Publications

2016
J. A. Rackers, Wang, Q., Liu, C., Piquemal, J. P., Ren, P., and Ponder, J. W., “An optimized charge penetration model for use with the AMOEBA force field,” Phys Chem Chem PhysPhys Chem Chem Phys, vol. 19, pp. 276-291, 2016.Abstract
The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol-1 to 1.3 kcal mol-1. The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.
A. Kiendler-Scharr, Mensah, A. A., Friese, E., Topping, D., Nemitz, E., Prevot, A. S. H., Äijälä, M., Allan, J., Canonaco, F., Canagaratna, M., Carbone, S., Crippa, M., Dall'Osto, M., Day, D. A., DeCarlo, P. F., Di Marco, C. F., Elbern, H., Eriksson, A., Freney, E., Hao, L., Herrmann, H., Hildebrandt, L., Hillamo, R., Jimenez, J. L., Laaksonen, A., McFiggans, G., Mohr, C., O'Dowd, C., Otjes, R., Ovadnevaite, J., Pandis, S. N., Poulain, L., Schlag, P., Sellegri, K., Swietlicki, E., Tiitta, P., Vermeulen, A., Wahner, A., Worsnop, D. R., and Wu, H. - C., “Organic nitrates from night-time chemistry are a ubiquitous component of the European submicron aerosol mass,” Geophyiscal Research Letters, vol. 43, 2016.
C. Zhu, Daigle, H., and Bryant, S. L., “Paramagnetic nanoparticles as nuclear magnetic resonance contrast agents in sandstone: Importance of nanofluid-rock interactions,” Interpretation, vol. 4, no. 2, pp. SF55-SF65, 2016.
A. L'Afflito, Haddad, W. M., and Bakolas, E., “Partial-State Stabilization and Optimal Feedback Control,” International Journal of Robust and Nonlinear Control, vol. 26, pp. 1026-1050, 2016. Publisher's Version
C. G. Cameron, Karpatne, A., and Sirohi, J., “Performance of a Mach-Scale Coaxial Counter-Rotating Rotor in Hover,” Journal of Aircraft, pp. 1–10, 2016.
B. Ghanbarian and Daigle, H., “Permeability in two-component porous media: Effective-medium approximation compared with lattice-Boltzmann simulations,” Vadose Zone Journal, vol. 15, no. 2, 2016.
O. Ajayi and Torres-Verdín, C., “Petrophysical interpretation of LWD, neutron-induced gamma-ray spectroscopy measurements: an inversion-based approach,” Petrophysics, vol. 56, no. 4, pp. 358-378, 2016.
Y. Chen, Elhag, A. S., Reddy, P. P., Chen, H., Cui, L., Worthen, A. J., Ma, K., Quintanilla, H., Noguera, J. A., and Hirasaki, G. J., “Phase behavior and interfacial properties of a switchable ethoxylated amine surfactant at high temperature and effects on CO 2-in-water foams,” Journal of colloid and interface science, vol. 470, pp. 80-91, 2016. Publisher's VersionAbstract
The interfacial properties for surfactants at the supercritical CO2–water (C–W) interface at temperatures above 80 °C have very rarely been reported given limitations in surfactant solubility and chemical stability. These limitations, along with the weak solvent strength of CO2, make it challenging to design surfactants that adsorb at the C–W interface, despite the interest in CO2-in-water (C/W) foams (also referred to as macroemulsions). Herein, we examine the thermodynamic, interfacial and rheological properties of the surfactant C12–14N(EO)2 in systems containing brine and/or supercritical CO2 at elevated temperatures and pressures. Because the surfactant is switchable from the nonionic state to the protonated cationic state as the pH is lowered over a wide range in temperature, it is readily soluble in brine in the cationic state below pH 5.5, even up to 120 °C, and also in supercritical CO2 in the nonionic state. As a consequence of the affinity for both phases, the surfactant adsorption at the CO2–water interface was high, with an area of 207 Å2/molecule. Remarkably, the surfactant lowered the interfacial tension (IFT) down to ∼5 mN/m at 120 °C and 3400 psia (23 MPa), despite the low CO2 density of 0.48 g/ml, indicating sufficient solvation of the surfactant tails. The phase behavior and interfacial properties of the surfactant in the cationic form were favorable for the formation and stabilization of bulk C/W foam at high temperature and high salinity. Additionally, in a 1.2 Darcy glass bead pack at 120 °C, a very high foam apparent viscosity of 146 cP was observed at low interstitial velocities given the low degree of shear thinning. For a calcium carbonate pack, C/W foam was formed upon addition of Ca2+ and Mg2+ in the feed brine to keep the pH below 4, by the common ion effect, in order to sufficiently protonate the surfactant. The ability to form C/W foams at high temperatures is of interest for a variety of applications in chemical synthesis, separations, materials science, and subsurface energy production.
L. Lin, Wang, M., Wei, X., Peng, X., Xie, C., and Zheng, Y., “Photoswitchable Rabi Splitting in Hybrid Plasmon–Waveguide Modes,” Nano Letters, vol. 16, no. 12, 2016. Publisher's VersionAbstract
Rabi splitting that arises from strong plasmon–molecule coupling has attracted tremendous interests. However, it has remained elusive to integrate Rabi splitting into the hybrid plasmon–waveguide modes (HPWMs), which have advantages of both subwavelength light confinement of surface plasmons and long-range propagation of guided modes in dielectric waveguides. Herein, we explore a new type of HPWMs based on hybrid systems of Al nanodisk arrays covered by PMMA thin films that are doped with photochromic molecules and demonstrate the photoswitchable Rabi splitting with a maximum splitting energy of 572 meV in the HPWMs by controlling the photoisomerization of the molecules. Through our experimental measurements combined with finite-difference time-domain (FDTD) simulations, we reveal that the photoswitchable Rabi splitting arises from the switchable coupling between the HPWMs and molecular excitons. By harnessing the photoswitchable Rabi splitting, we develop all-optical light modulators and rewritable waveguides. The demonstration of Rabi splitting in the HPWMs will further advance scientific research and device applications of hybrid plasmon–molecule systems.
W. J. Baars, Tinney, C. E., and Hamilton, M. F., “A piecewise spreading regime model for calculating effective Gol'dberg numbers for supersonic jet noise.,” AIAA Journal, vol. 54, no. 9, pp. 2833-2842, 2016.Abstract
A method for calculating the effective Gol’dberg number for diverging waveforms is presented, which leveragesknown features of a high-speed jet and its associated sound field. The approach employs a ray tube situated along the Mach wave angle where the sound field is not only most intense, but advances from undergoing cylindrical decay to spherical decay. Unlike other efforts, a “piecewise-spreading regime” model is employed, which yields, separately, effective Gol’dberg numbers for the cylindrically and spherically spreading regions in the far field. The new approach is applied to a plethora of experimental databases, encompassing both laboratory- and full-scale jet noise studies. The findings demonstrate how cumulative nonlinear distortion is expected to form in the acoustic near field of laboratory scale round jets where pressure amplitudes decay cylindrically; waveform distortion is not expected in the acoustic far field where waveform amplitudes diverge spherically. On the other hand, where full-scale jet studies are concerned, effective Gol’dberg number calculations demonstrate how cumulative waveform distortion is significant in both the cylindrical- and spherical-spreading regimes. The laboratory-scale studies also reveal a pronounced sensitivity to humidity conditions, relative to the full-scale counterpart.
W. Goth, Yang, B., Lesicko, J., Allen, A., Sacks, M. S., and Tunnell, J. W., “Polarized spatial frequency domain imaging of heart valve fiber structure,” Proc. SPIE, vol. 9710. pp. 971019-971019-8, 2016. Publisher's VersionAbstract
Our group previously introduced Polarized Spatial Frequency Domain Imaging (PSFDI), a wide-field, reflectance imaging technique which we used to empirically map fiber direction in porcine pulmonary heart valve leaflets (PHVL) without optical clearing or physical sectioning of the sample. Presented is an extended analysis of our PSFDI results using an inverse Mueller matrix model of polarized light scattering that allows additional maps of fiber orientation distribution, along with instrumentation permitting increased imaging speed for dynamic PHVL fiber measurements. We imaged electrospun fiber phantoms with PSFDI, and then compared these measurements to SEM data collected for the same phantoms. PHVL was then imaged and compared to results of the same leaflets optically cleared and imaged with small angle light scattering (SALS). The static PHVL images showed distinct regional variance of fiber orientation distribution, matching our SALS results. We used our improved imaging speed to observe bovine tendon subjected to dynamic loading using a biaxial stretching device. Our dynamic imaging experiment showed trackable changes in the fiber microstructure of biological tissue under loading. Our new PSFDI analysis model and instrumentation allows characterization of fiber structure within heart valve tissues (as validated with SALS measurements), along with imaging of dynamic fiber remodeling. The experimental data will be used as inputs to our constitutive models of PHVL tissue to fully characterize these tissues' elastic behavior, and has immediate application in determining the mechanisms of structural and functional failure in PHVLs used as bio-prosthetic implants.
M. Oostrom, Mehmani, Y., Romero-Gomez, P., Tang, Y., Liu, H., Yoon, H., Kang, Q., Joekar-Niasar, V., Balhoff, M. T., Dewers, T., Tartakovsky, G. D., Leist, E. A., Hess, N. J., Perkins, W. A., Rakowski, C. L., Richmond, M. C., Serkowski, J. A., Werth, C. J., Valocchi, A. J., Wietsma, T. W., and Zhang, C., “Pore-scale and continuum simulations of solute transport micromodel benchmark experiments,” Computational Geosciences, vol. 20, no. 4, pp. 857-879, 2016. Publisher's VersionAbstract
Four sets of nonreactive solute transport experiments were conducted with micromodels. Each set consisted of three experiments with one variable, i.e., flow velocity, grain diameter, pore-aspect ratio, and flow-focusing heterogeneity. The data sets were offered to pore-scale modeling groups to test their numerical simulators. Each set consisted of two learning experiments, for which all results were made available, and one challenge experiment, for which only the experimental description and base input parameters were provided. The experimental results showed a nonlinear dependence of the transverse dispersion coefficient on the Peclet number, a negligible effect of the pore-aspect ratio on transverse mixing, and considerably enhanced mixing due to flow focusing. Five pore-scale models and one continuum-scale model were used to simulate the experiments. Of the pore-scale models, two used a pore-network (PN) method, two others are based on a lattice Boltzmann (LB) approach, and one used a computational fluid dynamics (CFD) technique. The learning experiments were used by the PN models to modify the standard perfect mixing approach in pore bodies into approaches to simulate the observed incomplete mixing. The LB and CFD models used the learning experiments to appropriately discretize the spatial grid representations. For the continuum modeling, the required dispersivity input values were estimated based on published nonlinear relations between transverse dispersion coefficients and Peclet number. Comparisons between experimental and numerical results for the four challenge experiments show that all pore-scale models were all able to satisfactorily simulate the experiments. The continuum model underestimated the required dispersivity values, resulting in reduced dispersion. The PN models were able to complete the simulations in a few minutes, whereas the direct models, which account for the micromodel geometry and underlying flow and transport physics, needed up to several days on supercomputers to resolve the more complex problems.
M. N. Murshed, Imelda Barrett, P. E., and Randy B. Machemehl, P. E., “Predicting Priorities for Installing Over-height Vehicle Detection/Warning Systems for Bridges,” TRB 95th Annual Meeting Compendium of Papers, 2016. Publisher's VersionAbstract
Although collisions of over-height vehicles or vehicles carrying over-height loads with a bridge 3 superstructure may be considered a rare event, occurrences of such events are not uncommon. 4 When such an event takes place, the damage sustained by the bridge superstructure may be 5 substantial- sometimes even leading to total collapse of the bridge. Out of the available solutions 6 to this problem the most promising and attractive one involves the installation of over-height 7 vehicle detection and warning systems, however, such systems have diverse installation costs, 8 effectiveness and longevity. Moreover, yearly budget constraints limit the number of such 9 installations and there is no guideline as to which bridges should be equipped with such devices. 10 In this study a relatively simple but effective method is developed using only two basic items of 11 information about the bridge (minimum vertical under-clearance) and total number of traffic 12 lanes under the bridge to produce a priority ranking based upon the likelihood of the bridge being 13 hit by an over-height truck. Bridge collision datasets were obtained from three state DOTs- New 14 York, Missouri and Texas and these were used to develop the predictive procedure.
B. Ghanbarian, Torres-Verdín, C., and Skaggs, T., “Quantifying tight-gas sandstone permeability via critical path analysis.,” Advances in Water Research, vol. 92, no. June, pp. 316-322, 2016.
B. Ghanbarian, Torres-Verdín, C., and Skaggs, T., “Quantifying tight-gas sandstone permeability via critical path analysis.,” Advances in Water Research, vol. 92, no. June, pp. 316-322, 2016.
M. M. Sadeghi, Park, S., Huang, Y., Akinwande, D., Yao, Z., Murthy, J., and Shi, L., “Quantitative scanning thermal microscopy of graphene devices on flexible polyimide substrates,” Journal of Applied Physics, vol. 119, pp. 235101, 2016. Publisher's Version
H. Daigle, “Relative permeability to water or gas in the presence of hydrates in porous media from critical path analysis,” Journal of Petroleum Science and Engineering, vol. 146, pp. 526-535, 2016.
W. Wu, He, F., and Wang, Y., “Reversible ultrafast melting in bulk CdSe,” Journal of Applied Physics, vol. 119, pp. 055701, 2016. Publisher's VersionAbstract
In this work, transient reflectivity changes in bulk CdSe have been measured with two-color femtosecond pump-probe spectroscopy under a wide range of pump fluences. Three regions of reflectivity change with pump fluences have been consistently revealed for excited carrier density, coherent phonon amplitude, and lattice temperature. For laser fluences from 13 to 19.3 mJ/cm2, ultrafast melting happens in first several picoseconds. This melting process is purely thermal and reversible. A complete phase transformation in bulk CdSe may be reached when the absorbed laser energy is localized long enough, as observed in nanocrystallineCdSe.
H. Daigle, Hayman, N. W., Spikes, K., Gale, J., Eichhubl, P., and Milliken, K. L., “RPSEA FINAL TECHNICAL REPORT,” 2016.
C. Narth, Lagardere, L., Polack, E., N Gresh, Q Wang,, Wang, Q., Bell, D. R., Rackers, J. A., Ponder, J. W., Ren, P. Y., and Piquemal, J. P., “Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles,” J Comput ChemJ Comput Chem, vol. 37, pp. 494-506, 2016.Abstract
We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.

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