Browsing by Author "Liu, C"

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Open Access
A phase field model for mass transport with semi-permeable interfaces
(Journal of Computational Physics, 2022-09-01) Qin, Y; Huang, H; Zhu, Y; Liu, C; Xu, S
In this paper, a thermaldynamical consistent model for mass transfer across permeable moving interfaces is proposed by using the energy variation method. We consider a restricted diffusion problem where the flux across the interface depends on its conductance and the difference of the concentration on each side. The diffusive interface phase-field framework used here has several advantages over the sharp interface method. First of all, explicit tracking of the interface is no longer necessary. Secondly, interfacial conditions can be incorporated with a variable diffusion coefficient. Finally, topological changes of interfaces can be handed easily. A detailed asymptotic analysis confirms the diffusive interface model converges to the existing sharp interface model as the interface thickness goes to zero. An energy stable numerical scheme is developed to solve this highly nonlinear coupled system.Numerical simulations first illustrate the consistency of theoretical results on the sharp interface limit. Then a convergence study and energy decay test are conducted to ensure the efficiency and stability of the numerical scheme. To illustrate the effectiveness of our phase-field approach, several examples are provided, including a study of a two-phase mass transfer problem where droplets with deformable interfaces are suspended in a moving fluid.
Open Access
An energetic variational approach for ION transport
(Communications in Mathematical Sciences, 2014-03-06) Xu, S; Sheng, P; Liu, C
The transport and distribution of charged particles are crucial in the study of many physical and biological problems. In this paper, we employ an Energy Variational Approach to derive the coupled Poisson-Nernst-Planck-Navier-Stokes system. All of the physics is included in the choices of corresponding energy law and kinematic transport of particles. The variational derivations give the coupled force balance equations in a unique and deterministic fashion. We also discuss the situations with different types of boundary conditions. Finally, we show that the Onsager's relation holds for the electrokinetics, near the initial time of a step function applied field. © 2014 International Press.
Open Access
Behavior of different numerical schemes for random genetic drift
(BIT Numerical Mathematics, 2019-09-01) Xu, S; Chen, M; Liu, C; Zhang, R; Yue, X
In the problem of random genetic drift, the probability density of one gene is governed by a degenerated convection-dominated diffusion equation. Dirac singularities will always be developed at boundary points as time evolves, which is known as the fixation phenomenon in genetic evolution. Three finite volume methods: FVM1-3, one central difference method: FDM1 and three finite element methods: FEM1-3 are considered. These methods lead to different equilibrium states after a long time. It is shown that only schemes FVM3 and FEM3, which are the same, preserve probability, expectation and positiveness and predict the correct probability of fixation. FVM1-2 wrongly predict the probability of fixation due to their intrinsic viscosity, even though they are unconditionally stable. Contrarily, FDM1 and FEM1-2 introduce different anti-diffusion terms, which make them unstable and fail to preserve positiveness.
Open Access
Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores
(Computational and Mathematical Biophysics, 2014-01-01) Xu, S; Chen, M; Majd, S; Yue, X; Liu, C
Gramicidin A is a small and well characterized peptide that forms an ion channel in lipid membranes. An important feature of gramicidin A (gA) pore is that its conductance is affected by the electric charges near the its entrance. This property has led to the application of gramicidin A as a biochemical sensor for monitoring and quantifying a number of chemical and enzymatic reactions. Here, a mathematical model of conductance changes of gramicidin A pores in response to the presence of electrical charges near its entrance, either on membrane surface or attached to gramicidin A itself, is presented. In this numerical simulation, a two dimensional computational domain is set to mimic the structure of a gramicidin A channel in the bilayer surrounded by electrolyte. The transport of ions through the channel is modeled by the Poisson-Nernst-Planck (PNP) equations that are solved by Finite Element Method (FEM). Preliminary numerical simulations of this mathematical model are in qualitative agreement with the experimental results in the literature. In addition to the model and simulations, we also present the analysis of the stability of the solution to the boundary conditions and the convergence of FEM method for the two dimensional PNP equations in our model.
Open Access
Numerical method for multi-alleles genetic drift problem
(SIAM Journal on Numerical Analysis, 2019-01-01) Xu, S; Chen, X; Liu, C; Yue, X
Genetic drift describes random fluctuations in the number of genes variants in a population. One of the most popular models is the Wright-Fisher model. The diffusion limit of this model is a degenerate diffusion-convection equation. Due to the degeneration and convection, Dirac singularities will always develop at the boundaries as time evolves, i.e., the fixation phenomenon occurs. Theoretical analysis has proven that the weak solution of this equation, regarded as measure, conserves total probability and expectations. In the current work, we propose a scheme for 3-alleles model with absolute stability and generalize it to N-alleles case (N > 3). Our method can conserve not only total probability and expectations, but also positivity. We also prove that the discrete solution converges to a measure as the mesh size tends to zero, which is the exact measure solution of the original problem. The simulations illustrate that the probability density decays to zero first on the inner nodes, then also on the edge nodes except at the three vertex nodes, on which the density finally concentrates. The results correctly predict the fixation probability and are consistent with theoretical ones and with direct Monte Carlo simulations.
Open Access
Protective astrogenesis from the SVZ niche after injury is controlled by Notch modulator Thbs4
(Nature, 2013) Benner, EJ; Luciano, D; Jo, R; Abdi, K; Paez-Gonzalez, P; Sheng, H; Warner, DS; Liu, C; Eroglu, C; Kuo, CT
Postnatal/adult neural stem cells (NSCs) within the rodent subventricular zone (SVZ; also called subependymal zone) generate doublecortin (Dcx) + neuroblasts that migrate and integrate into olfactory bulb circuitry. Continuous production of neuroblasts is controlled by the SVZ microenvironmental niche. It is generally thought that enhancing the neurogenic activities of endogenous NSCs may provide needed therapeutic options for disease states and after brain injury. However, SVZ NSCs can also differentiate into astrocytes. It remains unclear whether there are conditions that favour astrogenesis over neurogenesis in the SVZ niche, and whether astrocytes produced there have different properties compared with astrocytes produced elsewhere in the brain. Here we show in mice that SVZ-generated astrocytes express high levels of thrombospondin 4 (Thbs4), a secreted homopentameric glycoprotein, in contrast to cortical astrocytes, which express low levels of Thbs4. We found that localized photothrombotic/ischaemic cortical injury initiates a marked increase in Thbs4 hi astrocyte production from the postnatal SVZ niche. Tamoxifen-inducible nestin-creER tm 4 lineage tracing demonstrated that it is these SVZ-generated Thbs4 hi astrocytes, and not Dcx + neuroblasts, that home-in on the injured cortex. This robust post-injury astrogenic response required SVZ Notch activation modulated by Thbs4 via direct Notch1 receptor binding and endocytosis to activate downstream signals, including increased Nfia transcription factor expression important for glia production. Consequently, Thbs4 homozygous knockout mice (Thbs4 KO/KO) showed severe defects in cortical-injury-induced SVZ astrogenesis, instead producing cells expressing Dcx migrating from SVZ to the injury sites. These alterations in cellular responses resulted in abnormal glial scar formation after injury, and significantly increased microvascular haemorrhage into the brain parenchyma of Thbs4 KO/KO mice. Taken together, these findings have important implications for post-injury applications of endogenous and transplanted NSCs in the therapeutic setting, as well as disease states where Thbs family members have important roles. © 2013 Macmillan Publishers Limited. All rights reserved.
Open Access
Road Traffic Injury Prevention Initiatives: A Systematic Review and Metasummary of Effectiveness in Low and Middle Income Countries.
(PLoS One, 2016) Staton, C; Vissoci, J; Gong, E; Toomey, N; Wafula, R; Abdelgadir, J; Zhou, Y; Liu, C; Pei, F; Zick, B; Ratliff, CD; Rotich, C; Jadue, N; de Andrade, L; von Isenburg, M; Hocker, M
BACKGROUND: Road traffic injuries (RTIs) are a growing but neglected global health crisis, requiring effective prevention to promote sustainable safety. Low- and middle-income countries (LMICs) share a disproportionately high burden with 90% of the world's road traffic deaths, and where RTIs are escalating due to rapid urbanization and motorization. Although several studies have assessed the effectiveness of a specific intervention, no systematic reviews have been conducted summarizing the effectiveness of RTI prevention initiatives specifically performed in LMIC settings; this study will help fill this gap. METHODS: In accordance with PRISMA guidelines we searched the electronic databases MEDLINE, EMBASE, Scopus, Web of Science, TRID, Lilacs, Scielo and Global Health. Articles were eligible if they considered RTI prevention in LMICs by evaluating a prevention-related intervention with outcome measures of crash, RTI, or death. In addition, a reference and citation analysis was conducted as well as a data quality assessment. A qualitative metasummary approach was used for data analysis and effect sizes were calculated to quantify the magnitude of emerging themes. RESULTS: Of the 8560 articles from the literature search, 18 articles from 11 LMICs fit the eligibility and inclusion criteria. Of these studies, four were from Sub-Saharan Africa, ten from Latin America and the Caribbean, one from the Middle East, and three from Asia. Half of the studies focused specifically on legislation, while the others focused on speed control measures, educational interventions, enforcement, road improvement, community programs, or a multifaceted intervention. CONCLUSION: Legislation was the most common intervention evaluated with the best outcomes when combined with strong enforcement initiatives or as part of a multifaceted approach. Because speed control is crucial to crash and injury prevention, road improvement interventions in LMIC settings should carefully consider how the impact of improvements will affect speed and traffic flow. Further road traffic injury prevention interventions should be performed in LMICs with patient-centered outcomes in order to guide injury prevention in these complex settings.
Open Access
Self-consistent approach to global charge neutrality in electrokinetics: A surface potential trap model
(Physical Review X, 2014-01-01) Wan, L; Xu, S; Liao, M; Liu, C; Sheng, P
In this work, we treat the Poisson-Nernst-Planck (PNP) equations as the basis for a consistent framework of the electrokinetic effects. The static limit of the PNP equations is shown to be the charge-conserving Poisson-Boltzmann (CCPB) equation, with guaranteed charge neutrality within the computational domain. We propose a surface potential trap model that attributes an energy cost to the interfacial charge dissociation. In conjunction with the CCPB, the surface potential trap can cause a surface-specific adsorbed charge layer σ. By defining a chemical potential μ that arises from the charge neutrality constraint, a reformulated CCPB can be reduced to the form of the Poisson-Boltzmann equation, whose prediction of the Debye screening layer profile is in excellent agreement with that of the Poisson-Boltzmann equation when the channel width is much larger than the Debye length. However, important differences emerge when the channel width is small, so the Debye screening layers from the opposite sides of the channel overlap with each other. In particular, the theory automatically yields a variation of σ that is generally known as the "charge regulation" behavior, attendant with predictions of force variation as a function of nanoscale separation between two charged surfaces that are in good agreement with the experiments, with no adjustable or additional parameters. We give a generalized definition of the ξ potential that reflects the strength of the electrokinetic effect; its variations with the concentration of surface-specific and surfacenonspecific salt ions are shown to be in good agreement with the experiments. To delineate the behavior of the electro-osmotic (EO) effect, the coupled PNP and Navier-Stokes equations are solved numerically under an applied electric field tangential to the fluid-solid interface. The EO effect is shown to exhibit an intrinsic time dependence that is noninertial in its origin. Under a step-function applied electric field, a pulse of fluid flow is followed by relaxation to a new ion distribution, owing to the diffusive counter current. We have numerically evaluated the Onsager coefficients associated with the EO effect, L21, and its reverse streaming potential effect, L12, and show that L12 = L21 in accordance with the Onsager relation. We conclude by noting some of the challenges ahead.
Open Access
Tissue distribution of a cord blood-derived cell product following intrathecal transplantation
(Cytotherapy, 2014-04) Storms, R; Liu, C; Gentry, T; Zhou, J; Ozamiz, A; Rusche, B; Balber, A; Kurtzberg, J
Open Access
Using Cost-Effectiveness Analysis in Mixed Methods Research: An Evaluation of an Integrated Care Program for Frequently Hospitalized Older Adults in Singapore
(Journal of Mixed Methods Research, 2020-04-01) Penkunas, MJ; Matchar, DB; Wong, CH; Liu, C; Chan, AWM
Traditional evaluation techniques are often not suitable for studying health interventions operating in real-world settings, particularly when interventions operate through complex causal pathways. We describe a mixed methods design for evaluating an integrated home care and social support service targeting mature and older adults (55+ years) in Singapore. Here, nurses and community health workers visit patients’ homes to address health and social needs while facilitating linkages to community-based services and providing caregiver support. Our mixed methods evaluation plan is composed of three components: quantitative comparison of hospital-based service utilization, cost-effectiveness analysis, and qualitative investigation into the experiences of patients, caregivers, and individuals who declined services. This article contributes a description of how cost-effectiveness analysis adds value when incorporated into mixed methods studies.
Open Access
White Matter Changes Related to Subconcussive Impact Frequency during a Single Season of High School Football.
(AJNR Am J Neuroradiol, 2017-12-21) Kuzminski, SJ; Clark, MD; Fraser, MA; Haswell, CC; Morey, RA; Liu, C; Choudhury, KR; Guskiewicz, KM; Petrella, JR
BACKGROUND AND PURPOSE: The effect of exposing the developing brain of a high school football player to subconcussive impacts during a single season is unknown. The purpose of this pilot study was to use diffusion tensor imaging to assess white matter changes during a single high school football season, and to correlate these changes with impacts measured by helmet accelerometer data and neurocognitive test scores collected during the same period. MATERIALS AND METHODS: Seventeen male athletes (mean age, 16 ± 0.73 years) underwent MR imaging before and after the season. Changes in fractional anisotropy across the white matter skeleton were assessed with Tract-Based Spatial Statistics and ROI analysis. RESULTS: The mean number of impacts over a 10-g threshold sustained was 414 ± 291. Voxelwise analysis failed to show significant changes in fractional anisotropy across the season or a correlation with impact frequency, after correcting for multiple comparisons. ROI analysis showed significant (P < .05, corrected) decreases in fractional anisotropy in the fornix-stria terminalis and cingulum hippocampus, which were related to impact frequency. The effects were strongest in the fornix-stria terminalis, where decreases in fractional anisotropy correlated with worsening visual memory. CONCLUSIONS: Our findings suggest that subclinical neurotrauma related to participation in American football may result in white matter injury and that alterations in white matter tracts within the limbic system may be detectable after only 1 season of play at the high school level.