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Browsing College of Science (COS) by Subject "02 Physical Sciences"
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- Capillary forces on a small particle at a liquid-vapor interface: Theory and simulationTang, Yanfei; Cheng, Shengfeng (American Physical Society, 2018-09-24)
- Conformational Analysis of Fluoro-, Chloro-, and Proteo-Alkene Gly-Pro and Pro-Pro Isosteres to Mimic CollagenArcoria, Paul J.; Ware, Rachel I.; Makwana, Sunny V.; Troya, Diego; Etzkorn, Felicia A. (American Chemical Society, 2021-12-30)Collagen is the most abundant human protein, with the canonical sequence (Gly-Pro-Hyp)n in its triple helix region. Cis-trans isomerization of the Xaa-Pro amide has made two of these amide bonds the target of alkene replacement: the Gly-Pro and the Pro-Hyp positions. The conformations of Gly-Pro and Pro-Pro (as a Pro-Hyp model) fluoro-, chloro-, and proteo-alkene mimic models were investigated computationally to determine whether these alkenes can stabilize the polyproline type II (PPII) conformation of collagen. Second-order Møller-Plesset (MP2) calculations with various basis sets were used to perform the conformational analyses and locate stationary points. The calculation results predict that fluoro- and chloro-alkene mimics of Gly-Pro and Pro-Pro can participate in n→π* donation to stabilize PPII conformations, yet they are poor n→π* acceptors, shifting the global minima away from PPII conformations. For the proteo-alkene mimics, the lack of significant n→π* interactions and unstable PPII-like geometries explains their known destabilization of the triple helix in collagen-like peptides.
- Crossover From Self-Similar to Self-Affine Structures in PercolationFrey, E.; Täuber, Uwe C.; Schwabl, Franz (Editions Physique, 1994-05-20)We study the crossover from self-similar scaling behavior to asymptotically self-affine (anisotropic) structures. As an example, we consider bond percolation with one preferred direction. Our theory is based on a field-theoretical representation, and takes advantage of a renormalization group approach designed for crossover phenomena. We calculate effective exponents for the connectivity describing the entire crossover region from isotropic to directed percolation, and predict at which scale of the anisotropy the crossover should occur. We emphasize the broad range of applicability of our method.
- High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration DynamicsCharkhesht, Ali; Regmi, Chola K.; Mitchell-Koch, Katie R.; Cheng, Shengfeng; Vinh, Nguyen Q. (American Chemical Society, 2018-06-21)The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly bound and loosely bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 Å distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins.
- John Cardy's scale-invariant journey in low dimensions: a special issue for his 70th birthday PrefaceCalabrese, Pasquale; Fendley, Paul; Täuber, Uwe C. (IOP, 2018-07-13)
- The meniscus on the outside of a circular cylinder: From microscopic to macroscopic scalesTang, Yanfei; Cheng, Shengfeng (Academic Press – Elsevier, 2019-01-01)We systematically study the meniscus on the outside of a small circular cylinder vertically immersed in a liquid bath in a cylindrical container that is coaxial with the cylinder. The cylinder has a radius R much smaller than the capillary length, κ-1, and the container radius, L, is varied from a small value comparable to R to ∞. In the limit of L≪κ-1, we analytically solve the general Young-Laplace equation governing the meniscus profile and show that the meniscus height, Δh, scales approximately with Rln(L/R). In the opposite limit where L≫κ-1,Δh becomes independent of L and scales with Rln(κ-1/R). We implement a numerical scheme to solve the general Young-Laplace equation for an arbitrary L and demonstrate the crossover of the meniscus profile between these two limits. The crossover region has been determined to be roughly 0.4κ-1≲L≲4κ-1. An approximate analytical expression has been found for Δh, enabling its accurate prediction at any values of L that ranges from microscopic to macroscopic scales.
- Requirements for the containment of COVID-19 disease outbreaks through periodic testing, isolation, and quarantineMukhamadiarov, Ruslan I.; Deng, Shengfeng; Serrao, Shannon R.; Priyanka; Childs, Lauren M.; Täuber, Uwe C. (IOP, 2022-01-21)We employ individual-based Monte Carlo computer simulations of a stochastic SEIR model variant on a two-dimensional Newman–Watts small-world network to investigate the control of epidemic outbreaks through periodic testing and isolation of infectious individuals, and subsequent quarantine of their immediate contacts. Using disease parameters informed by the COVID-19 pandemic, we investigate the effects of various crucial mitigation features on the epidemic spreading: fraction of the infectious population that is identifiable through the tests; testing frequency; time delay between testing and isolation of positively tested individuals; and the further time delay until quarantining their contacts as well as the quarantine duration. We thus determine the required ranges for these intervention parameters to yield effective control of the disease through both considerable delaying the epidemic peak and massively reducing the total number of sustained infections.
- The role of the non-linearity in controlling the surface roughness in the one-dimensional Kardar-Parisi-Zhang growth processPriyanka; Täuber, Uwe C.; Pleimling, Michel J. (IOP, 2021-04-16)We explore linear control of the one-dimensional non-linear Kardar-Parisi-Zhang (KPZ) equation with the goal to understand the effects the control process has on the dynamics and on the stationary state of the resulting stochastic growth kinetics. In linear control, the intrinsic non-linearity of the system is maintained at all times. In our protocol, the control is applied to only a small number nc of Fourier modes. The stationary-state roughness is obtained analytically in the small-nc regime with weak non-linear coupling wherein the controlled growth process is found to result in Edwards-Wilkinson dynamics. Furthermore, when the non-linear KPZ coupling is strong, we discern a regime where the controlled dynamics shows scaling in accordance to the KPZ universality class. We perform a detailed numerical analysis to investigate the controlled dynamics subject to weak as well as strong non-linearity. A first-order perturbation theory calculation supports the simulation results in the weak non-linear regime. For strong non-linearity, we find a temporal crossover between KPZ and dispersive growth regimes, with the crossover time scaling with the number nc of controlled Fourier modes. We observe that the height distribution is positively skewed, indicating that as a consequence of the linear control, the surface morphology displays fewer and smaller hills than in the uncontrolled growth process, and that the inherent size-dependent stationary-state roughness provides an upper limit for the roughness of the controlled system.
- Stabilizing spiral structures and population diversity in the asymmetric May-Leonard model through immigrationSerrao, Shannon R.; Täuber, Uwe C. (Springer, 2021-08-01)We study the induction and stabilization of spiral structures for the cyclic three-species stochastic May-Leonard model with asymmetric predation rates on a spatially inhomogeneous two-dimensional toroidal lattice using Monte Carlo simulations. In an isolated setting, strongly asymmetric predation rates lead to rapid extinction from coexistence of all three species to a single surviving population. Even for weakly asymmetric predation rates, only a fraction of ecologies in a statistical ensemble manages to maintain full three-species coexistence. However, when the asymmetric competing system is coupled via diffusive proliferation to a fully symmetric May-Leonard patch, the stable spiral patterns from this region induce transient plane-wave fronts and ultimately quasi-stationary spiral patterns in the vulnerable asymmetric region. Thus the endangered ecological subsystem may effectively become stabilized through immigration from even a much smaller stable region. To describe the stabilization of spiral population structures in the asymmetric region, we compare the increase in the robustness of these topological defects at extreme values of the asymmetric predation rates in the spatially coupled system with the corresponding asymmetric May{Leonard model in isolation. We delineate the quasi-stationary nature of coexistence induced in the asymmetric subsystem by its diffusive coupling to a symmetric May{Leonard patch, and propose a (semi-)quantitative criterion for the spiral oscillations to be sustained in the asymmetric region.
- Tunable Gap Plasmons in Gold Nanospheres Adsorbed into a pH-Responsive Polymer FilmJao, Chih-Yu; Robinson, Hans D.; Samaimongkol, Panupon (Elsevier, 2019-06)Hypothesis Plasmon nanorules are exquisitely sensitive distance sensors that are based on the electromagnetic interaction between metal nanoparticles and surfaces. We hypothesize that nanorulers can act as quantitative probes of processes such as particle aggregation and adsorption, and deploy them to investigate particle adsorption onto stimulus-responsive polymer films. While such systems have previously been qualitatively investigated with plasmon nanorulers, our quantitative analysis should provide deeper insights. Experiment Gold nanospheres are adsorbed from solution onto pH-responsive, amine-rich polyelectrolyte multilayer (PEM) films that are either directly deposited on a gold substrate or onto an intermediate self-assembled monolayer (SAM) of charged thiols. Fitting the optical scattering spectrum to a full-wave calculation, we quantify the sphere-substrate gap distance with good accuracy. Findings We find that the gold spheres partially embed into the PEMs rather than ride on top of them, and that although the amount of actuation of the spheres afforded by tuning the pH is well controlled, it is significantly smaller than the corresponding thickness changes in unstrained films. Further, the presence of a SAM below the PEM increases the amount of polymer in the PEM, except for the thickest and most highly charged films, where the SAM instead appears to displace from the area below the nanospheres.
- Variation of the subsidence parameters, effective thermal conductivity, and mantle dynamicsAdam, Claudia; King, Scott D.; Vidal, Valérie; Rabinowicz, Michel; Jalobeanu, André; Yoshida, Masaki (Elsevier, 2015-09-15)The subsidence of young seafloor is generally considered to be a passive phenomenon related to the conductive cooling of the lithosphere after its creation at mid-oceanic ridges. Recent alternative theories suggest that the mantle dynamics plays an important role in the structure and depth of the oceanic lithosphere. However, the link between mantle dynamics and seafloor subsidence has still to be quantitatively assessed. Here we provide a statistical study of the subsidence parameters (subsidence rate and ridge depth) for all the oceans. These parameters are retrieved through two independent methods, the positive outliers method, a classical method used in signal processing, and through the MiFil method. From the subsidence rate, we compute the effective thermal conductivity, k , which ranges between 1 and 7 W m K . We also model the mantle flow pattern from the S40RTS tomography model. The density anomalies derived from S40RTS are used to compute the instantaneous flow in a global 3D spherical geometry. We show that departures from the k =3 Wm K standard value are systematically related to mantle processes and not to lithospheric structure. Regions characterized by k >3 Wm K are associated with mantle uplifts (mantle plumes or other local anomalies). Regions characterized by k <3 Wm K are related to large-scale mantle downwellings such as the Australia-Antarctic Discordance (AAD) or the return flow from the South Pacific Superswell to the East Pacific Rise. This demonstrates that mantle dynamics plays a major role in the shaping of the oceanic seafloor. In particular, the parameters generally considered to quantify the lithosphere structure, such as the thermal conductivity, are not only representative of this structure but also incorporate signals from the mantle convection occurring beneath the lithosphere. The dynamic topography computed from the S40RTS tomography model reproduces the subsidence pattern observed in the bathymetry. Overall we find a good correlation between the subsidence parameters derived from the bathymetry and the dynamic topography. This demonstrates that these parameters are strongly dependent on mantle dynamics.