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Articles by Lucy Zhang in JoVE
Other articles by Lucy Zhang on PubMed
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Temperature Control Algorithms in Dual Control Volume Grand Canonical Molecular Dynamics Simulations of Hydrogen Diffusion in Palladium
The Journal of Chemical Physics.
Oct, 2007 |
Pubmed ID: 17979385 The effectiveness of five temperature control algorithms for dual control volume grand canonical molecular dynamics is investigated in the study of hydrogen atom diffusion in a palladium bulk. The five algorithms, namely, Gaussian, generalized Gaussian moment thermostat (GGMT), velocity scaling, Nosé-Hoover (NH), and its enhanced version Nosé-Hoover chain (NHC) are examined in both equilibrium and nonequilibrium simulation studies. Our numerical results show that Gaussian yields the most inaccurate solutions for the hydrogen-palladium system due to the high friction coefficient generated from the large velocity fluctuation of hydrogen, while NHC, NH, and GGMT produce the most accurate temperature and density profiles in both equilibrium and nonequilibrium cases with their feedback control mechanisms. However, this feedback control also overestimates the self-diffusion coefficients in equilibrium systems and the diffusion coefficient in nonequilibrium systems. Velocity scaling thermostat produces slight inhomogeneities in the temperature and density profiles, but due to the dissipated heat accumulated in the control volumes it still yields accurate self-diffusion coefficients that are in good agreement with the experimental data at a wide range of temperatures while others tend to deviate.
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Characterizing Left Atrial Appendage Functions in Sinus Rhythm and Atrial Fibrillation Using Computational Models
Journal of Biomechanics.
Aug, 2008 |
Pubmed ID: 18579148 Clinical studies show that the left atrial appendage, a blind-ended structure that is attached to the left atrium, may be the cause of 90% of atrial thrombi in atrial fibrillation (abnormal heart rhythm), and it is much reduced in sinus (normal) rhythm. In this paper, the effects of blood flows in left atrium and left atrial appendage are studied to help characterize the atrial appendage functions in sinus rhythm and atrial fibrillation using mathematical models. Our results show that the left atrial appendage is not functional in sinus rhythm because the atrial transmitral velocities remained almost identical for atria with and without appendage, which agrees with the current clinical observations. However, in atrial fibrillation, a proper atrial contraction is absent, which causes the second emptying velocity (A-wave) to be missing in both transmitral velocity and appendage filling/emptying velocity. Without the proper emptying of the blood, vortices generated in the chamber remain high strengths and with longer durations. They induce ineffective emptying of the blood in the atrium and appendage, which then lead to blood stagnation and subsequent thrombus formation.
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Nanoscale Wetting on Groove-patterned Surfaces
Langmuir : the ACS Journal of Surfaces and Colloids.
May, 2009 |
Pubmed ID: 19326936 In this paper, nanoscale wetting on groove-patterned surfaces is thoroughly studied using molecular dynamics simulations. The results are compared with Wenzel's and Cassie's predictions to determine whether these continuum theories are still valid at the nanoscale for both hydrophobic and hydrophilic types of surfaces when the droplet size is comparable to the groove size. A system with a liquid mercury droplet and grooved copper substrate is simulated. The wetting properties are determined by measuring contact angles of the liquid droplet at equilibrium states. Correlations are established between the contact angle, roughness factor r, and surface fraction f. The results show that, for hydrophobic surfaces, the contact angle as a function of roughness factor and surface fraction on nanogrooved surfaces obeys the predictions from Wenzel's theory for wetted contacts and Cassie's theory for composite contacts. However, slight deviations occur in composite contacts when a small amount of liquid penetration is observed. The contact angle of this partial wetting cannot be accurately predicted using either Cassie's or Wenzel's theories. For hydrophilic surfaces, only wetted contacts are observed. In most cases, the resulting contact angles are found to be higher than Wenzel's predictions. At the nanoscale, high surface edge density plays an important role, which results in contact line pinning near plateau edges. For both hydrophobic and hydrophilic surfaces, substantial amount of anistropic spreading is found in the direction that is parallel to the grooves, especially at wetted or partially wetted contacts.
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Nanoscale Simple-fluid Behavior Under Steady Shear
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics.
May, 2012 |
Pubmed ID: 23004740 In this study, we use two nonequilibrium molecular dynamics algorithms, boundary-driven shear and homogeneous shear, to explore the rheology and flow properties of a simple fluid undergoing steady simple shear. The two distinct algorithms are designed to elucidate the influences of nanoscale confinement. The results of rheological material functions, i.e., viscosity and normal pressure differences, show consistent Newtonian behaviors at low shear rates from both systems. The comparison validates that confinements of the order of 10 nm are not strong enough to deviate the simple fluid behaviors from the continuum hydrodynamics. The non-Newtonian phenomena of the simple fluid are further investigated by the homogeneous shear simulations with much higher shear rates. We observe the "string phase" at high shear rates by applying both profile-biased and profile-unbiased thermostats. Contrary to other findings where the string phase is found to be an artifact of the thermostats, we perform a thorough analysis of the fluid microstructures formed due to shear, which shows that it is possible to have a string phase and second shear thinning for dense simple fluids.
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The Long-term Effects of Phage Concentration on the Inhibition of Planktonic Bacterial Cultures
Environmental Science. Processes & Impacts.
Jan, 2014 |
Pubmed ID: 24301469 Since the early 1920s there has been an interest in using bacteriophages (phages) for the control of bacterial pathogens. While there are many factors that have limited the success of phage bio-control, one particular problem is the variability of outcomes between phages and bacteria. Specifically, there is a significant need for a better understanding of how initial phage concentrations affect long-term bacterial inhibition. In work reported herein three phages were isolated for Escherichia coli K12, Pseudomonas aeruginosa PAO1, as well as Bacillus cereus and bio-control experiments were performed with phage concentrations ranging from 10(5) to 10(8) plaque forming units per mL over the course of 72 h. For four of the nine phages isolated there was a linear relationship between inhibition and phage concentration, suggesting the effect of phage concentration is important at longer time scales. For three of the isolated phages, phage concentrations had no effect on bacterial inhibition suggesting that even at the lowest concentration the method of action was saturated and lower concentrations might still be effective. Additionally, a cocktail was created and was compared to the previously isolated phages. There was no statistical difference between the cocktail and the best performing phage highlighting the importance of selecting the appropriate phages for treatment. These results suggest that, for certain phages, there is a strong relationship between phage concentration and long-term bacterial growth inhibition and the initial phage concentration is an important indicator of the long-term outcome.
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