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Journal articles on the topic 'Time-dependent point interactions'
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1
Correggi, Michele, Gianfausto Dell’Antonio, Rodolfo Figari, and Andrea Mantile. "Ionization for Three Dimensional Time-Dependent Point Interactions." Communications in Mathematical Physics 257, no. 1 (February 18, 2005): 169–92. http://dx.doi.org/10.1007/s00220-005-1293-x.
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Carlone, Raffaele, Michele Correggi, Marco Falconi, and Marco Olivieri. "Emergence of Time-Dependent Point Interactions in Polaron Models." SIAM Journal on Mathematical Analysis 53, no. 4 (January 2021): 4657–91. http://dx.doi.org/10.1137/20m1381344.
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Dell'Antonio, G. F., R. Figari, and A. Teta. "A Limit Evolution Problem for Time-Dependent Point Interactions." Journal of Functional Analysis 142, no. 1 (November 1996): 249–75. http://dx.doi.org/10.1006/jfan.1996.0149.
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Kuhn, J., F. M. Zanetti, A. L. Azevedo, A. G. M. Schmidt, Bin Kang Cheng, and M. G. E. da Luz. "Time-dependent point interactions and infinite walls: some results for wavepacket scattering." Journal of Optics B: Quantum and Semiclassical Optics 7, no. 3 (March 1, 2005): S77—S85. http://dx.doi.org/10.1088/1464-4266/7/3/011.
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RENARD, V. T., T. OTA, N. KUMADA, and H. HIRAYAMA. "POSITIVE MAGNETO-RESISTANCE IN A POINT CONTACT: POSSIBLE MANIFESTATION OF INTERACTIONS." International Journal of High Speed Electronics and Systems 17, no. 03 (September 2007): 495–99. http://dx.doi.org/10.1142/s0129156407004680.
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We report a non-monotonic and strongly temperature dependent magneto-resistance observed in clean quantum point contacts. At the same time the conductance of the point contact varies linearly with temperature. This unexpected behavior may be related to electron-electron interactions.
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Rudra, P. "Symmetry group of point transformations for the time-dependent Schrödinger equation: Harmonic interactions among nucleons." Physical Review C 44, no. 4 (October 1, 1991): 1486–92. http://dx.doi.org/10.1103/physrevc.44.1486.
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Flick, Johannes, Michael Ruggenthaler, Heiko Appel, and Angel Rubio. "Kohn–Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space." Proceedings of the National Academy of Sciences 112, no. 50 (December 1, 2015): 15285–90. http://dx.doi.org/10.1073/pnas.1518224112.
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The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron–photon interactions in terms of effective Kohn–Sham potentials. In this work, we numerically construct the exact electron–photon Kohn–Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light–matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account.
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Hofmeister, Anne M., and Everett M. Criss. "Constraints on Newtonian Interplanetary Point-Mass Interactions in Multicomponent Systems from the Symmetry of Their Cycles." Symmetry 13, no. 5 (May 11, 2021): 846. http://dx.doi.org/10.3390/sym13050846.
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Interplanetary interactions are the largest forces in our Solar System that disturb the planets from their elliptical orbits around the Sun, yet are weak (<10−3 Solar). Currently, these perturbations are computed in pairs using Hill’s model for steady-state, central forces between one circular and one elliptical ring of mass. However, forces between rings are not central. To represent interplanetary interactions, which are transient, time-dependent, and cyclical, we build upon Newton’s model of interacting point-mass pairs, focusing on circular orbits of the eight largest bodies. To probe general and evolutionary behavior, we present analytical and numerical models of the interplanetary forces and torques generated during the planetary interaction cycles. From symmetry, over a planetary interaction cycle, radial forces dominate while tangential forces average to zero. Our calculations show that orbital perturbations require millennia to quantify, but observations are only over ~165 years. Furthermore, these observations are compromised because they are predominantly made from Earth, whose geocenter occupies a complex, non-Keplerian orbit. Eccentricity and inclination data are reliable and suggest that interplanetary interactions have drawn orbital planes together while elongating the orbits of the two smallest planets. This finding is consistent with conservation principles governing the eight planets, which formed as a system and evolve as a system.
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Declémy, A., C. Rulliére, and Ph Kottis. "Solvation Dynamics Studied by Picosecond Fluorescence: Microscopic Reorientation and Longitudinal Relaxation of the Solvent." Laser Chemistry 10, no. 5-6 (January 1, 1990): 413–29. http://dx.doi.org/10.1155/1990/86536.
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The dynamics of the Time-Dependent Fluorescence Shift (TDFS) of a rigid polar excited probe dissolved in alcohol solvents at different temperatures have been studied by picosecond time-resolved spectroscopy. The results are compared to previously published results on well characterized polar systems. These results show that solvation dynamics in such systems are strongly scaled by the microscopic (singleparticle) reorientation time τM of the solvent molecules and/or by the (macroscopic) longitudinal relaxation time τL of the solvent. The key point governing this scaling is the relative interaction between the solvent molecules and the probe compared to the interaction between the solvent molecules. It is also shown that specific interactions, such as hydrogen bonded-complex formation, may play an important role.
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Burkitt, Anthony N., Hamish Meffin, and David B. Grayden. "Spike-Timing-Dependent Plasticity: The Relationship to Rate-Based Learning for Models with Weight Dynamics Determined by a Stable Fixed Point." Neural Computation 16, no. 5 (May 1, 2004): 885–940. http://dx.doi.org/10.1162/089976604773135041.
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Experimental evidence indicates that synaptic modification depends on the timing relationship between the presynaptic inputs and the output spikes that they generate. In this letter, results are presented for models of spike-timing-dependent plasticity (STDP) whose weight dynamics is determined by a stable fixed point. Four classes of STDP are identified on the basis of the time extent of their input-output interactions. The effect on the potentiation of synapses with different rates of input is investigated to elucidate the relationship of STDP with classical studies of long-term potentiation and depression and rate-based Hebbian learning. The selective potentiation of higher-rate synaptic inputs is found only for models where the time extent of the input-output interactions is input restricted (i.e., restricted to time domains delimited by adjacent synaptic inputs) and that have a time-asymmetric learning window with a longer time constant for depression than for potentiation. The analysis provides an account of learning dynamics determined by an input-selective stable fixed point. The effect of suppressive interspike interactions on STDP is also analyzed and shown to modify the synaptic dynamics.
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Scott, R. K., and D. G. Dritschel. "Vortex–Vortex Interactions in the Winter Stratosphere." Journal of the Atmospheric Sciences 63, no. 2 (February 1, 2006): 726–40. http://dx.doi.org/10.1175/jas3632.1.
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Abstract This paper examines the interaction of oppositely signed vortices in the compressible (non-Boussinesq) quasigeostrophic system, with a view to understanding vortex interactions in the polar winter stratosphere. A series of simplifying approximations leads to a two-vortex system whose dynamical properties are determined principally by two parameters: the ratio of the circulation of the vortices and the vertical separation of their centroids. For each point in this two-dimensional parameter space a family of equilibrium solutions exists, further parameterized by the horizontal separation of the vortex centroids, which are stable for horizontal separations greater than a critical value. The stable equilibria are characterized by vortex deformations that generally involve stronger deformations of the larger and/or lower of the two vortices. For smaller horizontal separations, the equilibria are unstable and a strongly nonlinear, time-dependent interaction takes place, typically involving the shedding of material from the larger vortex while the smaller vortex remains coherent. Qualitatively, the interactions resemble previous observations of certain stratospheric sudden warmings that involved the interaction of a growing anticyclonic circulation with the cyclonic polar vortex.
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Fang, Jim, and Karen Mosier. "Literature Values of Terminal Half-Lives of Clozapine are Dependent on the Time of the Last Data Point." Journal of Pharmacy & Pharmaceutical Sciences 17, no. 2 (April 16, 2014): 187. http://dx.doi.org/10.18433/j3kc7p.
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The pharmacokinetics of clozapine is a subject of intensive research because of its narrow therapeutic window and susceptibility to drug-drug interactions. A systematic literature search was conducted in PubMed and Google Scholar for half-life values of clozapine in humans. Twenty-one publications were found to contain terminal half-life information of clozapine in humans along with the time of the last plasma sample. Average values of the terminal half-lives of clozapine were calculated to be 10.2, 13.2, 14.2, 18.3 and 29.2 hours with a last data point at 12, 24, 48, 72 and 120 hours, respectively. This confirms the notion that one would arrive at longer terminal half-lives when longer blood sampling times are used in pharmacokinetic studies on clozapine. “Terminal half-lives” of therapeutic agent are routinely computed and reported in literature. For drugs with a third deep compartment such as clozapine, one should remember to consider the time of the last data point when comparing the “terminal” half-life.
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Zhang, Kuilin, Hani S. Mahmassani, and Chung-Cheng Lu. "Probit-Based Time-Dependent Stochastic User Equilibrium Traffic Assignment Model." Transportation Research Record: Journal of the Transportation Research Board 2085, no. 1 (January 2008): 86–94. http://dx.doi.org/10.3141/2085-10.
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This study presents a time-dependent stochastic user equilibrium (TDSUE) traffic assignment model within a probit-based path choice decision framework that explicitly takes into account temporal and spatial correlation (traveler interactions) in travel disutilities across a set of paths. The TDSUE problem, which aims to find time-dependent SUE path flows, is formulated as a fixed-point problem and solved by a simulation-based method of successive averages algorithm. A mesoscopic traffic simulator is employed to determine (experienced) time-dependent travel disutilities. A time-dependent shortest-path algorithm is applied to generate new paths and augment a grand path set. Two vehicle-based implementation techniques are proposed and compared in order to show their impact on solution quality and computational efficiency. One uses the classical Monte Carlo simulation approach to explicitly compute path choice probabilities, and the other determines probabilities by sampling vehicles’ path travel costs from an assumed perception error distribution (also using a Monte Carlo simulation process). Moreover, two types of variance-covariance error structures are discussed: one considers temporal and spatial path choice correlation (due to path overlapping) in terms of aggregated path travel times, and the other uses experienced (or empirical) path travel times from a sample of individual vehicle trajectories. A set of numerical experiments are conducted to investigate the convergence pattern of the solution algorithms and to examine the impact of temporal and spatial correlation on path choice behavior.
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Cha, Chae Young, Enrique Santos, Akira Amano, Takao Shimayoshi, and Akinori Noma. "Time-dependent changes in membrane excitability during glucose-induced bursting activity in pancreatic β cells." Journal of General Physiology 138, no. 1 (June 27, 2011): 39–47. http://dx.doi.org/10.1085/jgp.201110612.
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In our companion paper, the physiological functions of pancreatic β cells were analyzed with a new β-cell model by time-based integration of a set of differential equations that describe individual reaction steps or functional components based on experimental studies. In this study, we calculate steady-state solutions of these differential equations to obtain the limit cycles (LCs) as well as the equilibrium points (EPs) to make all of the time derivatives equal to zero. The sequential transitions from quiescence to burst–interburst oscillations and then to continuous firing with an increasing glucose concentration were defined objectively by the EPs or LCs for the whole set of equations. We also demonstrated that membrane excitability changed between the extremes of a single action potential mode and a stable firing mode during one cycle of bursting rhythm. Membrane excitability was determined by the EPs or LCs of the membrane subsystem, with the slow variables fixed at each time point. Details of the mode changes were expressed as functions of slowly changing variables, such as intracellular [ATP], [Ca2+], and [Na+]. In conclusion, using our model, we could suggest quantitatively the mutual interactions among multiple membrane and cytosolic factors occurring in pancreatic β cells.
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Lo, Chun-Min, Jun-Chih Lo, Priscila Y. Sato, Tsz-Lun Yeung, Samuel C. Mok, and Kay-Pong Yip. "Monitoring of ovarian cancer cell invasion in real time with frequency-dependent impedance measurement." American Journal of Physiology-Cell Physiology 311, no. 6 (December 1, 2016): C1040—C1047. http://dx.doi.org/10.1152/ajpcell.00211.2016.
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The conventional approach to assessing cancer invasion is primarily for end-point analysis, which does not provide temporal information on the invasion process or any information on the interactions between invading cells and the underlying adherent cells. To alleviate these limitations, the present study exploited electric cell-substrate impedance sensing (ECIS) to monitor the invasion of ovarian cancer cells (SKOV-3) through an adherent monolayer of human umbilical vein endothelial cells (HUVECs). Impedance was measured at 4 kHz of AC voltage or was measured as a function of AC frequency (25 Hz to 60 kHz). By measuring impedance at 4-kHz AC, we found that the invasion of SKOV-3 cells through the HUVEC monolayer was manifested as a rapid decrease in transendothelial electrical resistance in real time. The invasion was augmented in the presence of hepatocyte growth factor (HGF). The enhancing effect of HGF was attenuated by c-Met inhibitor (SU11274). By measuring the frequency-dependent impedance of SKOV-3 cells over time, we found that HGF-enhanced SKOV-3 cell invasion was accomplished with reduced junctional resistance ( Rb), increased average cell-substrate separation ( h), and increased micromotion. SU11274 attenuated the effects of HGF on Rb, h, and micromotion in the SKOV-3 monolayer. SU11274 also increased the barrier function of the HUVEC monolayer by increasing Rb and decreasing h. In conclusion, this study demonstrated an improved method for monitoring and studying the interactions between cancer cells and the underlying adherent cells during invasion in real time. Alterations in cellular biophysical properties ( Rb, h) associated with cancer transendothelial invasion were detected.
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Costa, João, Josep Valls-Solé, Francesc Valldeoriola, and Jordi Rumià. "Subcortical Interactions Between Somatosensory Stimuli of Different Modalities and Their Temporal Profile." Journal of Neurophysiology 100, no. 3 (September 2008): 1610–21. http://dx.doi.org/10.1152/jn.90412.2008.
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Interactions between inputs of different sensory modality occur along the sensory pathway, including the thalamus. However, the temporal profile of such interaction has not been fully studied. In eight patients who had been implanted an intrathalamic electrode for deep brain stimulation as symptomatic treatment of tremor, we investigated the interactions between mechanical taps and electrical nerve stimuli. Somatosensory evoked potentials (SEPs) were recorded from Erb's point, cervical spinal cord, nucleus ventrointermedialis of the thalamus, and parietal cortex. A handheld electronic reflex hammer was used to deliver a mechanical tap to the skin overlying the first dorsal interosseous muscle and to trigger an ipsilateral digital median nerve electrical stimulus time-locked to the mechanical tap with a variable delay of 0 to 50 ms. There were significant time-dependent interactions between the two sensory volleys at the subcortical level. Thalamic SEPs were decreased in amplitude at interstimulus intervals (ISIs) from 10 to 40 ms with maximum effect at 20 ms (−42.8 ± 10.5%; P < 0.001). A similar decrease was also seen in the number and frequency of the high-frequency components of thalamic SEPs (−25 ± 4%). A smaller reduction (−18.1 ± 5.8%; P < 0.001) was present in upper cervical response at ISI = 20 ms. There were no changes in peripheral responses. Cortical SEPs were almost completely absent in some subjects at ISIs from 20 to 50 ms. There were no changes in SEP latencies. Our results indicate that significant time-dependent interactions between sensory volleys occur at the subcortical level. These observations provide further insight into the physiological mechanisms underlying afferent gating between sensory volleys of different modality.
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Chang, Andrew, and Simon Y. Tang. "Determination of the Depth- and Time- Dependent Mechanical Behavior of Mouse Articular Cartilage Using Cyclic Reference Point Indentation." CARTILAGE 11, no. 3 (July 18, 2018): 358–63. http://dx.doi.org/10.1177/1947603518786554.
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Mouse models of osteoarthritis and cartilage degeneration are important and powerful tools for investigating the molecular mechanisms of the disease pathology. Because of the vast number of genetically modified mouse models that are available for research, the ability to use these models is particularly attractive for the mechanobiologic interactions in the pathogenesis of osteoarthritis. However, the very small scale of mouse articular cartilage, where the healthy tissue is only 80 µm in thickness, poses challenges in quantifying mechanical characteristics of the tissue. We introduce here a novel approach that combines experimental and analytical methods to quantify the nuanced mechanical changes during cartilage degeneration at this scale. Cyclic reference point indentation is used to directly test the murine articular cartilage to obtain the force-deformation and the phase-shift characteristics of the tissue. The cartilage zonal thicknesses are confirmed from histology. These data are then fitted to a parallel spring model to determine the depth-dependent tissue stiffness and modulus. Using this approach, we investigated the effects of trypsin degradation on the zonal mechanical behavior of mouse articular cartilage. We observe a decline of the superficial zone stiffness coupled with the loss of the superficial layer. Subsequent degradation by trypsin allowed the identification of middle- and deep- zone properties. Taken together, this approach can be a useful tool for understanding the disease mechanisms of cartilage homeostasis and degeneration, and for monitoring of therapies for osteoarthritis.
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Mun, Seyoung, Kyudong Han, and Jung Keun Hyun. "The Time Sequence of Gene Expression Changes after Spinal Cord Injury." Cells 11, no. 14 (July 18, 2022): 2236. http://dx.doi.org/10.3390/cells11142236.
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Gene expression changes following spinal cord injury (SCI) are time-dependent, and an accurate understanding of these changes can be crucial in determining time-based treatment options in a clinical setting. We performed RNA sequencing of the contused spinal cord of rats at five different time points from the very acute to chronic stages (1 hour, 1 day, 1 week, 1 month, and 3 months) following SCI. We identified differentially expressed genes (DEGs) and Gene Ontology (GO) terms at each time point, and 14,257 genes were commonly expressed at all time points. The biological process of the inflammatory response was increased at 1 hour and 1 day, and the cellular component of the integral component of the synaptic membrane was increased at 1 day. DEGs associated with cell activation and the innate immune response were highly enriched at 1 week and 1 month, respectively. A total of 2841 DEGs were differentially expressed at any of the five time points, and 18 genes (17 upregulated and 1 downregulated) showed common expression differences at all time points. We found that interleukin signaling, neutrophil degranulation, eukaryotic translation, collagen degradation, LGI–ADAM interactions, GABA receptor, and L1CAM-ankyrin interactions were prominent after SCI depending on the time post injury. We also performed gene–drug network analysis and found several potential antagonists and agonists which can be used to treat SCI. We expect to discover effective treatments in the clinical field through further studies revealing the efficacy and safety of potential drugs.
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HÓRVÖLGYI, Z., and M. ZRINYI. "INTERFACIAL AGGREGATION OF FLOATING MICROPARTICLES UNDER THE CONTROL OF SHORT-RANGE COLLOID AND VERY LONG-RANGE CAPILLARY FORCES." Fractals 01, no. 03 (September 1993): 460–69. http://dx.doi.org/10.1142/s0218348x93000484.
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Interfacial aggregation of surface modified glass beads (62–74 μm diameter) at water/air interface was carried out by using two differently hydrophobic samples, respectively. The effect of aggregation time on the self-similar structure of forming aggregates was studied comparing the actual results to those obtained previously.1 The time dependence of restructuring from the point of view of fractal geometry has been proved but the results call attention to another time dependent process— orientation of growing clusters during their collisions due to anisotropy of cluster-cluster interactions.
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Shishkin, I., T. Alon, R. Dagan, and P. Ginzburg. "Temperature and Phase Transition Sensing in Liquids with Fluorescent Probes." MRS Advances 2, no. 44 (2017): 2391–99. http://dx.doi.org/10.1557/adv.2017.391.
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ABSTRACTLocal environment of fluorescent dyes could strongly affects emission dynamics of the latter. In particular, both signal intensities and emission lifetimes are highly sensitive to solvent temperatures. Here, temperature-dependent behavior Rhodamine B fluorescence in water and ethanol solutions was experimentally investigated. Phase transition point between liquid water and ice was shown to have a dramatic impact on both in intensity (30-fold drop) and in lifetime (from 2.68 ns down to 0.13 ns) of the dye luminescence along with the shift of spectral maxima from 590 to 625 nm. At the same time, use of ethanol as solvent does not lead to any similar behavior. The reported results and approaches enable further investigations of dye-solvent interactions and studies of physical properties at phase transition points.
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Karlsson, Jan Olof G., Per Jynge, and Louis J. Ignarro. "The Damaging Outcome of the POLAR Phase III Trials Was Due to Avoidable Time-Dependent Redox Interaction between Oxaliplatin and PledOx." Antioxidants 10, no. 12 (December 3, 2021): 1937. http://dx.doi.org/10.3390/antiox10121937.
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On 2 July 2021, highly negative results were reported from the POLAR A and M phase III trials in patients with colorectal cancer, treated with an oxaliplatin-based regimen and co-treated with calmangafodipir (CaM; PledOx®; PledPharma AB/Egetis Therapeutics AB) or placebo. The results revealed persistent chemotherapy-induced peripheral neuropathy (CIPN) in 54.8% of the patients treated with PledOx, compared with 40.0% of the patients treated with the placebo (p < 0.05), i.e., a 37% increase in incidence of the side effect that the trial was aimed to prevent. The damaging outcome of the trials differed diametrically from an in-parallel conducted mice study and from a clinical trial with mangafodipir, the active ingredient of CaM. According to the authors of the POLAR report, the etiology of the profound increase in CIPN in the PledOx arm is unclear. However, these devastating effects are presumably explained by intravenous administrations of PledOx and oxaliplatin being too close in time and, thereby, causing unfavorable redox interactions between Mn2+ and Pt2−. In the mice study as well as in the preceding phase II clinical trial (PLIANT), PledOx was administered 10 min before the start of the oxaliplatin infusion; this was clearly an administration procedure, where the devastating interactions between PledOx and oxaliplatin could be avoided. However, when it comes to the POLAR trials, PledOx was administered, for incomprehensible reasons, “on Top of Modified FOLFOX6” at day one, i.e., after the two-hour oxaliplatin infusion instead of before oxaliplatin. This is a time point when the plasma concentration of oxaliplatin and Pt2+-metabolites is at its highest, and where the risk of devastating redox interactions between PledOx and oxaliplatin, in turn, is at its highest.
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Cammack, Alexander J., Arnav Moudgil, Jiayang Chen, Michael J. Vasek, Mark Shabsovich, Katherine McCullough, Allen Yen, et al. "A viral toolkit for recording transcription factor–DNA interactions in live mouse tissues." Proceedings of the National Academy of Sciences 117, no. 18 (April 16, 2020): 10003–14. http://dx.doi.org/10.1073/pnas.1918241117.
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Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF-occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only end-point snapshots of TF binding. Alternatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do not require TF-specific antibodies and offer the potential for unique applications, such as recording of TF occupancy over time and cell type specificity through conditional expression of the TF–enzyme fusion. Here, we create a viral toolkit for one such method, calling cards, and demonstrate that these reagents can be delivered to the live mouse brain and used to report TF occupancy. Further, we establish a Cre-dependent calling cards system and, in proof-of-principle experiments, show utility in defining cell type-specific TF profiles and recording and integrating TF-binding events across time. This versatile approach will enable unique studies of TF-mediated gene regulation in live animal models.
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LE DIZÈS, STÉPHANE, and ALBERTO VERGA. "Viscous interactions of two co-rotating vortices before merging." Journal of Fluid Mechanics 467 (September 24, 2002): 389–410. http://dx.doi.org/10.1017/s0022112002001532.
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The viscous evolution of two co-rotating vortices is analysed using direct two-dimensional numerical simulations of the Navier–Stokes equations. The article focuses on vortex interaction regimes before merging. Two parameters are varied: a steepness parameter n which measures the steepness of the initial vorticity profiles in a given family of profiles, and the Reynolds number Re (between 500 and 16 000). Two distinct relaxation processes are identified. The first one is non-viscous and corresponds to a rapid adaptation of each vortex to the external (strain) field generated by the other vortex. This adaptation process, which is profile dependent, is described and explained using the damped Kelvin modes of each vortex. The second relaxation process is a slow diffusion phenomenon. It is similar to the relaxation of any non-Gaussian axisymmetrical vortex towards the Gaussian. The quasi-stationary solution evolves on a viscous-time scale toward a single attractive solution which corresponds to the evolution from two initially Gaussian vortices. The attractive solution is analysed in detail up to the merging threshold a/b ≈ 0.22 where a and b are the vortex radius and the separation distance respectively. The vortex core deformations are quantified and compared to those induced by a single vortex in a rotating strain field. A good agreement with the asymptotic predictions is demonstrated for the eccentricity of vortex core streamlines. A weak anomalous Reynolds number dependence of the solution is also identified. This dependence is attributed to the advection–diffusion of vorticity towards the hyperbolic points of the system and across the separatrix connecting these points. A Re1/3 scaling for the vorticity at the central hyperbolic point is obtained. These findings are discussed in the context of a vortex merging criterion.
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Moscou, Matthew J., Nick Lauter, Rico A. Caldo, Dan Nettleton, and Roger P. Wise. "Quantitative and Temporal Definition of the Mla Transcriptional Regulon During Barley–Powdery Mildew Interactions." Molecular Plant-Microbe Interactions® 24, no. 6 (June 2011): 694–705. http://dx.doi.org/10.1094/mpmi-09-10-0211.
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Barley Mildew resistance locus a (Mla) is a major determinant of immunity to the powdery mildew pathogen, Blumeria graminis f. sp. hordei. Alleles of Mla encode cytoplasmic- and membrane-localized coiled-coil, nucleotide binding site, leucine-rich repeat proteins that mediate resistance when complementary avirulence effectors (AVRa) are present in the pathogen. Presence of an appropriate AVRa protein triggers nuclear relocalization of MLA, in which MLA binds repressing host transcription factors. Timecourse expression profiles of plants harboring Mla1, Mla6, and Mla12 wild-type alleles versus paired loss-of-function mutants were compared to discover conserved transcriptional targets of MLA and downstream signaling cascades. Pathogen-dependent gene expression was equivalent or stronger in susceptible plants at 20 h after inoculation (HAI) and was attenuated at later timepoints, whereas resistant plants exhibited a time-dependent strengthening of the transcriptional response, increasing in both fold change and the number of genes differentially expressed. Deregulation at 20 HAI implicated 16 HAI as a crucial point in determining the future trajectory of this interaction and was interrogated by quantitative analysis. In total, 28 potential transcriptional targets of the MLA regulon were identified. These candidate targets possess a diverse set of predicted functions, suggesting that multiple pathways are required to mediate the hypersensitive reaction.
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Smale, Scott, Peiru He, Ben A. Olsen, Kenneth G. Jackson, Haille Sharum, Stefan Trotzky, Jamir Marino, Ana Maria Rey, and Joseph H. Thywissen. "Observation of a transition between dynamical phases in a quantum degenerate Fermi gas." Science Advances 5, no. 8 (August 2019): eaax1568. http://dx.doi.org/10.1126/sciadv.aax1568.
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A proposed paradigm for out-of-equilibrium quantum systems is that an analog of quantum phase transitions exists between parameter regimes of qualitatively distinct time-dependent behavior. Here, we present evidence of such a transition between dynamical phases in a cold-atom quantum simulator of the collective Heisenberg model. Our simulator encodes spin in the hyperfine states of ultracold fermionic potassium. Atoms are pinned in a network of single-particle modes, whose spatial extent emulates the long-range interactions of traditional quantum magnets. We find that below a critical interaction strength, magnetization of an initially polarized fermionic gas decays quickly, while above the transition point, the magnetization becomes long-lived because of an energy gap that protects against dephasing by the inhomogeneous axial field. Our quantum simulation reveals a nonequilibrium transition predicted to exist but not yet directly observed in quenched s-wave superconductors.
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Szmidt, Kazimierz, and Benedykt Hedzielski. "Nonlinear Interactions between Gravity Waves in Water of Constant Depth." Archives of Hydro-Engineering and Environmental Mechanics 62, no. 1-2 (June 1, 2015): 3–25. http://dx.doi.org/10.1515/heem-2015-0016.
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AbstractThe paper deals with interactions between water waves propagating in fluid of constant depth. In formulation of this problem, a nonlinear character of these interactions is taken into account. In particular, in order to simplify a solution to nonlinear boundary conditions at the free surface, a system of material coordinates is employed as independent variables in the description of the phenomenon. The main attention is focused on the transient solutions corresponding to fluid motion starting from rest. With respect to the initial value problem considered, we confine our attention to a finite fluid domain. For a finite elapse of time, measured from the starting point, the solution in a finite fluid area mimics a solution within an infinite domain, inherent for wave propagation problems. Because of the complicated structure of equations describing nonlinear waves, an approximate formulation is considered, which is based on a power series expansion of dependent variables with respect to a small parameter. Such a solution is assumed to be accurate in describing the main features of the phenomenon. Numerical experiments are conducted to illustrate the approximate formulation developed in this paper.
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Fernández, Berta, Zulema Fernández, Emilio Quiñoá, and Félix Freire. "From Oligo(Phenyleneethynylene) Monomers to Supramolecular Helices: The Role of Intermolecular Interactions in Aggregation." Molecules 26, no. 12 (June 9, 2021): 3530. http://dx.doi.org/10.3390/molecules26123530.
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Supramolecular helices that arise from the self-assembly of small organic molecules via non-covalent interactions play an important role in the structure and properties of the corresponding materials. Here we study the supramolecular helical aggregation of oligo(phenyleneethynylene) monomers from a theoretical point of view, always guiding the studies with experimentally available data. In this way, by systematically increasing the number of monomer units, optimized n-mer geometries are obtained along with the corresponding absorption and circular dichroism spectra. For the geometry optimizations we use density functional theory together with the B3LYP-D3 functional and the 6–31G** basis set. For obtaining the spectra we resort to time-dependent density functional theory using the CAM-B3LYP functional and the 3–21G basis set. These combinations of density functional and basis set were selected after systematic convergence studies. The theoretical results are analyzed and compared to the experimentally available spectra, observing a good agreement.
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Lazaryan, N., and H. Sedaghat. "Dynamics of Planar Systems That Model Stage-Structured Populations." Discrete Dynamics in Nature and Society 2015 (2015): 1–14. http://dx.doi.org/10.1155/2015/137182.
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We study a general discrete planar system for modeling stage-structured populations. Our results include conditions for the global convergence of orbits to zero (extinction) when the parameters (vital rates) are time and density dependent. When the parameters are periodic we obtain weaker conditions for extinction. We also study a rational special case of the system for Beverton-Holt type interactions and show that the persistence equilibrium (in the positive quadrant) may be globally attracting even in the presence of interstage competition. However, we determine that with a sufficiently high level of competition, the persistence equilibrium becomes unstable (a saddle point) and the system exhibits period two oscillations.
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Welsh, Rory M., Stephanie M. Rosales, Jesse R. Zaneveld, Jérôme P. Payet, Ryan McMinds, Steven L. Hubbs, and Rebecca L. Vega Thurber. "Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled byHalobacteriovoraxpredators." PeerJ 5 (May 31, 2017): e3315. http://dx.doi.org/10.7717/peerj.3315.
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Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. The coral microbiome contains diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the mechanism and controls of overall structure, stability, and function of the microbiome. We sought to test how coral microbiome dynamics were affected by interactions between two bacteria:Vibrio coralliilyticus, a known temperature-dependent pathogen of some corals, andHalobacteriovorax, a unique bacterial predator ofVibrioand other gram-negative bacteria. We challenged reef-building coral withV. coralliilyticusin the presence or absence ofHalobacteriovoraxpredators, and monitored microbial community dynamics with 16S rRNA gene profiling time-series.Vibrio coralliilyticusinoculation increased the mean relative abundance ofVibriosby greater than 35% from the 4 to 8 hour time point, but not in the 24 & 32 hour time points. However, strong secondary effects of theVibriochallenge were also observed for the rest of the microbiome such as increased richness (observed species), and reduced stability (increased beta-diversity). Moreover, after the transient increase inVibrios,two lineages of bacteria (RhodobacteralesandCytophagales) increased in coral tissues, suggesting thatV. coralliilyticuschallenge opens niche space for these known opportunists.Rhodobacteralesincreased from 6.99% (±0.05 SEM) to a maximum mean relative abundance of 48.75% (±0.14 SEM) in the final time point andCytophagalesfrom <0.001% to 3.656%.Halobacteriovoraxpredators are commonly present at low-abundance on coral surfaces. Based on the keystone role of predators in many ecosystems, we hypothesized thatHalobacteriovoraxpredators might help protect corals by consuming foreign or “alien” gram negative bacteria.Halobacteriovoraxinoculation also altered the microbiome but to a lesser degree thanV. coralliilyticus, andHalobacteriovoraxwere never detected after inoculation. Simultaneous challenge with bothV. coralliilyticusand predatoryHalobacteriovoraxeliminated the increase inV. coralliilyticus, ameliorated changes to the rest of the coral microbiome, and prevented the secondary blooms of opportunisticRhodobacteralesandCytophagalesseen in theV. coralliilyticuschallenge. These data suggest that, under certain circumstances, host-associated bacterial predators may mitigate the ability of other bacteria to destabilize the microbiome.
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Knopoff, Damián A., and Germán A. Torres. "On an optimal control strategy in a kinetic social dynamics model." Communications in Applied and Industrial Mathematics 9, no. 2 (December 1, 2018): 22–33. http://dx.doi.org/10.2478/caim-2018-0014.
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Abstract Kinetic models have so far been used to model wealth distribution in a society. In particular, within the framework of the kinetic theory for active particles, some important models have been developed and proposed. They involve nonlinear interactions among individuals that are modeled according to game theoretical tools by introducing parameters governing the temporal dynamics of the system. In this present paper we propose an approach based on optimal control tools that aims to optimize this evolving dynamics from a social point of view. Namely, we look for time dependent control variables concerning the distribution of wealth that can be managed, for instance, by the government, in order to obtain a given social profile.
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Gozal, Evelyne, and David Gozal. "Invited Review: Respiratory plasticity following intermittent hypoxia: developmental interactions." Journal of Applied Physiology 90, no. 5 (May 1, 2001): 1995–99. http://dx.doi.org/10.1152/jappl.2001.90.5.1995.
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Intermittent hypoxia (IH) is the most frequent form of hypoxia occurring in the developing mammal. On one hand, the maturational process of neural, mechanical, pulmonary, and sleep state-dependent factors will favor the occurrence of IH during early postnatal life. On the other hand, it has also become clear that hypoxia, even when short lasting, can modify subsequent respiratory responses to hypoxia and induce a variety of genes whose consequences will persist for much longer periods than the duration of the hypoxic stimulus itself, i.e., functional and adaptive plasticities. The dynamic interactions between the overall duration and recurring frequency of IH, the severity of IH, and the level of neural maturity at the time of IH will modify the ventilatory, metabolic, and cardiovascular responses to hypoxia. We propose that the earlier IH will occur in the developmental course the more likely that the physiological responses to an ulterior hypoxic challenge will be altered even into adulthood. At this point in time, a critical examination of the field would suggest that the short-term alterations of the hypoxic ventilatory response (HVR) of the developing mammal to IH are qualitatively similar to those of the adult and display a biphasic pattern, namely, initial enhancement of the HVR followed by a reduction in HVR. However, the short- and long-term effects of IH on the modulation of neurotransmitter release, receptor binding and expression, intracellular signaling cascades, transcriptional regulation, and gene expression as a function of animal maturity are almost completely unknown. Further delineation of such complex responses to IH may permit the formulation of interventional strategies aiming at reducing the overall vulnerability of the young infant and child to apnea and sudden death.
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García-Valdivia, Antonio A., Estitxu Echenique-Errandonea, Gloria B. Ramírez-Rodríguez, José M. Delgado-López, Belén Fernández, Sara Rojas, Javier Cepeda, and Antonio Rodríguez-Diéguez. "Photoluminescent Coordination Polymers Based on Group 12 Metals and 1H-Indazole-6-Carboxylic Acid." Inorganics 9, no. 3 (March 22, 2021): 20. http://dx.doi.org/10.3390/inorganics9030020.
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Two new coordination polymers (CPs) based on Zn(II) and Cd(II) and 1H-indazole-6-carboxylic acid (H2L) of general formulae [Zn(L)(H2O)]n (1) and [Cd2(HL)4]n (2) have been synthesized and fully characterized by elemental analyses, Fourier transformed infrared spectroscopy and single crystal X-ray diffraction. The results indicate that compound 1 possesses double chains in its structure whereas 2 exhibits a 3D network. The intermolecular interactions, including hydrogen bonds, C–H···π and π···π stacking interactions, stabilize both crystal structures. Photoluminescence (PL) properties have shown that compounds 1 and 2 present similar emission spectra compared to the free-ligand. The emission spectra are also studied from the theoretical point of view by means of time-dependent density-functional theory (TD-DFT) calculations to confirm that ligand-centred π-π* electronic transitions govern emission of compound 1 and 2. Finally, the PL properties are also studied in aqueous solution to explore the stability and emission capacity of the compounds.
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Oleszko-Torbus, Natalia, Marcelina Bochenek, Alicja Utrata-Wesołek, Agnieszka Kowalczuk, Andrzej Marcinkowski, Andrzej Dworak, Agnieszka Fus-Kujawa, Aleksander L. Sieroń, and Wojciech Wałach. "Poly(2-oxazoline) Matrices with Temperature-Dependent Solubility—Interactions with Water and Use for Cell Culture." Materials 13, no. 12 (June 13, 2020): 2702. http://dx.doi.org/10.3390/ma13122702.
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In this work, we studied the stability of matrices with temperature-dependent solubility and their interactions with water at physiological temperature for their application in cell culture in vitro. Gradient copolymers of 2-isopropyl- with 2-n-propyl-2-oxazoline (P(iPrOx-nPrOx)) were used to prepare the matrices. The comonomer ratio during polymerization was chosen such that the cloud point temperature (TCP) of the copolymer was below 37 °C while the glass transition (Tg) was above 37 °C. The role of the support for matrices in the context of their stability in aqueous solution was examined. Therefore, matrices in the form of both self-supported bulk polymer materials (fibrillar mats and molds) and polymer films supported on the silica slides were examined. All of the matrices remained undissolved when incubated in water at a temperature above TCP. For the self-supported mats and molds, we observed the loss of shape stability, but, in the case of films supported on silica slides, only slight changes in morphology were observed. For a more in-depth investigation of the origin of the shape deformation of self-supported matrices, we analyzed the wettability, thickness, and water uptake of films on silica support because the matrices remained undeformed under these conditions. It was found that, above the TCP of P(iPrOx-nPrOx), the wettability of the films decreased, but at the same time the films absorbed water and swelled. We examined how this specific behavior of the supported films influenced the culture of fibroblasts. The temperature-dependent solubility of the matrices and the possibility of noninvasive cell separation were also examined.
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Noor, Shahani, J. Nance, David Lo, Monica Carson, and Emma Wilson. "CCL21 dependent CD4+ T cell migration plays a role in protective immune responses against Toxoplasma infection in the brain. (99.22)." Journal of Immunology 186, no. 1_Supplement (April 1, 2011): 99.22. http://dx.doi.org/10.4049/jimmunol.186.supp.99.22.
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Abstract The chemokine receptor, CCR7 and interactions with its ligands CCL19 and CCL21 are well known to facilitate priming of T cells in lymphoid tissue. Our data demonstrate upregulation of CCR7, CCL19 and CCL21 in the brain during Toxoplasma gondii infection at a time point coincident with the peak of T cell infiltration in the CNS. CNS resident astrocytes significantly upregulate CCL21 following direct infection with Toxoplasma tachyzoites and in the absence of CCL21, plt/plt mice were less efficient in controlling parasite replication during chronic infection. Although T cells enter the infected brain in a CCR7 independent manner, migration of extravasated CD4+T cells from the perivascular area into the CNS parenchyma is CCL21-dependent. Our data also demonstrate accumulation of CD4+CCR7 expressing T cells in the infected brain. A significant proportion of these CCR7+T cells express memory T cell markers including IL-7R (Interleukin 7 Receptor) and CD103 (tissue resident memory phenotype). These data indicate CCR7-CCL21 interactions play a role in guiding CD4+CCR7+ memory T cell migration in the brain to prevent parasite reactivation and disease. Analysis of the behavior and phenotype of this memory T cell population in the absence of CCR7 or CCL21 will be presented. These data address the potential contribution of CCR7/CCL21 mediated interactions to maximize memory responses in the brain during Toxoplasma infection.
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Albeverio, S., Z. Brzezniak, and L. Dabrowski. "Time-dependent propagator with point interaction." Journal of Physics A: Mathematical and General 27, no. 14 (July 21, 1994): 4933–43. http://dx.doi.org/10.1088/0305-4470/27/14/021.
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Bubu, O. M., A. K. Mbah, N. J. Williams, A. D. Turner, A. Parekh, A. E. Mullins, K. Kam, et al. "1153 Association Of Nocturnal Sleep Disturbance And Prospective Cognitive Decline In Cognitive Normal Elderly: Findings From The National Alzheimer’s Coordinating Center Uniform Dataset." Sleep 43, Supplement_1 (April 2020): A439—A440. http://dx.doi.org/10.1093/sleep/zsaa056.1147.
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Abstract Introduction We determined whether nocturnal sleep disturbance (NSD) is associated with prospective cognitive decline in clinically normal older adults Methods Prospective longitudinal study utilizing data from the National Alzheimer’s Coordinating Center (NACC) Uniform Data set (UDS). NSD data, as characterized by the Neuropsychiatric Inventory Questionnaire (NPI-Q), were derived from 10,600 participants at baseline, with at least one UDS follow-up visit, from 32 National Institute of Aging Alzheimer’s Disease Research Centers (ADRC). Prospective cognitive decline was characterized as incident mild cognitive impairment (MCI) diagnosis during UDS follow-up. Logistic mixed-effects model with random intercept and slope examined associations between the NSD and longitudinal cognitive decline. All models included age at baseline, sex, years of education, APOE ε4 status and their interactions with time. Time was operationalized as years from baseline for each participant. Results Of the 10,600 cognitively normal participants at baseline, 1,017 (8.6%) had NSD. The proportion of males versus females with sleep problems was 10.1% vs. 9.3% respectively. For participants with NSD and no NSD, the mean (SD) age was 71 (7.3) and 70 (5.7) years and average follow-up time was 5.2 (2.6) and 4.9 (2.7) years, respectively. Participants with NSD were significantly more likely to develop incident MCI during UDS follow-up (OR: 1.42, p =.003). The interaction of NSD with time was significant (p< .001) suggesting an increase in the likelihood of conversion to MCI increased over time. Furthermore, there were significant differences in mean conversion rates to MCI in the NSD group when the previous time-point was compared to the next (p<01), with a time dependent dose response in the risk of conversion to MCI observed. Conclusion In elderly cognitive-normal individuals, nocturnal sleep disturbance is associated with a time-dependent progression risk to MCI. These findings are consistent with the role of disturbed sleep in the development of Alzheimer’s Disease. Support NIH/NIA/NHLBI (L30-AG064670, CIRAD P30AG059303 Pilot, T32HL129953, R01HL118624, R21AG049348, R21AG055002, R01AG056031, R01AG022374, R21AG059179, R01AG056682, R01AG056531, K07AG05268503, K23HL125939)
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Moore, L. E., K. Yoshii, and B. N. Christensen. "Transfer impedances between different regions of branched excitable cells." Journal of Neurophysiology 59, no. 3 (March 1, 1988): 689–705. http://dx.doi.org/10.1152/jn.1988.59.3.689.
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1. The excitable properties of branched cells were measured using a combination of voltage-clamp and frequency-domain techniques. Point impedance functions from either the soma or growth cone of NG-108 cells were curve fitted with a reduced cable model at different membrane potentials to establish kinetic parameters. 2. Transfer impedance functions between the soma and growth cone were measured and simulated with a morphologically determined model. In these experiments the membrane potential was controlled by a single-electrode voltage clamp thus allowing an estimate of transfer functions for any arbitrary input, such as a single synaptic current for differing degrees of tonic synaptic drive. Furthermore, the integration of different regional inputs was evaluated based on the transfer functions between different locations on an individual cell. 3. The activation of an outward steady-state current leads to resonating impedance functions that were used to evaluate the kinetic properties of ionic channels in different regions of branched excitable cells. For simple branching patterns the point and transfer impedances show lower resonant frequencies for active growth cones compared with active somas. 4. More complex branching patterns showed the unexpected result that the voltage-dependent resonant frequency was higher for the growth cone recording than the soma. The presence of a higher resonant frequency when the growth cone is activated does not require more rapid kinetics of the active potassium conductance, since the time constant of the active conductance can be the same in the growth cone and the soma membrane. 5. In conclusion, the resonant frequencies, as well as all other aspects of the impedance functions, are complicated interactions of the detailed branching patterns and active conductances. In general, these interactions are not predictable from a passive electrotonic analysis, especially when the voltage-dependent conductances are distributed throughout the dendritic tree.
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SUN, JIN, WAN-ZHEN LIANG, and YU LIU. "THEORETICAL STUDIES ON THE LASER-DRIVEN MANY-ELECTRON DYNAMICS OF FINITE-SIZE BORON-NITRIDE NANOTUBES." Journal of Theoretical and Computational Chemistry 07, no. 04 (August 2008): 579–93. http://dx.doi.org/10.1142/s0219633608003976.
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We present a theoretical study on the electronic dynamics of finite-size Boron-Nitride Nanotubes (BNNTs) driven by the linearly polarized (LP) and circularly polarized (CP) intense laser fields. The many-electron dynamics is described by propagating the reduced one-electron density matrix in real-time domain. The high harmonic generation (HHG) spectra and the time evolution of charge density during harmonic generation are demonstrated. Comparison is made with Carbon Nanotubes (CNTs). The selection rules (SRs) for HHG of finite-size nanotubes are established. One of the important consequences of our results is that HHG of finite-size nanotubes are dependent not only on the molecular point-groups but also on the strength of inter chain interactions. The characteristic difference in nonlinear optical properties between finite and infinitely extended zigzag and armchair BNNTs is significant. Another important consequence is that the laser pulse can drive the electrons to move along or normal to tube axis and produce a charge current on the tube wall.
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Blake, R. J., P. V. Coveney, P. Clarke, and S. M. Pickles. "The TeraGyroid Experiment – Supercomputing 2003." Scientific Programming 13, no. 1 (2005): 1–17. http://dx.doi.org/10.1155/2005/435602.
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Amphiphiles are molecules with hydrophobic tails and hydrophilic heads. When dispersed in solvents, they self assemble into complex mesophases including the beautiful cubic gyroid phase. The goal of the TeraGyroid experiment was to study defect pathways and dynamics in these gyroids. The UK's supercomputing and USA's TeraGrid facilities were coupled together, through a dedicated high-speed network, into a single computational Grid for research work that peaked around the Supercomputing 2003 conference. The gyroids were modeled using lattice Boltzmann methods with parameter spaces explored using many 1283and3grid point simulations, this data being used to inform the world's largest three-dimensional time dependent simulation with 10243-grid points. The experiment generated some 2 TBytes of useful data. In terms of Grid technology the project demonstrated the migration of simulations (using Globus middleware) to and fro across the Atlantic exploiting the availability of resources. Integration of the systems accelerated the time to insight. Distributed visualisation of the output datasets enabled the parameter space of the interactions within the complex fluid to be explored from a number of sites, informed by discourse over the Access Grid. The project was sponsored by EPSRC (UK) and NSF (USA) with trans-Atlantic optical bandwidth provided by British Telecommunications.
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Dutta, Goutam, and Yashasvi Giridhar. "Nuclear coupled thermal hydraulic analysis of fast transient depressurization in supercritical channels." International Journal of Numerical Methods for Heat & Fluid Flow 27, no. 5 (May 2, 2017): 1158–71. http://dx.doi.org/10.1108/hff-03-2016-0121.
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Purpose The objective of the present work is to simulate the nuclear coupled thermal–hydraulic fast transient case studies for a vertically up-flowing supercritical pressure water channel of circular cross section. The emphasis is on analyzing the phenomenon of the deterioration in heat transfer (DHT) inside the channel subjected to sharp pressure variations. Design/methodology/approach The thermal–hydraulic model, THRUST, is integrated with the neutron point kinetic (NPK) solver to account for the non-linear interactions between the thermal–hydraulic and neutronic temperature and density reactivity feedback effects. The model implemented and studied accounts for the time-dependent reactor power and is used to analyze various steady-state and flow-induced transient case studies (time-dependent and step change in exit pressure). Findings There is good agreement in the predicted behavior of the supercritical water pressure system with that of the available experimental data for the steady-state case. The event of DHT in the second transient case (step decrease in exit pressure) is found to be more severe than that of exponential pressure decrease. Originality/value This study evaluated a novel implementation of the thermal–hydraulic model, THRUST, integrated with NPKs applied to supercritical pressure water systems for predicting DHT.
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Li, R., Z. Chen, Q. Yu, M. Weng, and Z. Chen. "The Function and Regulatory Network of Pax9 Gene in Palate Development." Journal of Dental Research 98, no. 3 (December 24, 2018): 277–87. http://dx.doi.org/10.1177/0022034518811861.
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Cleft palate, a common congenital deformity, can arise from disruptions in any stage of palatogenesis, including palatal shelf growth, elevation, adhesion, and fusion. Paired box gene 9 (Pax9) is recognized as a vital regulator of palatogenesis with great relevance to cleft palate in humans and mice. Pax9-deficient murine palatal shelves displayed deficient elongation, postponed elevation, failed contact, and fusion. Pax9 is expressed in epithelium and mesenchyme, exhibiting a dynamic expression pattern that changes according to the proceeding of palatogenesis. Recent studies highlighted the Pax9-related genetic interactions and their critical roles during palatogenesis. During palate growth, PAX9 interacts with numerous molecules and members of pathways (e.g., OSR2, FGF10, SHOS2, MSX1, BARX1, TGFβ3, LDB1, BMP, WNT β-catenin dependent, and EDA) in the mesenchyme and functions as a key mediator in epithelial-mesenchymal communications with FGF8, TBX1, and the SHH pathway. During palate elevation, PAX9 is hypothesized to mediate the time point of the elevation event in the anterior and posterior parts of the palatal shelves. The delayed elevation of Pax9 mutant palatal shelves probably results from abnormal expressions of a series of genes ( Osr2 and Bmpr1a) leading to deficient palate growth, abnormal tongue morphology, and altered hyaluronic acid distribution. The interactions between PAX9 and genes encoding the OSR2, TGFβ3, and WNT β-catenin-dependent pathways provide evidence that PAX9 might participate in the regulation of palate fusion. This review summarizes the current understanding of PAX9’s functions and emphasizes the interactions between PAX9 and vital genes during palatogenesis. We hope to provide some clues for further exploration of the function and mechanism of PAX9, especially during palate elevation and fusion events.
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Bouvier, Marlene, and Mingnan Chen. "Analysis of interactions in a soluble tapasin/HLA-B*0801 complex provides a mechanism for peptide selection (93.10)." Journal of Immunology 178, no. 1_Supplement (April 1, 2007): S167. http://dx.doi.org/10.4049/jimmunol.178.supp.93.10.
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Abstract The cell-surface presentation of peptides by class I molecules is the culmination of a complex series of events that take place in the endoplasmic reticulum and involves specialized proteins, including tapasin (TPN). Although it is uncontested that TPN plays a critical role in class I maturation, a mechanistic understanding of TPN is lacking. We examined interactions in a soluble TPN/class I complex using real-time fluorescence measurements. Results show that TPN increases the association and dissociation rates of some, but not all, peptides. TPN acts as a chaperone by increasing the concentration of peptide-deficient class I molecules in solution. We also show that a TPN-assisted mechanism of peptide selection relies on disruption of conserved hydrogen bonds at the C-terminal end of the groove; peptide sequence-dependent interactions along the entire length of the groove also play an important role. Overall, our results suggest that the presence of TPN in the class I assembly complex ensures that bound candidate peptides that cannot meet a certain minimum energy threshold, as needed to conformationally disengage TPN, are excluded from the repertoire. We propose that the net outcome of a TPN-assisted mechanism of peptide selection is to maximize at any point in time, and according to the pool of peptides available, the diversity of minimally stable class I/peptide molecules on the cell surface. Funded by NIH-AI45070
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Pinto, Camila B., Leonardo H. R. Dos Santos, and Bernardo L. Rodrigues. "Understanding metal–ligand interactions in coordination polymers using Hirshfeld surface analysis." Acta Crystallographica Section C Structural Chemistry 75, no. 6 (May 20, 2019): 707–16. http://dx.doi.org/10.1107/s2053229619005874.
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Properties related to the size and shape of Hirshfeld surfaces provide insight into the nature and strength of interactions among the building blocks of molecular crystals. In this work, we demonstrate that functions derived from the curvatures of the surface at a point, namely, shape index (S) and curvedness (C), as well as the distances from the surface to the nearest external (d e) and internal (d i) nuclei, can be used to help understand metal–ligand interactions in coordination polymers. The crystal structure of catena-poly[[[(1,10-phenanthroline-κ2 N,N′)copper(II)]-μ-4-nitrophthalato-κ2 O 1:O 2] trihydrate], {[Cu(C8H3NO6)(C12H8N2)]·3H2O} n , described here for the first time, was used as a prototypical system for our analysis. Decomposition of the coordination polymer into its metal centre and ligand molecules followed by joint analysis of the Hirshfeld surfaces generated for each part unveil qualitative and semi-quantitative information that cannot be easily obtained either from conventional crystal packing analysis or from Hirshfeld surface analysis of the entire polymeric units. The shape index function S is particularly sensitive to the coordination details and its mapping on the surface of the metallic centre is highly dependent on the nature of the ligand and the coordination bond distance. Correlations are established between the shape of the Hirshfeld surface of the metal and the geometry of the metal–ligand contacts in the crystals. This could be applied not only to estimate limiting coordination distances in metal–organic compounds, but also to help establish structure–property relationships potentially useful for the crystal engineering of such materials.
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Veres, Bálint. "Intermedia and Intermittency." Acta Universitatis Sapientiae, Film and Media Studies 9, no. 1 (December 1, 2014): 155–69. http://dx.doi.org/10.1515/ausfm-2015-0008.
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Abstract It is commonly known that medial reflections have been initiated by attempts to secure the borders of discrete medial forms and to define the modus operandi of each essentialized medial area. Later on, the focus of study has shifted to plurimedial formations and the interactions between predefined medial genres. In the last few decades, taxonomic approaches to various multi-, inter-, and transmedial phenomena dominated the discussions, which offered invaluable support in mapping the terrain, but at the same time hindered the analysis of the ephemeral, time-dependent aspects of plurimedial operations. While we explore the properties of each medial configuration, we lose sight of the actual historical drivers that produce ever-new configurations. My thesis is that any discourse on intermediality should be paralleled by a discourse on cultural intermittency, and consequently, media studies should involve an approach that focuses on the “ecosystem” of the constantly renewing media configurations from the point of view of their vitalizing potential and capability to trigger heightened experiences. This approach draws much inspiration from K. Ludwig Pfeiffer’s media anthropology that gives orientation in my paper.
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Batishchev, O. V., L. A. Shilova, M. V. Kachala, V. Y. Tashkin, V. S. Sokolov, N. V. Fedorova, L. A. Baratova, D. G. Knyazev, J. Zimmerberg, and Y. A. Chizmadzhev. "pH-Dependent Formation and Disintegration of the Influenza A Virus Protein Scaffold To Provide Tension for Membrane Fusion." Journal of Virology 90, no. 1 (October 14, 2015): 575–85. http://dx.doi.org/10.1128/jvi.01539-15.
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ABSTRACTInfluenza virus is taken up from a pH-neutral extracellular milieu into an endosome, whose contents then acidify, causing changes in the viral matrix protein (M1) that coats the inner monolayer of the viral lipid envelope. At a pH of ∼6, M1 interacts with the viral ribonucleoprotein (RNP) in a putative priming stage; at this stage, the interactions of the M1 scaffold coating the lipid envelope are intact. The M1 coat disintegrates as acidification continues to a pH of ∼5 to clear a physical path for the viral genome to transit from the viral interior to the cytoplasm. Here we investigated the physicochemical mechanism of M1's pH-dependent disintegration. In neutral media, the adsorption of M1 protein on the lipid bilayer was electrostatic in nature and reversible. The energy of the interaction of M1 molecules with each other in M1 dimers was about 10 times as weak as that of the interaction of M1 molecules with the lipid bilayer. Acidification drives conformational changes in M1 molecules due to changes in the M1 charge, leading to alterations in their electrostatic interactions. Dropping the pH from 7.1 to 6.0 did not disturb the M1 layer; dropping it lower partially desorbed M1 because of increased repulsion between M1 monomers still stuck to the membrane. Lipid vesicles coated with M1 demonstrated pH-dependent rupture of the vesicle membrane, presumably because of the tension generated by this repulsive force. Thus, the disruption of the vesicles coincident with M1 protein scaffold disintegration at pH 5 likely stretches the lipid membrane to the point of rupture, promoting fusion pore widening for RNP release.IMPORTANCEInfluenza remains a top killer of human beings throughout the world, in part because of the influenza virus's rapid binding to cells and its uptake into compartments hidden from the immune system. To attack the influenza virus during this time of hiding, we need to understand the physical forces that allow the internalized virus to infect the cell. In particular, we need to know how the protective coat of protein inside the viral surface reacts to the changes in acid that come soon after internalization. We found that acid makes the molecules of the protein coat push each other while they are still stuck to the virus, so that they would like to rip the membrane apart. This ripping force is known to promote membrane fusion, the process by which infection actually occurs.
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Göçken, Mustafa, Ayşe Tuğba Dosdoğru, Aslı Boru, and Faruk Geyik. "Characterizing continuous (s, S) policy with supplier selection using Simulation Optimization." SIMULATION 93, no. 5 (January 23, 2017): 379–96. http://dx.doi.org/10.1177/0037549716687044.
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A real-world inventory control system, due to its nonlinear, stochastic, time-dependent nature, and the presence of complex interactions between supply chain members, can become quite challenging to optimize and requires a complex model. At this point, the Simulation Optimization (SO) model gains a better understanding of the complex and messy phenomenon of the inventory control of supply chain members. By creating SO models for Distribution Center (DC)s and Suppliers, we wish to present flexible and comprehensible research on the important decision of whether to minimize the differences between total overordering cost and total underordering cost (Model 1) or to minimize the total supply chain cost (Model 2). We also try to point out several important issues: the optimal value of the initial inventory, the reorder point, and the order-up-to level in continuous (s, S) policy for each DC and each Supplier; whether SO models can successfully integrate the supplier selection and continuous (s, S) policy for the supply chain environment; how to apply statistical analysis skills to compare these SO models with a greater level of detail. According to the cost analysis, the total supply chain cost of Model 1 is improved approximately 22% with Model 2. Also, Model 2 is the best one according to quantity-based analysis, order-based analysis, probability-based analysis, and lead-time-based analysis. Model 2 can be successfully applied for the actual situation of the supply chain inventory system and companies can obtain a remarkable amount of saving while increasing their competitive edge.
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Torrens-Fontanals, Mariona, Alejandro Peralta-García, Carmine Talarico, Ramon Guixà-González, Toni Giorgino, and Jana Selent. "SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions." Nucleic Acids Research 50, no. D1 (November 11, 2021): D858—D866. http://dx.doi.org/10.1093/nar/gkab977.
Full textAbstract:
Abstract SCoV2-MD (www.scov2-md.org) is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome. The database includes simulations produced by leading groups using molecular dynamics (MD) methods to investigate the structure-dynamics-function relationships of viral proteins. SCoV2-MD cross-references the molecular data with the pandemic evolution by tracking all available variants sequenced during the pandemic and deposited in the GISAID resource. SCoV2-MD enables the interactive analysis of the deposited trajectories through a web interface, which enables users to search by viral protein, isolate, phylogenetic attributes, or specific point mutation. Each mutation can then be analyzed interactively combining static (e.g. a variety of amino acid substitution penalties) and dynamic (time-dependent data derived from the dynamics of the local geometry) scores. Dynamic scores can be computed on the basis of nine non-covalent interaction types, including steric properties, solvent accessibility, hydrogen bonding, and other types of chemical interactions. Where available, experimental data such as antibody escape and change in binding affinities from deep mutational scanning experiments are also made available. All metrics can be combined to build predefined or custom scores to interrogate the impact of evolving variants on protein structure and function.
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Bella, Francesco, and Manuel Silvestri. "VEHICLE–PEDESTRIAN INTERACTIONS INTO AND OUTSIDE OF CROSSWALKS: EFFECTS OF DRIVER ASSISTANCE SYSTEMS." Transport 36, no. 2 (April 30, 2021): 98–109. http://dx.doi.org/10.3846/transport.2021.14739.
Full textAbstract:
This study aimed to analyse the driver’s behaviour during the interaction with a pedestrian crossing into and outside the zebra crossing, and evaluate the effectiveness of two kinds of Advanced Driver Assistance System (ADAS) that provided to the driver an auditory alert, and a visual alert to detect the pedestrian. 42 participants joined the experiment conducted using the fixed-base driving simulator of the Department of Engineering (Roma Tre University). They experienced different crossing conditions (legal and illegal) and ADAS conditions (no ADAS, visual warning and auditory warning) in an urban scenario. The parameters Time-To-Arrive (TTA) and Speed Reduction Time (SRT) were obtained from the drivers’ speed profiles in the last 150 m in advance of the conflict point with the pedestrian. Results clearly showed the criticality of illegal crossings. When the pedestrian crossed outside of the crosswalk, the highest number of collision occurred and the ANalysis Of VAriance (ANOVA) returned significant effects on both the dependent variables TTA and SRT, highlighting the higher criticality of the vehicle–pedestrian interaction and the more abrupt yielding manoeuvre. Positive effects (the vehicle–pedestrian interaction was less critical and the yielding manoeuvre was smoother) emerged for both the driver assistance systems, although not statistically significant. Besides, both the driver assistance systems positively affected the behaviour of the average cautious drivers. No significant effects of the warning systems were recorded on the aggressive drivers, which because of their behavioural characteristics ignored the warning alarm. In addition, no significant effects of the warning systems were recorded for the very cautious drivers, which adjusted their behaviour even before the alarm trigger. Finally, the outcomes of the questionnaire submitted to the participants highlighted the clear preference for the auditory warning, probably because of the different physical stimuli that are solicited by the warning signal. The results confirm that adequate pedestrian paths should be planned to avoid jaywalker conditions, which induce the driver to assume critical driving behaviour and provide useful findings of the effectiveness of driver assistance systems for pedestrian detection.
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Karunasena, Enusha, K. Wyatt McMahon, David Chang, and Mindy M. Brashears. "Host Responses to the Pathogen Mycobacterium avium subsp. paratuberculosis and Beneficial Microbes Exhibit Host Sex Specificity." Applied and Environmental Microbiology 80, no. 15 (May 9, 2014): 4481–90. http://dx.doi.org/10.1128/aem.01229-14.
Full textAbstract:
ABSTRACTDifferences between microbial pathogenesis in male and female hosts are well characterized in disease conditions connected to sexual transmission. However, limited biological insight is available on variances attributed to sex specificity in host-microbe interactions, and it is most often a minimized variable outside these transmission events. In this work, we studied two gut microbes—a pathogen,Mycobacterium aviumsubsp.paratuberculosis, and a probiotic,Lactobacillus animalisNP-51—and the interaction between each agent and the male and female gastrointestinal systems. This trial was conducted in BALB/c mice (n= 5 per experimental group and per sex at a given time point), with analysis at four time points over 180 days. Host responses toM. aviumsubsp.paratuberculosisandL. animaliswere sensitive to sex. Cytokines that were significantly different (P≤ 0.05) between the sexes included interleukin-1α/β (IL-1α/β), IL-17, IL-6, IL-10, IL-12, and gamma interferon (IFN-γ) and were dependent on experimental conditions. However, granulocyte-macrophage colony-stimulating factor (GM-CSF), vascular endothelial growth factor (VEGF), and IL-13/23 showed no sex specificity. A metabolomics study indicated a 0.5- to 2.0-fold (log2scale) increase in short-chain fatty acids (butyrate and acetate) in males and greater increases ino-phosphocholine or histidine from female colon tissues; variances distinct to each sex were observed with age or long-term probiotic consumption. Two genera,StaphylococcusandRoseburia, were consistently overrepresented in females compared to males; other species were specific to one sex but fluctuated depending on experimental conditions. The differences observed suggest that male and female gut tissues and microbiota respond to newly introduced microorganisms differently and that gut-associated microorganisms with host immune system responses and metabolic activity are supported by biology distinct to the host sex.
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Jensen, O. E. "Instabilities of flow in a collapsed tube." Journal of Fluid Mechanics 220 (November 1990): 623–59. http://dx.doi.org/10.1017/s0022112090003408.
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In a previous paper (Jensen & Pedley 1989) a model was analysed describing the effects of longitudinal wall tension and energy loss through flow separation on the existence and nature of steady flow in a finite length of externally pressurized, elastic-walled tube. The stability of these steady flows to small time-dependent perturbations is now determined. A linear analysis shows that the tube may be unstable to at least three different modes of oscillation, with frequencies in distinct bands, depending on the governing parameters; neutral stability curves for each mode are calculated. The motion of the separation point at a constriction in the tube appears to play an important role in the mechanism of these oscillations. A weakly nonlinear analysis is used to examine the instabilities in a neighbourhood of their neutral curves and to investigate mode interactions. The existence of multiple independent oscillations indicates that very complex dynamical behaviour may occur.