynamics in Taiwan's subtropical zone. A vector-host transmission model was used to examine how temperature fluctuations influence the development of pre-adult mosquitoes, their egg-laying rates, adult mortality, and the incubation rate of viruses within them. This study showed that although estimations of entomological parameters were positively correlated with slow temperature rises, no such correlation was detected with mosquito mortality or maturation rates, underscoring the slow rate of maturation of pre-adult mosquitoes. The findings suggest that the dynamic modeling of vector-host interactions is significantly influenced by temperature. Additionally, our modeling indicates that a temperature range of about 32°C is ideal for dengue transmission. In the future, control measure modeling and cost-effectiveness assessments may benefit from these insights.
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Neverova, G. P., and O. L. Zhdanova. "Comparative Dynamics Analysis of Simple Mathematical Models of the Plankton Communities Considering Various Types of Response Function." Mathematical Biology and Bioinformatics 17, no. 2 (December 19, 2022): 465–80. http://dx.doi.org/10.17537/2022.17.465.
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The paper proposes a two-component discrete-time model of the plankton community, taking into account features of the development and interaction of phytoplankton and zooplankton. To describe the interaction between these species and to compare the system dynamics, we use the following set of response functions: type II and III Holling function and the Arditi–Ginzburg response function, each of which describes trophic interactions between phytoplankton and zooplankton. An analytical and numerical study of the model proposed is made. The analysis shows that the variation of trophic functions does not change the dynamic behavior of the model fundamentally. The stability loss of nontrivial fixed point corresponding to the coexistence of phytoplankton and zooplankton can occur through a cascade of period-doubling bifurcations and according to the Neimark–Saker scenario, which allows us to observe the appearance of long-period oscillations representing the alternation of peaks and reduction in the number of species as a result of the predator-prey interaction. As well, the model has multistability areas, where a variation in initial conditions with the unchanged values of all model parameters can result in a shift of the current dynamic mode. Each of the models is shown to demonstrate conditional coexistence when a variation of the current community structure can lead to the extinction of the entire community or its part. Considering the characteristics of the species composition, the model with the type II Holling function seems a more suitable for describing the dynamics of the plankton community. Such a system is consistent with the idea that phytoplankton is a fast variable and predator dynamics is slow; thus, long-period fluctuations occur at high phytoplankton growth rates and low zooplankton ones. The model with the Arditi–Ginzburg functional response demonstrates quasi-periodic fluctuations in a narrow parametric aria with a high predator growth rate and low prey growth rate. The quasi-periodic dynamics regions in the model with the Holling type III functional response correspond to the conception of fast and slow variables, however in this case, the stability of the system increases, and the Neimark-Sacker bifurcation occurs even at a higher growth rate of zooplankton.
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Leleu, Timothée, and Kazuyuki Aihara. "Spontaneous Slow Oscillations and Sequential Patterns Due to Short-Term Plasticity in a Model of the Cortex." Neural Computation 25, no. 12 (December 2013): 3131–82. http://dx.doi.org/10.1162/neco_a_00513.
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We study a realistic model of a cortical column taking into account short-term plasticity between pyramidal cells and interneurons. The simulation of leaky integrate-and-fire neurons shows that low-frequency oscillations emerge spontaneously as a result of intrinsic network properties. These oscillations are composed of prolonged phases of high and low activity reminiscent of cortical up and down states, respectively. We simplify the description of the network activity by using a mean field approximation and reduce the system to two slow variables exhibiting some relaxation oscillations. We identify two types of slow oscillations. When the combination of dynamic synapses between pyramidal cells and those between interneurons accounts for the generation of these slow oscillations, the end of the up phase is characterized by asynchronous fluctuations of the membrane potentials. When the slow oscillations are mainly driven by the dynamic synapses between interneurons, the network exhibits fluctuations of membrane potentials, which are more synchronous at the end than at the beginning of the up phase. Additionally, finite size effect and slow synaptic currents can modify the irregularity and frequency, respectively, of these oscillations. Finally, we consider possible roles of a slow oscillatory input modeling long-range interactions in the brain. Spontaneous slow oscillations of local networks are modulated by the oscillatory input, which induces, notably, synchronization, subharmonic synchronization, and chaotic relaxation oscillations in the mean field approximation. In the case of forced oscillations, the slow population-averaged activity of leaky integrate-and-fire neurons can have both deterministic and stochastic temporal features. We discuss the possibility that long-range connectivity controls the emergence of slow sequential patterns in local populations due to the tendency of a cortical column to oscillate at low frequency.
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Yeon, Jun-Hee, Cheon-Gyu Park, Bertil Hille, and Byung-Chang Suh. "Translocatable voltage-gated Ca2+ channel β subunits in α1–β complexes reveal competitive replacement yet no spontaneous dissociation." Proceedings of the National Academy of Sciences 115, no. 42 (September 26, 2018): E9934—E9943. http://dx.doi.org/10.1073/pnas.1809762115.
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β subunits of high voltage-gated Ca2+ (CaV) channels promote cell-surface expression of pore-forming α1 subunits and regulate channel gating through binding to the α-interaction domain (AID) in the first intracellular loop. We addressed the stability of CaV α1B–β interactions by rapamycin-translocatable CaV β subunits that allow drug-induced sequestration and uncoupling of the β subunit from CaV2.2 channel complexes in intact cells. Without CaV α1B/α2δ1, all modified β subunits, except membrane-tethered β2a and β2e, are in the cytosol and rapidly translocate upon rapamycin addition to anchors on target organelles: plasma membrane, mitochondria, or endoplasmic reticulum. In cells coexpressing CaV α1B/α2δ1 subunits, the translocatable β subunits colocalize at the plasma membrane with α1B and stay there after rapamycin application, indicating that interactions between α1B and bound β subunits are very stable. However, the interaction becomes dynamic when other competing β isoforms are coexpressed. Addition of rapamycin, then, switches channel gating and regulation by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] lipid. Thus, expression of free β isoforms around the channel reveals a dynamic aspect to the α1B–β interaction. On the other hand, translocatable β subunits with AID-binding site mutations are easily dissociated from CaV α1B on the addition of rapamycin, decreasing current amplitude and PI(4,5)P2 sensitivity. Furthermore, the mutations slow CaV2.2 current inactivation and shift the voltage dependence of activation to more positive potentials. Mutated translocatable β subunits work similarly in CaV2.3 channels. In sum, the strong interaction of CaV α1B–β subunits can be overcome by other free β isoforms, permitting dynamic changes in channel properties in intact cells.
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Zmigrod, Leor, and Amit Goldenberg. "Cognition and Emotion in Extreme Political Action: Individual Differences and Dynamic Interactions." Current Directions in Psychological Science 30, no. 3 (May 4, 2021): 218–27. http://dx.doi.org/10.1177/0963721421993820.
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Who is most likely to join and engage in extreme political action? Although traditional theories have focused on situational factors or group identity, an emerging science illustrates that tendencies for extreme political action may also be rooted in individuals’ idiosyncratic cognitive and affective dispositions. This article synthesizes cutting-edge evidence demonstrating that individuals’ cognitive and affective architecture shapes their willingness to support ideological violence. In the cognitive domain, traits such as cognitive rigidity, slow perceptual strategies, and poor executive functions are linked to heightened endorsement for ideological violence. In the emotion domain, characteristics associated with emotional reactivity and impaired emotional regulation, such as sensation seeking and impulsivity, can facilitate readiness for extreme political action. The review homes in on the roles of cognitive rigidity and sensation seeking as traits heightening proclivities for extreme pro-group behavior and recommends that future research should assess cognition-emotion interactions to reveal different subprofiles of political actors. A theoretical framework focused on cognitive and affective information-processing traits—and their interactions—opens up tractable empirical questions and a future research agenda. Identifying subsets of ideologues is an endeavor with potential to inform the design of evidence-based interventions aimed at reducing ideological extremism and fostering social understanding.
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Zeng, Zhen, Elisa L. Hill-Yardin, David Williams, Terence O'Brien, Andris Serelis, and Christopher R. French. "Effect of phenytoin on sodium conductances in rat hippocampal CA1 pyramidal neurons." Journal of Neurophysiology 116, no. 4 (October 1, 2016): 1924–36. http://dx.doi.org/10.1152/jn.01060.2015.
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The antiepileptic drug phenytoin (PHT) is thought to reduce the excitability of neural tissue by stabilizing sodium channels (NaV) in inactivated states. It has been suggested the fast-inactivated state (IF) is the main target, although slow inactivation (IS) has also been implicated. Other studies on local anesthetics with similar effects on sodium channels have implicated the NaV voltage sensor interactions. In this study, we reexamined the effect of PHT in both equilibrium and dynamic transitions between fast and slower forms of inactivation in rat hippocampal CA1 pyramidal neurons. The effects of PHT were observed on fast and slow inactivation processes, as well as on another identified “intermediate” inactivation process. The effect of enzymatic removal of IF was also studied, as well as effects on the residual persistent sodium current ( INaP). A computational model based on a gating charge interaction was derived that reproduced a range of PHT effects on NaV equilibrium and state transitions. No effect of PHT on IF was observed; rather, PHT appeared to facilitate the occupancy of other closed states, either through enhancement of slow inactivation or through formation of analogous drug-bound states. The overall significance of these observations is that our data are inconsistent with the commonly held view that the archetypal NaV channel inhibitor PHT stabilizes fast inactivation states, and we demonstrate that conventional slow activation “IS” and the more recently identified intermediate-duration inactivation process “II” are the primary functional targets of PHT. In addition, we show that the traditional explanatory frameworks based on the “modulated receptor hypothesis” can be substituted by simple, physiologically plausible interactions with voltage sensors. Additionally, INaP was not preferentially inhibited compared with peak INa at short latencies (50 ms) by PHT.
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Li, Xin, Wei Huang, Elizabeth A. Morris, Luminita A. Tudorica, Venkatraman E. Seshan, William D. Rooney, Ian Tagge, Ya Wang, Jingang Xu, and Charles S. Springer. "Dynamic NMR effects in breast cancer dynamic-contrast-enhanced MRI." Proceedings of the National Academy of Sciences 105, no. 46 (November 13, 2008): 17937–42. http://dx.doi.org/10.1073/pnas.0804224105.
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The passage of a vascular-injected paramagnetic contrast reagent (CR) bolus through a region-of-interest affects tissue 1H2O relaxation and thus MR image intensity. For longitudinal relaxation [R1 ≡ (T1)−1], the CR must have transient molecular interactions with water. Because the CR and water molecules are never uniformly distributed in the histological-scale tissue compartments, the kinetics of equilibrium water compartmental interchange are competitive. In particular, the condition of the equilibrium trans cytolemmal water exchange NMR system sorties through different domains as the interstitial CR concentration, [CRo], waxes and wanes. Before CR, the system is in the fast-exchange-limit (FXL). Very soon after CRo arrival, it enters the fast-exchange-regime (FXR). Near maximal [CRo], the system could enter even the slow-exchange-regime (SXR). These conditions are defined herein, and a comprehensive description of how they affect quantitative pharmacokinetic analyses is presented. Data are analyzed from a population of 22 patients initially screened suspicious for breast cancer. After participating in our study, the subjects underwent biopsy/pathology procedures and only 7 (32%) were found to have malignancies. The transient departure from FXL to FXR (and apparently not SXR) is significant in only the malignant tumors, presumably because of angiogenic capillary leakiness. Thus, if accepted, this analysis would have prevented the 68% of the biopsies that proved benign.
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Xie, Mouzhe, Lei Yu, Lei Bruschweiler-Li, Xinyao Xiang, Alexandar L. Hansen, and Rafael Brüschweiler. "Functional protein dynamics on uncharted time scales detected by nanoparticle-assisted NMR spin relaxation." Science Advances 5, no. 8 (August 2019): eaax5560. http://dx.doi.org/10.1126/sciadv.aax5560.
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Protein function depends critically on intrinsic internal dynamics, which is manifested in distinct ways, such as loop motions that regulate protein recognition and catalysis. Under physiological conditions, dynamic processes occur on a wide range of time scales from subpicoseconds to seconds. Commonly used NMR spin relaxation in solution provides valuable information on very fast and slow motions but is insensitive to the intermediate nanosecond to microsecond range that exceeds the protein tumbling correlation time. Presently, very little is known about the nature and functional role of these motions. It is demonstrated here how transverse spin relaxation becomes exquisitely sensitive to these motions at atomic resolution when studying proteins in the presence of nanoparticles. Application of this novel cross-disciplinary approach reveals large-scale dynamics of loops involved in functionally critical protein-protein interactions and protein-calcium ion recognition that were previously unobservable.
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Dupraz, Christian, Kevin Wolz, Isabelle Lecomte, Grégoire Talbot, Grégoire Vincent, Rachmat Mulia, François Bussière, et al. "Hi-sAFe: A 3D Agroforestry Model for Integrating Dynamic Tree–Crop Interactions." Sustainability 11, no. 8 (April 16, 2019): 2293. http://dx.doi.org/10.3390/su11082293.
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Agroforestry, the intentional integration of trees with crops and/or livestock, can lead to multiple economic and ecological benefits compared to trees and crops/livestock grown separately. Field experimentation has been the primary approach to understanding the tree–crop interactions inherent in agroforestry. However, the number of field experiments has been limited by slow tree maturation and difficulty in obtaining consistent funding. Models have the potential to overcome these hurdles and rapidly advance understanding of agroforestry systems. Hi-sAFe is a mechanistic, biophysical model designed to explore the interactions within agroforestry systems that mix trees with crops. The model couples the pre-existing STICS crop model to a new tree model that includes several plasticity mechanisms responsive to tree–tree and tree–crop competition for light, water, and nitrogen. Monoculture crop and tree systems can also be simulated, enabling calculation of the land equivalent ratio. The model’s 3D and spatially explicit form is key for accurately representing many competition and facilitation processes. Hi-sAFe is a novel tool for exploring agroforestry designs (e.g., tree spacing, crop type, tree row orientation), management strategies (e.g., thinning, branch pruning, root pruning, fertilization, irrigation), and responses to environmental variation (e.g., latitude, climate change, soil depth, soil structure and fertility, fluctuating water table). By improving our understanding of the complex interactions within agroforestry systems, Hi-sAFe can ultimately facilitate adoption of agroforestry as a sustainable land-use practice.
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Kruteva, Margarita. "Dynamics studied by Quasielastic Neutron Scattering (QENS)." Adsorption 27, no. 5 (February 2, 2021): 875–89. http://dx.doi.org/10.1007/s10450-020-00295-4.
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AbstractQuasielastic neutron scattering (QENS) allows measurement of the molecular displacements in time and space, from pico- to tens of nanoseconds and from Ångstroms to nanometers, respectively. The method probes dynamics from fast vibrational modes down to slow diffusive motion. Every scattering experiment leads to a dynamic structure factor $$S\left( {\vec Q,\omega } \right)$$ S Q → , ω or its spatial and temporal Fourier transform (van Hove correlation function $$G\left( {\vec r,t} \right)$$ G r → , t ). This shows exactly where the atoms are and how they move. In this manuscript the basics of the QENS method are presented and a few examples highlighting the potentials of QENS are given: (i) diffusion of liquids and gases in nano- and mesoporous materials; (ii) hydrogen dynamics in a high temperature polymer electrolyte fuel cell (HT-PEFC) and (iii) influence of the surface interactions on polymer dynamics in nanopores.
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Grebowsky, Joseph M., and Arthur C. Aikin. "Planetary ionospheres – sources and dynamic drivers." Proceedings of the International Astronomical Union 4, S257 (September 2008): 499–510. http://dx.doi.org/10.1017/s1743921309029780.
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AbstractExternal energy inputs into all planetary upper atmospheres (including more than a half dozen moons with atmospheres) are comprised of combinations of solar EUV, soft x-rays, solar energetic particles, solar wind charged particles, magnetospherically accelerated particles, solar wind electric field, interplanetary dust particles as well as propagating lower atmosphere disturbances. Each input has analogous physical interactions with all planetary ionospheres and upper atmospheres, but the integrated consequences of the multiple energy inputs vary from planet to planet. The Earth forms the framework for most fundamental processes because of extensive measurements of the effects of each of the inputs. However the conditions at Earth are far different from those at the carbon dioxide atmosphere of magnetic field-free, slow-rotating Venus, the carbon dioxide atmosphere of Mars with patchy remnant magnetic fields, while the outer planets have hydrogen atmospheres, are fast rotating with intrinsic magnetic fields, and encompass moons that interact with the magnetospheres and have exotic atmospheres. Although the physical processes are known, our understanding of our solar system's ionospheres diminishes with increasing distance from the Sun.
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Liu, Shuang, Jun-Fang Wu, and Chao Li. "Reconfigurable optical diode based on asymmetrically coupled slow-light waveguide." Journal of Applied Physics 133, no. 4 (January 28, 2023): 043105. http://dx.doi.org/10.1063/5.0133804.
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Controlling the flow of light is fundamental for on-chip optical signal processing. In this paper, we investigate how to realize high contrast, high unidirectional transmission rate, and reconfigurable nonreciprocal light transmission, based on a nonlinear nanocavity asymmetrically side-coupled with a specially designed slow-light waveguide. We analytically and numerically demonstrate that the unusual multiple threshold pump power points for trigging the photon transitions between bistable states, as well as the sensitivity of the dynamic interactions to the relative delay time between the signal light and pump pulse, play crucial roles in this optical diode system. Based on these findings, a high contrast (over 22 dB) and high unidirectional transmission rate (over 70%) optical diode is achieved. More importantly, the conducting direction of the optical diode can be controllably reversed, without the need of changing the signal's wavelength or power as usually done. This approach is promising in the fields of optical information processing and quantum computing.
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Pimentel, Sam, and Gwenn E. Flowers. "A numerical study of hydrologically driven glacier dynamics and subglacial flooding." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 467, no. 2126 (August 4, 2010): 537–58. http://dx.doi.org/10.1098/rspa.2010.0211.
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A hydrologically coupled flowband model of ‘higher order’ ice dynamics is used to explore perturbations in response to supraglacial water drainage and subglacial flooding. The subglacial drainage system includes interacting ‘fast’ and ‘slow’ drainage elements. The fast drainage system is assumed to be composed of ice-walled conduits and the slow system of a macroporous water sheet. Under high subglacial water pressures, flexure of the overlying ice is modelled using elastic beam theory. A regularized Coulomb friction law describes basal boundary conditions that enable hydrologically driven acceleration. We demonstrate the modelled interactions between hydrology and ice dynamics by means of three observationally inspired examples: (i) simulations of meltwater drainage at an Alpine-type glacier produce seasonal and diurnal variability, and exhibit drainage evolution characteristic of the so-called ‘spring transition’; (ii) horizontal and vertical diurnal accelerations are modelled in response to summer meltwater input at a Greenland-type outlet glacier; and (iii) short-lived perturbations to basal water pressure and ice-flow speed are modelled in response to the prescribed drainage of a supraglacial lake. Our model supports the suggestion that a channelized drainage system can form beneath the margins of the Greenland ice sheet, and may contribute to reducing the dynamic impact of floods derived from supraglacial lakes.
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Joseph, Prem, Leo Spyracopoulos, and Krishna Rajarathnam. "Dynamics-Derived Insights into Complex Formation between the CXCL8 Monomer and CXCR1 N-Terminal Domain: An NMR Study." Molecules 23, no. 11 (October 31, 2018): 2825. http://dx.doi.org/10.3390/molecules23112825.
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Interleukin-8 (CXCL8), a potent neutrophil-activating chemokine, exerts its function by activating the CXCR1 receptor that belongs to class A G protein-coupled receptors (GPCRs). Receptor activation involves interactions between the CXCL8 N-terminal loop and CXCR1 N-terminal domain (N-domain) residues (Site-I) and between the CXCL8 N-terminal and CXCR1 extracellular/transmembrane residues (Site-II). CXCL8 exists in equilibrium between monomers and dimers, and it is known that the monomer binds CXCR1 with much higher affinity and that Site-I interactions are largely responsible for the differences in monomer vs. dimer affinity. Here, using backbone 15N-relaxation nuclear magnetic resonance (NMR) data, we characterized the dynamic properties of the CXCL8 monomer and the CXCR1 N-domain in the free and bound states. The main chain of CXCL8 appears largely rigid on the picosecond time scale as evident from high order parameters (S2). However, on average, S2 are higher in the bound state. Interestingly, several residues show millisecond-microsecond (ms-μs) dynamics only in the bound state. The CXCR1 N-domain is unstructured in the free state but structured with significant dynamics in the bound state. Isothermal titration calorimetry (ITC) data indicate that both enthalpic and entropic factors contribute to affinity, suggesting that increased slow dynamics in the bound state contribute to affinity. In sum, our data indicate a critical and complex role for dynamics in driving CXCL8 monomer-CXCR1 Site-I interactions.
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Gupta, Shamik, and Stefano Ruffo. "The world of long-range interactions: A bird’s eye view." International Journal of Modern Physics A 32, no. 09 (March 23, 2017): 1741018. http://dx.doi.org/10.1142/s0217751x17410184.
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In recent years, studies of long-range interacting (LRI) systems have taken center stage in the arena of statistical mechanics and dynamical system studies, due to new theoretical developments involving tools from as diverse a field as kinetic theory, non-equilibrium statistical mechanics, and large deviation theory, but also due to new and exciting experimental realizations of LRI systems. In the first, introductory, Section 1, we discuss the general features of long-range interactions, emphasizing in particular the main physical phenomenon of non-additivity, which leads to a plethora of distinct effects, both thermodynamic and dynamic, that are not observed with short-range interactions: Ensemble inequivalence, slow relaxation, broken ergodicity. In Section 2, we discuss several physical systems with long-range interactions: mean-field spin systems, self-gravitating systems, Euler equations in two dimensions, Coulomb systems, one-component electron plasma, dipolar systems, free-electron lasers. In Section 3, we discuss the general scenario of dynamical evolution of generic LRI systems. In Section 4, we discuss an illustrative example of LRI systems, the Kardar–Nagel spin system, which involves discrete degrees of freedom, while in Section 5, we discuss a paradigmatic example involving continuous degrees of freedom, the so-called Hamiltonian mean-field (HMF) model. For the former, we demonstrate the effects of ensemble inequivalence and slow relaxation, while for the HMF model, we emphasize in particular the occurrence of the so-called quasistationary states (QSSs) during relaxation towards the Boltzmann–Gibbs equilibrium state. The QSSs are non-equilibrium states with lifetimes that diverge with the system size, so that in the thermodynamic limit, the systems remain trapped in the QSSs, thereby making the latter the effective stationary states. In Section 5, we also discuss an experimental system involving atoms trapped in optical cavities, which may be modelled by the HMF system. In Section 6, we address the issue of ubiquity of the quasistationary behavior by considering a variety of models and dynamics, discussing in each case the conditions to observe QSSs. In Section 7, we investigate the issue of what happens when a long-range system is driven out of thermal equilibrium. Conclusions are drawn in Section 8.
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Luo, Feng, Yu-Mei Song, Hai-Xiao Huang, Xiao-Zhao Tian, Gong-Ming Sun, Yan Zhu, and Xue-Feng Feng. "Two New One-Dimensional Homospin Dy(III) Compounds Showing Slow Magnetic Relaxation." Australian Journal of Chemistry 65, no. 10 (2012): 1436. http://dx.doi.org/10.1071/ch12233.
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In this work, we present two new one-dimensional Dy(iii) compounds, namely [Dy3(L1)9]n (1, HL1 = benzoic acid) and {[Dy4(L2)14][Fe(phen)3]}n (2, HL2 = 3-nitrobenzoic acid, phen = 1,10-phenanthroline). In 1, three distinct coordination polyhedra for Dy(iii) sites including a six-coordinated DyO6 octahedron, a seven-coordinated DyO7 pentagonal bipyramid, and eight-coordinated DyO8 dodecahedron, are observed. These Dy(iii) ions are in turn bridged by L1––carboxylate to give rise to the 1D helical chain structure. Within 2, there are two crystallography-independent Dy(iii) ions that take the mono-capped trigonal bipyramidal geometry. Through L2-carboxylate bridges the Dy(iii) ions are associated together, resulting in the 1D chain structure. Direct current magnetic susceptibilities reveal ferromagnetic interactions, whilst dynamic magnetic studies via alternating current measurements disclose slow magnetic relaxation of these structures.
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Daumas, F., N. Destainville, C. Millot, A. Lopez, D. Dean, and L. Salomé. "Interprotein interactions are responsible for the confined diffusion of a G-protein-coupled receptor at the cell surface." Biochemical Society Transactions 31, no. 5 (October 1, 2003): 1001–5. http://dx.doi.org/10.1042/bst0311001.
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The monitoring of the movements of membrane proteins (or lipids) by single-particle tracking enables one to obtain reliable insights into the complex dynamic organization of the plasma membrane constituents. Using this technique, we investigated the diffusional behaviour of a G-protein-coupled receptor. The trajectories of the receptors revealed a diffusion mode combining a short-term rapid confined diffusion with a long-term slow diffusion. A detailed statistical analysis shows that the receptors have a diffusion confined to a domain which itself diffuses, the confinement being due to long-range attractive inter-protein interactions. The existing models of the dynamic organization of the cell membrane cannot explain our results. We propose a theoretical Brownian model of interacting proteins that is consistent with the experimental observations and accounts for the variations found as a function of the domain size of the short-term and long-term diffusion coefficients.
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Julien, Claude, Bruno Chapuis, Yong Cheng, and Christian Barrès. "Dynamic interactions between arterial pressure and sympathetic nerve activity: role of arterial baroreceptors." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 285, no. 4 (October 2003): R834—R841. http://dx.doi.org/10.1152/ajpregu.00102.2003.
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The role of arterial baroreceptors in controlling arterial pressure (AP) variability through changes in sympathetic nerve activity was examined in conscious rats. AP and renal sympathetic nerve activity (RSNA) were measured continuously during 1-h periods in freely behaving rats that had been subjected to sinoaortic baroreceptor denervation (SAD) or a sham operation 2 wk before study ( n = 10 in each group). Fast Fourier transform analysis revealed that chronic SAD did not alter high-frequency (0.75-5 Hz) respiratory-related oscillations of mean AP (MAP) and RSNA, decreased by ∼50% spectral power of both variables in the midfrequency band (MF, 0.27-0.74 Hz) containing the so-called Mayer waves, and induced an eightfold increase in MAP power without altering RSNA power in the low-frequency band (0.005-0.27 Hz). In both groups of rats, coherence between RSNA and MAP was maximal in the MF band and was usually weak at lower frequencies. In SAD rats, the transfer function from RSNA to MAP showed the characteristics of a second-order low-pass filter containing a fixed time delay (∼0.5 s). These results indicate that arterial baroreceptors are not involved in production of respiratory-related oscillations of RSNA but play a major role in the genesis of synchronous oscillations of MAP and RSNA at the frequency of Mayer waves. The weak coupling between slow fluctuations of RSNA and MAP in sham-operated and SAD rats points to the interference of noise sources unrelated to RSNA affecting MAP and of noise sources unrelated to MAP affecting RSNA.
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Sengel, Jason T., and Mark I. Wallace. "Imaging the dynamics of individual electropores." Proceedings of the National Academy of Sciences 113, no. 19 (April 25, 2016): 5281–86. http://dx.doi.org/10.1073/pnas.1517437113.
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Electroporation is a widely used technique to permeabilize cell membranes. Despite its prevalence, our understanding of the mechanism of voltage-mediated pore formation is incomplete; methods capable of visualizing the time-dependent behavior of individual electropores would help improve our understanding of this process. Here, using optical single-channel recording, we track multiple isolated electropores in real time in planar droplet interface bilayers. We observe individual, mobile defects that fluctuate in size, exhibiting a range of dynamic behaviors. We observe fast (25 s−1) and slow (2 s−1) components in the gating of small electropores, with no apparent dependence on the applied potential. Furthermore, we find that electropores form preferentially in the liquid disordered phase. Our observations are in general supportive of the hydrophilic toroidal pore model of electroporation, but also reveal additional complexity in the interactions, dynamics, and energetics of electropores.
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Siregar, Yusra Dewi, Ilham Aji Maulana, Deswita Saskia Humairah Manik, and Siti Syarah Hutasiot. "Pengaruh Masuknya Islam Terhadap Kebudayaan di Tanah Karo." Islam & Contemporary Issues 4, no. 1 (April 16, 2024): 28–34. http://dx.doi.org/10.57251/ici.v4i1.1415.
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This study aims to examine the influence of the arrival of Islam on the culture in Tanah Karo, which was previously dominated by animism and dynamism beliefs. Through the literature review method, this research analyzes changes in the belief system, customs, marriage patterns, education, and social dynamics after Islam was introduced in the region. The findings show that interactions between Islamic traders and scholars with the indigenous Karo community triggered a slow but significant process of acculturation. Traditional Karo culture underwent a transformation, adopting Islamic values in various aspects of life, including religious celebrations like Eid al-Fitr, as well as in arts, architecture, and language. Despite challenges in the acculturation process, the Karo people managed to maintain a balance between local traditions and Islamic values, creating a pluralistic and dynamic cultural identity. This study is important for understanding cultural and religious dynamics in a diverse society and provides insights into the cultural evolution in Tanah Karo.
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Gemmell, Brad J., Sean P. Colin, John H. Costello, and Kelly R. Sutherland. "A ctenophore (comb jelly) employs vortex rebound dynamics and outperforms other gelatinous swimmers." Royal Society Open Science 6, no. 3 (March 2019): 181615. http://dx.doi.org/10.1098/rsos.181615.
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Gelatinous zooplankton exhibit a wide range of propulsive swimming modes. One of the most energetically efficient is the rowing behaviour exhibited by many species of schyphomedusae, which employ vortex interactions to achieve this result. Ctenophores (comb jellies) typically use a slow swimming, cilia-based mode of propulsion. However, species within the genus Ocyropsis have developed an additional propulsive strategy of rowing the lobes, which are normally used for feeding, in order to rapidly escape from predators. In this study, we used high-speed digital particle image velocimetry to examine the kinematics and fluid dynamics of this rarely studied propulsive mechanism. This mechanism allows Ocyropsis to achieve size-adjusted speeds that are nearly double those of other large gelatinous swimmers. The investigation of the fluid dynamic basis of this escape mode reveals novel vortex interactions that have not previously been described for other biological propulsion systems. The arrangement of vortices during escape swimming produces a similar configuration and impact as that of the well-studied ‘vortex rebound’ phenomenon which occurs when a vortex ring approaches a solid wall. These results extend our understanding of how animals use vortex–vortex interactions and provide important insights that can inform the bioinspired engineering of propulsion systems.
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Flores-Aldama, Lisandra, Daniel Bustos, Deny Cabezas-Bratesco, Wendy Gonzalez, and Sebastian E. Brauchi. "Intracellular Helix-Loop-Helix Domain Modulates Inactivation Kinetics of Mammalian TRPV5 and TRPV6 Channels." International Journal of Molecular Sciences 24, no. 5 (February 24, 2023): 4470. http://dx.doi.org/10.3390/ijms24054470.
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TRPV5 and TRPV6 are calcium-selective ion channels expressed at the apical membrane of epithelial cells. Important for systemic calcium (Ca2+) homeostasis, these channels are considered gatekeepers of this cation transcellular transport. Intracellular Ca2+ exerts a negative control over the activity of these channels by promoting inactivation. TRPV5 and TRPV6 inactivation has been divided into fast and slow phases based on their kinetics. While slow inactivation is common to both channels, fast inactivation is characteristic of TRPV6. It has been proposed that the fast phase depends on Ca2+ binding and that the slow phase depends on the binding of the Ca2+/Calmodulin complex to the internal gate of the channels. Here, by means of structural analyses, site-directed mutagenesis, electrophysiology, and molecular dynamic simulations, we identified a specific set of amino acids and interactions that determine the inactivation kinetics of mammalian TRPV5 and TRPV6 channels. We propose that the association between the intracellular helix-loop-helix (HLH) domain and the TRP domain helix (TDh) favors the faster inactivation kinetics observed in mammalian TRPV6 channels.
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Horn, John P. "The integrative role of synaptic cotransmission in the bullfrog vasomotor C system: evidence for a synaptic gain hypothesis." Canadian Journal of Physiology and Pharmacology 70, S1 (May 15, 1992): S19—S26. http://dx.doi.org/10.1139/y92-239.
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Understanding the integrative significance of synaptic cotransmission is a central problem in autonomic physiology. What are the functional roles of slow synaptic potentials in autonomic ganglia? This paper reviews the problem and its historical roots by focusing on work in the amphibian paravertebral sympathetic system. The phenotypic properties that distinguish the sympathetic B and C cell systems are summarized. Then, a synaptic gain hypothesis is proposed for the integrative function of muscarinic and peptidergic synapses in the vasomotor C system. The model states that the peripheral output of the vasomotor system is subject to synaptic amplification by two gain stages in series. The first gain stage is postulated to arise in ganglia from interactions between two slow postsynaptic potentials; the excitatory response mediated by luteinizing hormone releasing hormone, and the inhibitory response mediated by the muscarinic action of acetylcholine. The second gain stage is postulated to arise in arteries from interactions between two postganglionic cotransmitters: epinephrine and neuropeptide Y. A circuit with these properties would enable preganglionic patterns of electrical activity to regulate the system's output over a wider dynamic range than possible without cotransmitters.Key words: vasomotor sympathetic neurons, muscarinic synapses, luteinizing hormone releasing hormone, neuropeptide Y, neuronal model.
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Nicolaidou, Evangelia, Thomas L. Hill, and Simon A. Neild. "Detecting internal resonances during model reduction." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 477, no. 2250 (June 2021): 20210215. http://dx.doi.org/10.1098/rspa.2021.0215.
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Model order reduction of geometrically nonlinear dynamic structures is often achieved via a static condensation procedure, whereby high-frequency modes are assumed to be quasi-statically coupled to a small set of lower frequency modes, which form the reduction basis. This approach is mathematically justifiable for structures characterized by slow/fast dynamics, such as thin plates and slender beams, and has been shown to provide highly accurate results. Nevertheless, selecting the reduction basis without a priori knowledge of the full-order dynamics is a challenging task; retaining redundant modes will lead to computationally suboptimal reduced-order models (ROMs), while omitting dynamically significant modes will lead to inaccurate results, and important features such as internal resonances may not be captured. In this study, we demonstrate how the error associated with static condensation can be efficiently approximated during model reduction. This approximate error can then be used as the basis of a method for predicting when dynamic modal interactions will occur, which will guide the reduction basis selection process. Equivalently, this may serve as a tool for verifying the accuracy of ROMs without the need for full-order simulations. The proposed method is demonstrated using a simple oscillator and a finite element model of a clamped–clamped beam.
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Agbemavor, Wisdom Selorm Kofi, and Elna Maria Buys. "Dynamic Interactions between Diarrhoeagenic Enteroaggregative Escherichia coli and Presumptive Probiotic Bacteria: Implications for Gastrointestinal Health." Microorganisms 11, no. 12 (December 8, 2023): 2942. http://dx.doi.org/10.3390/microorganisms11122942.
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This study delves into the temporal dynamics of bacterial interactions in the gastrointestinal tract, focusing on how probiotic strains and pathogenic bacteria influence each other and human health. This research explores adhesion, competitive exclusion, displacement, and inhibition of selected diarrhoeagenic Escherichia coli (D-EAEC) and potential probiotic strains under various conditions. Key findings reveal that adhesion is time-dependent, with both D-EAEC K2 and probiotic L. plantarum FS2 showing increased adhesion over time. Surprisingly, L. plantarum FS2 outperformed D-EAEC K2 in adhesion and exhibited competitive exclusion and displacement, with inhibition of adhesion surpassing competitive exclusion. This highlights probiotics’ potential to slow pathogen attachment when not in competition. Pre-infecting with L. plantarum FS2 before pathogenic infection effectively inhibited adhesion, indicating probiotics’ ability to prevent pathogen attachment. Additionally, adhesion correlated strongly with interleukin-8 (IL-8) secretion, linking it to the host’s inflammatory response. Conversely, IL-8 secretion negatively correlated with trans-epithelial electrical resistance (TEER), suggesting a connection between tight junction disruption and increased inflammation. These insights offer valuable knowledge about the temporal dynamics of gut bacteria interactions and highlight probiotics’ potential in competitive exclusion and inhibiting pathogenic bacteria, contributing to strategies for maintaining gastrointestinal health and preventing infections.
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Sangeeta and Arnab Bhattacherjee. "Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA." PLOS ONE 18, no. 1 (January 19, 2023): e0278396. http://dx.doi.org/10.1371/journal.pone.0278396.
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Human Replication Protein A (hRPA) is a multidomain protein that interacts with ssDNA intermediates to provide the latter much-needed stability during DNA metabolism and maintain genomic integrity. Although the ssDNA organization with hRPA was studied recently through experimental means, characterizing the underlying mechanism at the atomic level remains challenging because of the dynamic domain architecture of hRPA and poorly understood heterogeneity of ssDNA-protein interactions. Here, we used a computational framework, precisely tailored to capture protein-ssDNA interactions, and investigated the binding of hRPA with a 60 nt ssDNA. Two distinct binding mechanisms are realized based on the hRPA domain flexibility. For a rigid domain architecture of hRPA, ssDNA binds sequentially with hRPA domains, resulting in slow association kinetics. The binding pathway involves the formation of stable and distinct intermediate states. On contrary, for a flexible domain architecture of hRPA, ssDNA binds synergistically to the A and B domains followed by the rest of hRPA. The domain dynamics in hRPA alleviates the free energy cost of domain orientation necessary for specific binding with ssDNA, leading to fast association kinetics along a downhill binding free energy landscape. An ensemble of free energetically degenerate intermediate states is encountered that makes it arduous to characterize them structurally. An excellent match between our results with the available experimental observations provides new insights into the rich dynamics of hRPA binding to ssDNA and in general paves the way to investigate intricate details of ssDNA-protein interactions, crucial for cellular functioning.
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Salmon, Wendy C., Michael C. Adams, and Clare M. Waterman-Storer. "Dual-wavelength fluorescent speckle microscopy reveals coupling of microtubule and actin movements in migrating cells." Journal of Cell Biology 158, no. 1 (July 8, 2002): 31–37. http://dx.doi.org/10.1083/jcb.200203022.
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Interactions between microtubules (MTs) and filamentous actin (f-actin) are involved in directed cell locomotion, but are poorly understood. To test the hypothesis that MTs and f-actin associate with one another and affect each other's organization and dynamics, we performed time-lapse dual-wavelength spinning-disk confocal fluorescent speckle microscopy (FSM) of MTs and f-actin in migrating newt lung epithelial cells. F-actin exhibited four zones of dynamic behavior: rapid retrograde flow in the lamellipodium, slow retrograde flow in the lamellum, anterograde flow in the cell body, and no movement in the convergence zone between the lamellum and cell body. Speckle analysis showed that MTs moved at the same trajectory and velocity as f-actin in the cell body and lamellum, but not in the lamellipodium or convergence zone. MTs grew along f-actin bundles, and quiescent MT ends moved in association with f-actin bundles. These results show that the movement and organization of f-actin has a profound effect on the dynamic organization of MTs in migrating cells, and suggest that MTs and f-actin bind to one another in vivo.
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Qin, Huaguang, Wuxuan Hong, Zehua Qi, Yinghong Hu, Rui Shi, Shuyuan Wang, Yuxi Wang, et al. "A Temperature-Dependent Model for Tritrophic Interactions Involving Tea Plants, Tea Green Leafhoppers and Natural Enemies." Insects 13, no. 8 (July 29, 2022): 686. http://dx.doi.org/10.3390/insects13080686.
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The tea green leaf hopper, Empoasca onukii Matsuda, is a severe pest of tea plants. Volatile emissions from tea shoots infested by the tea green leafhopper may directly repel insect feeding or attract natural enemies. Many studies have been conducted on various aspects of the tritrophic relationship involving tea plants, tea green leafhoppers and natural enemies. However, mathematic models which could explain the dynamic mechanisms of this tritrophic interaction are still lacking. In the current work, we constructed a realistic and stochastic model with temperature-dependent features to characterize the tritrophic interactions in the tea agroecosystem. Model outputs showed that two leafhopper outbreaks occur in a year, with their features being consistent with field observations. Simulations showed that daily average effective accumulated temperature (EAT) might be an important metric for outbreak prediction. We also showed that application of slow-releasing semiochemicals, as either repellents or attractants, may be highly efficacious for pest biocontrol and can significantly increase tea yields. Furthermore, the start date of applying semiochemicals can be optimized to effectively increase tea yields. The current model qualitatively characterizes key features of the tritrophic interactions and provides critical insight into pest control in tea ecosystems.
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Nedyalkov, Michail, Caroline Sultanem, and Jean-Jacque Benattar. "Contact angles of protein black foam films under dynamic and equilibrium conditions." Open Chemistry 5, no. 3 (September 1, 2007): 748–65. http://dx.doi.org/10.2478/s11532-007-0014-z.
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AbstractThe contact angles of protein Newton black foam films from ALG (alpha-lactalbumin), BLG (beta-lactoglobulin) and BSA (bovine serum albumin) are measured here within. The measurements are carried out under dynamic and equilibrium conditions. For all proteins, a strong hystheresis effect of the contact angle is observed under dynamic conditions. An attempt is made to explain these results by the slow adsorption and desorption kinetics of the protein bilayers and by the dynamic structure and the rheology of the protein network forming the bubble walls. In addition, we propose a modification of the experimental device reported previously for contact angle measurements of large flat films in equilibrium. The advantages of this method are discussed in detail. Some shortcomings (precision, reproducibility) of this preliminary variant of the device in this initial stage of its application, do not allow one to draw reliable conclusions about the interactions of these films. Some improvements of the measurement quality are proposed.
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Schmidt, C. E., A. F. Horwitz, D. A. Lauffenburger, and M. P. Sheetz. "Integrin-cytoskeletal interactions in migrating fibroblasts are dynamic, asymmetric, and regulated." Journal of Cell Biology 123, no. 4 (November 15, 1993): 977–91. http://dx.doi.org/10.1083/jcb.123.4.977.
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We have used laser optical trapping and nanometer-level motion analysis to investigate the cytoskeletal associations and surface dynamics of beta 1 integrin, a cell-substrate adhesion molecule, on the dorsal surfaces of migrating fibroblast cells. A single-beam optical gradient trap (laser tweezers) was used to restrain polystyrene beads conjugated with anti-beta 1 integrin mAbs and place them at desired locations on the cell exterior. This technique was used to demonstrate a spatial difference in integrin-cytoskeleton interactions in migrating cells. We found a distinct increase in the stable attachment of beads, and subsequent rearward flow, on the lamellipodia of locomoting cells compared with the retracting portions. Complementary to the enhanced linkage of integrin at the cell lamellipodium, the membrane was more deformable at the rear versus the front of moving cells while nonmotile cells did not exhibit this asymmetry in membrane architecture. Video microscopy and nanometer-precision tracking routines were used to study the surface dynamics of integrin on the lamellipodia of migrating cells by monitoring the displacements of colloidal gold particles coated with anti-beta 1 integrin mAbs. Small gold aggregates were rapidly transported preferentially to the leading edge of the lamellipod where they resumed diffusion restricted along the edge. This fast transport was characterized by brief periods of directed movement ("jumps") having an instantaneous velocity of 37 +/- 15 microns/min (SD), separated by periods of diffusion. In contrast, larger aggregates of gold particles and the large latex beads underwent slow, steady rearward movement (0.85 +/- 0.44 micron/min) (SD) at a rate similar to that reported for other capping events and for migration of these cells. Cell lines containing mutated beta 1 integrins were used to show that the cytoplasmic domain is essential for an asymmetry in attachment of integrin to the underlying cytoskeletal network and is also necessary for rapid, intermittent transport. However, enhanced membrane deformability at the cell rear does not require integrin-cytoskeletal interactions. We also demonstrated that posttranslational modifications of integrin could potentially play a role in these phenomena. These results suggest a scheme for the role of dynamic integrin-mediated adhesive interactions in cell migration. Integrins are transported preferentially to the cell front where they form nascent adhesions. These adhesive structures grow in size and associate with the cytoskeleton that exerts a rearward force on them. Dorsal aggregates more rearward while those on the ventral side remain fixed to the substrate allowing the cell body to move forward. Detachment of the cell rear occurs by at least two modes: (a) weakened integrin-cytoskeleton interactions, potentially mediated by local modifications of linkage proteins, which lead to weakened cell-substratum interactions and (b) ripping of integrins and the highly deformable membrane from the cell body.
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Barà, Chiara, Laura Sparacino, Riccardo Pernice, Yuri Antonacci, Alberto Porta, Dimitris Kugiumtzis, and Luca Faes. "Comparison of discretization strategies for the model-free information-theoretic assessment of short-term physiological interactions." Chaos: An Interdisciplinary Journal of Nonlinear Science 33, no. 3 (March 2023): 033127. http://dx.doi.org/10.1063/5.0140641.
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This work presents a comparison between different approaches for the model-free estimation of information-theoretic measures of the dynamic coupling between short realizations of random processes. The measures considered are the mutual information rate (MIR) between two random processes [Formula: see text] and [Formula: see text] and the terms of its decomposition evidencing either the individual entropy rates of [Formula: see text] and [Formula: see text] and their joint entropy rate, or the transfer entropies from [Formula: see text] to [Formula: see text] and from [Formula: see text] to [Formula: see text] and the instantaneous information shared by [Formula: see text] and [Formula: see text]. All measures are estimated through discretization of the random variables forming the processes, performed either via uniform quantization (binning approach) or rank ordering (permutation approach). The binning and permutation approaches are compared on simulations of two coupled non-identical Hènon systems and on three datasets, including short realizations of cardiorespiratory (CR, heart period and respiration flow), cardiovascular (CV, heart period and systolic arterial pressure), and cerebrovascular (CB, mean arterial pressure and cerebral blood flow velocity) measured in different physiological conditions, i.e., spontaneous vs paced breathing or supine vs upright positions. Our results show that, with careful selection of the estimation parameters (i.e., the embedding dimension and the number of quantization levels for the binning approach), meaningful patterns of the MIR and of its components can be achieved in the analyzed systems. On physiological time series, we found that paced breathing at slow breathing rates induces less complex and more coupled CR dynamics, while postural stress leads to unbalancing of CV interactions with prevalent baroreflex coupling and to less complex pressure dynamics with preserved CB interactions. These results are better highlighted by the permutation approach, thanks to its more parsimonious representation of the discretized dynamic patterns, which allows one to explore interactions with longer memory while limiting the curse of dimensionality.
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MERCER, AARON J., and WALLACE B. THORESON. "The dynamic architecture of photoreceptor ribbon synapses: Cytoskeletal, extracellular matrix, and intramembrane proteins." Visual Neuroscience 28, no. 6 (November 2011): 453–71. http://dx.doi.org/10.1017/s0952523811000356.
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AbstractRod and cone photoreceptors possess ribbon synapses that assist in the transmission of graded light responses to second-order bipolar and horizontal cells of the vertebrate retina. Proper functioning of the synapse requires the juxtaposition of presynaptic release sites immediately adjacent to postsynaptic receptors. In this review, we focus on the synaptic, cytoskeletal, and extracellular matrix proteins that help to organize photoreceptor ribbon synapses in the outer plexiform layer. We examine the proteins that foster the clustering of release proteins, calcium channels, and synaptic vesicles in the presynaptic terminals of photoreceptors adjacent to their postsynaptic contacts. Although many proteins interact with one another in the presynaptic terminal and synaptic cleft, these protein–protein interactions do not create a static and immutable structure. Instead, photoreceptor ribbon synapses are remarkably dynamic, exhibiting structural changes on both rapid and slow time scales.
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Symons, Jane L., Julie Jamison, Jane Dening, Linda Murray, and Sue Pearson. "Improving care coordination in community physical rehabilitation: A qualitative study of the change framework." International Journal of Care Coordination 22, no. 3-4 (September 2019): 140–47. http://dx.doi.org/10.1177/2053434519895423.
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Introduction Contemporary rehabilitation change relies on effective collaboration and ongoing social interactions among stakeholders. The study objective was to explore the influence of the selected change framework and underlying social interactions during a care coordination improvement project. Methods A qualitative study collected data from 35 employees in a community physical rehabilitation service. Participants were not only undergoing change to improve client care coordination but were also facilitating the change processes themselves. Symbolic interactionism guided the research design, and data were collected using interviews and observation. Blumer’s six root beliefs were used for deductive data analysis and provided the framework for the findings. Results Findings highlight that the perceptions of the selected change framework were mixed yet dynamic, with modification occurring via social interaction. Elements of Kotter’s eight steps, lean thinking, and transformational change models were trialed. Implementation of the change processes required formal and informal group social interactions. Participants’ different outlooks explained their mixed response to the change processes. Participants who supported the implemented changes believed the processes and outcomes were clear, appropriate, and inclusive. Time, energy, and positive social interactions enabled employees to drive change, with more of these resources desired to refine the vision, problem-solve implementation, and further improve care coordination. Discussion This study enhances the understanding of how employees and the community physical rehabilitation service shaped each other during the change processes. The focus on social interactions highlights the slow rate of improved care coordination and need for increased resources and/or duration for successful change.
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Angelaki, D. E., and B. J. Hess. "Three-dimensional organization of otolith-ocular reflexes in rhesus monkeys. I. Linear acceleration responses during off-vertical axis rotation." Journal of Neurophysiology 75, no. 6 (June 1, 1996): 2405–24. http://dx.doi.org/10.1152/jn.1996.75.6.2405.
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1. The dynamic properties of otolith-ocular reflexes elicited by sinusoidal linear acceleration along the three cardinal head axes were studied during off-vertical axis rotations in rhesus monkeys. As the head rotates in space at constant velocity about an off-vertical axis, otolith-ocular reflexes are elicited in response to the sinusoidally varying linear acceleration (gravity) components along the interaural, nasooccipital, or vertical head axis. Because the frequency of these sinusoidal stimuli is proportional to the velocity of rotation, rotation at low and moderately fast speeds allows the study of the mid-and low-frequency dynamics of these otolith-ocular reflexes. 2. Animals were rotated in complete darkness in the yaw, pitch, and roll planes at velocities ranging between 7.4 and 184 degrees/s. Accordingly, otolith-ocular reflexes (manifested as sinusoidal modulations in eye position and/or slow-phase eye velocity) were quantitatively studied for stimulus frequencies ranging between 0.02 and 0.51 Hz. During yaw and roll rotation, torsional, vertical, and horizontal slow-phase eye velocity was sinusoidally modulated as a function of head position. The amplitudes of these responses were symmetric for rotations in opposite directions. In contrast, mainly vertical slow-phase eye velocity was modulated during pitch rotation. This modulation was asymmetric for rotations in opposite direction. 3. Each of these response components in a given rotation plane could be associated with an otolith-ocular response vector whose sensitivity, temporal phase, and spatial orientation were estimated on the basis of the amplitude and phase of sinusoidal modulations during both directions of rotation. Based on this analysis, which was performed either for slow-phase eye velocity alone or for total eye excursion (including both slow and fast eye movements), two distinct response patterns were observed: 1) response vectors with pronounced dynamics and spatial/temporal properties that could be characterized as the low-frequency range of “translational” otolith-ocular reflexes; and 2) response vectors associated with an eye position modulation in phase with head position ("tilt" otolith-ocular reflexes). 4. The responses associated with two otolith-ocular vectors with pronounced dynamics consisted of horizontal eye movements evoked as a function of gravity along the interaural axis and vertical eye movements elicited as a function of gravity along the vertical head axis. Both responses were characterized by a slow-phase eye velocity sensitivity that increased three- to five-fold and large phase changes of approximately 100-180 degrees between 0.02 and 0.51 Hz. These dynamic properties could suggest nontraditional temporal processing in utriculoocular and sacculoocular pathways, possibly involving spatiotemporal otolith-ocular interactions. 5. The two otolith-ocular vectors associated with eye position responses in phase with head position (tilt otolith-ocular reflexes) consisted of torsional eye movements in response to gravity along the interaural axis, and vertical eye movements in response to gravity along the nasooccipital head axis. These otolith-ocular responses did not result from an otolithic effect on slow eye movements alone. Particularly at high frequencies (i.e., high speed rotations), saccades were responsible for most of the modulation of torsional and vertical eye position, which was relatively large (on average +/- 8-10 degrees/g) and remained independent of frequency. Such reflex dynamics can be simulated by a direct coupling of primary otolith afferent inputs to the oculomotor plant. (ABSTRACT TRUNCATED)
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Sedlák, Marián. "On the possible role of nonelectrostatic interactions in the mechanism of the slow polyelectrolyte mode observed by dynamic light scattering." Journal of Chemical Physics 101, no. 11 (December 1994): 10140–44. http://dx.doi.org/10.1063/1.468003.
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Norris, Stephen R., Virupakshi Soppina, Aslan S. Dizaji, Kristin I. Schimert, David Sept, Dawen Cai, Sivaraj Sivaramakrishnan, and Kristen J. Verhey. "A method for multiprotein assembly in cells reveals independent action of kinesins in complex." Journal of Cell Biology 207, no. 3 (November 3, 2014): 393–406. http://dx.doi.org/10.1083/jcb.201407086.
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Teams of processive molecular motors are critical for intracellular transport and organization, yet coordination between motors remains poorly understood. Here, we develop a system using protein components to generate assemblies of defined spacing and composition inside cells. This system is applicable to studying macromolecular complexes in the context of cell signaling, motility, and intracellular trafficking. We use the system to study the emergent behavior of kinesin motors in teams. We find that two kinesin motors in complex act independently (do not help or hinder each other) and can alternate their activities. For complexes containing a slow kinesin-1 and fast kinesin-3 motor, the slow motor dominates motility in vitro but the fast motor can dominate on certain subpopulations of microtubules in cells. Both motors showed dynamic interactions with the complex, suggesting that motor–cargo linkages are sensitive to forces applied by the motors. We conclude that kinesin motors in complex act independently in a manner regulated by the microtubule track.