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Search Results: 1 - 10 of 4995 matches for " Jaehyuk Choi "
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Diffusion-Limited Aggregation on Curved Surfaces
Jaehyuk Choi,Darren Crowdy,Martin Z. Bazant
Physics , 2010, DOI: 10.1209/0295-5075/91/46005
Abstract: We develop a general theory of transport-limited aggregation phenomena occurring on curved surfaces, based on stochastic iterated conformal maps and conformal projections to the complex plane. To illustrate the theory, we use stereographic projections to simulate diffusion-limited-aggregation (DLA) on surfaces of constant Gaussian curvature, including the sphere ($K>0$) and pseudo-sphere ($K<0$), which approximate "bumps" and "saddles" in smooth surfaces, respectively. Although curvature affects the global morphology of the aggregates, the fractal dimension (in the curved metric) is remarkably insensitive to curvature, as long as the particle size is much smaller than the radius of curvature. We conjecture that all aggregates grown by conformally invariant transport on curved surfaces have the same fractal dimension as DLA in the plane. Our simulations suggest, however, that the multifractal dimensions increase from hyperbolic ($K<0$) to elliptic ($K>0$) geometry, which we attribute to curvature-dependent screening of tip branching.
Dynamics of Conformal Maps for a Class of Non-Laplacian Growth Phenomena
Martin Z. Bazant,Jaehyuk Choi,Benny Davidovitch
Physics , 2003, DOI: 10.1103/PhysRevLett.91.045503
Abstract: Time-dependent conformal maps are used to model a class of growth phenomena limited by coupled non-Laplacian transport processes, such as nonlinear diffusion, advection, and electro-migration. Both continuous and stochastic dynamics are described by generalizing conformal-mapping techniques for viscous fingering and diffusion-limited aggregation, respectively. A general notion of time in stochastic growth is also introduced. The theory is applied to simulations of advection-diffusion-limited aggregation in a background potential flow. A universal crossover in morphology is observed from diffusion-limited to advection-limited fractal patterns with an associated crossover in the growth rate, controlled by a time-dependent effective Peclet number. Remarkably, the fractal dimension is not affected by advection, in spite of dramatic increases in anisotropy and growth rate, due to the persistence of diffusion limitation at small scales.
The Average Shape of Transport-Limited Aggregates
Benny Davidovitch,Jaehyuk Choi,Martin Z. Bazant
Physics , 2005, DOI: 10.1103/PhysRevLett.95.075504
Abstract: We study the relation between stochastic and continuous transport-limited growth models, which generalize conformal-mapping formulations of diffusion-limited aggregation (DLA) and viscous fingering, respectively. We derive a nonlinear integro-differential equation for the asymptotic shape (average conformal map) of stochastic aggregates, whose mean-field approximation is the corresponding continuous equation, where the interface moves at its local expected velocity. Our equation accurately describes advection-diffusion-limited aggregation (ADLA), and, due to nonlinear averaging over fluctuations, the average ADLA cluster is similar, but not identical, to an exact solution of the mean-field dynamics. Similar results should apply to all models in our class, thus explaining the known discrepancies between average DLA clusters and viscous fingers in a channel geometry.
Velocity profile of granular flows inside silos and hoppers
Jaehyuk Choi,Arshad Kudrolli,Martin Z. Bazant
Physics , 2005, DOI: 10.1088/0953-8984/17/24/011
Abstract: We measure the flow of granular materials inside a quasi-two dimensional silo as it drains and compare the data with some existing models. The particles inside the silo are imaged and tracked with unprecedented resolution in both space and time to obtain their velocity and diffusion properties. The data obtained by varying the orifice width and the hopper angle allows us to thoroughly test models of gravity driven flows inside these geometries. All of our measured velocity profiles are smooth and free of the shock-like discontinuities ("rupture zones") predicted by critical state soil mechanics. On the other hand, we find that the simple Kinematic Model accurately captures the mean velocity profile near the orifice, although it fails to describe the rapid transition to plug flow far away from the orifice. The measured diffusion length $b$, the only free parameter in the model, is not constant as usually assumed, but increases with both the height above the orifice and the angle of the hopper. We discuss improvements to the model to account for the differences. From our data, we also directly measure the diffusion of the particles and find it to be significantly less than predicted by the Void Model, which provides the classical microscopic derivation of the Kinematic Model in terms of diffusing voids in the packing. However, the experimental data is consistent with the recently proposed Spot Model, based on a simple mechanism for cooperative diffusion. Finally, we discuss the flow rate as a function of the orifice width and hopper angles. We find that the flow rate scales with the orifice size to the power of 1.5, consistent with dimensional analysis. Interestingly, the flow rate increases when the funnel angle is increased.
Diffusion and mixing in gravity-driven dense granular flows
Jaehyuk Choi,A. Kudrolli,R. R. Rosales,Martin Z. Bazant
Mathematics , 2003, DOI: 10.1103/PhysRevLett.92.174301
Abstract: We study the transport properties of particles draining from a silo using imaging and direct particle tracking. The particle displacements show a universal transition from super-diffusion to normal diffusion, as a function of the distance fallen, independent of the flow speed. In the super-diffusive (but sub-ballistic) regime, which occurs before a particle falls through its diameter, the displacements have fat-tailed and anisotropic distributions. In the diffusive regime, we observe very slow cage breaking and Peclet numbers of order 100, contrary to the only previous microscopic model (based on diffusing voids). Overall, our experiments show that diffusion and mixing are dominated by geometry, consistent with fluctuating contact networks but not thermal collisions, as in normal fluids.
Steady advection-diffusion around finite absorbers in two-dimensional potential flows
Jaehyuk Choi,Dionisios Margetis,Todd M. Squires,Martin Z. Bazant
Mathematics , 2004, DOI: 10.1017/S0022112005005008
Abstract: We perform an exhaustive study of the simplest, nontrivial problem in advection-diffusion -- a finite absorber of arbitrary cross section in a steady two-dimensional potential flow of concentrated fluid. This classical problem has been studied extensively in the theory of solidification from a flowing melt, and it also arises in Advection-Diffusion-Limited Aggregation. In both cases, the fundamental object is the flux to a circular disk, obtained by conformal mapping from more complicated shapes. We construct the first accurate numerical solution using an efficient new method, which involves mapping to the interior of the disk and using a spectral method in polar coordinates. Our method also combines exact asymptotics and an adaptive mesh to handle boundary layers. Starting from a well-known integral equation in streamline coordinates, we also derive new, high-order asymptotic expansions for high and low P\'eclet numbers ($\Pe$). Remarkably, the `high' $\Pe$ expansion remains accurate even for such low $\Pe$ as $10^{-3}$. The two expansions overlap well near $\Pe = 0.1$, allowing the construction of an analytical connection formula that is uniformly accurate for all $\Pe$ and angles on the disk with a maximum relative error of 1.75%. We also obtain an analytical formula for the Nusselt number ($\Nu$) as a function of the P\'eclet number with a maximum relative error of 0.53% for all possible geometries. Because our finite-plate problem can be conformally mapped to other geometries, the general problem of two-dimensional advection-diffusion past an arbitrary finite absorber in a potential flow can be considered effectively solved.
Regulation of Cellular Diacylglycerol through Lipid Phosphate Phosphatases Is Required for Pathogenesis of the Rice Blast Fungus, Magnaporthe oryzae
Md. Abu Sadat, Junhyun Jeon, Albely Afifa Mir, Jaeyoung Choi, Jaehyuk Choi, Yong-Hwan Lee
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0100726
Abstract: Considering implication of diacylglycerol in both metabolism and signaling pathways, maintaining proper levels of diacylglycerol (DAG) is critical to cellular homeostasis and development. Except the PIP2-PLC mediated pathway, metabolic pathways leading to generation of DAG converge on dephosphorylation of phosphatidic acid catalyzed by lipid phosphate phosphatases. Here we report the role of such enzymes in a model plant pathogenic fungus, Magnaporthe oryzae. We identified five genes encoding putative lipid phosphate phosphatases (MoLPP1 to MoLPP5). Targeted disruption of four genes (except MoLPP4) showed that MoLPP3 and MoLPP5 are required for normal progression of infection-specific development and proliferation within host plants, whereas MoLPP1 and MoLPP2 are indispensable for fungal pathogenicity. Reintroduction of MoLPP3 and MoLPP5 into individual deletion mutants restored all the defects. Furthermore, exogenous addition of saturated DAG not only restored defect in appressorium formation but also complemented reduced virulence in both mutants. Taken together, our data indicate differential roles of lipid phosphate phosphatase genes and requirement of proper regulation of cellular DAGs for fungal development and pathogenesis.
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics
Kyongyong Jung, Jongsun Park, Jaeyoung Choi, Bongsoo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang, Yong-Hwan Lee
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-586
Abstract: The Seoul National University Genome Browser (SNUGB) integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets) and 34 plant and animal (38 datasets) species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion.The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/ webcite.As the number of sequenced genomes rapidly increases, search and comparison of sequence features within and between species has become an integral part of most biological inquires. To facilitate uses of the sequenced genomes, numerous bioinformatics tools have been developed; among these, genome browser plays an essential role by providing various means for viewing genome sequences and annotated features (e.g., chromosomal position and context of individual genes, protein/nucleotide sequences, structures of exon/intron, and promoters) via graphical and text interfaces. Widely utilized genome browsers include: (i) Ensembl http://www.ensembl.org/ webcite, which is specialized for mammalian genomics and comparative genomics [1], (ii) UCSC Genome Browser http://genome.ucsc.edu/ webcite, which archives genome sequences of 30 vertebrate and 24 non-vertebrate species [2], (iii) GBrowse http://g
Kaposin-B Enhances the PROX1 mRNA Stability during Lymphatic Reprogramming of Vascular Endothelial Cells by Kaposi's Sarcoma Herpes Virus
Jaehyuk Yoo,Jinjoo Kang,Ha Neul Lee,Berenice Aguilar,Darren Kafka,Sunju Lee,Inho Choi,Juneyong Lee,Swapnika Ramu,Juergen Haas,Chester J. Koh,Young-Kwon Hong
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1001046
Abstract: Kaposi's sarcoma (KS) is the most common cancer among HIV-positive patients. Histogenetic origin of KS has long been elusive due to a mixed expression of both blood and lymphatic endothelial markers in KS tumor cells. However, we and others discovered that Kaposi's sarcoma herpes virus (KSHV) induces lymphatic reprogramming of blood vascular endothelial cells by upregulating PROX1, which functions as the master regulator for lymphatic endothelial differentiation. Here, we demonstrate that the KSHV latent gene kaposin-B enhances the PROX1 mRNA stability and plays an important role in KSHV-mediated PROX1 upregulation. We found that PROX1 mRNA contains a canonical AU-rich element (ARE) in its 3′-untranslated region that promotes PROX1 mRNA turnover and that kaposin-B stimulates cytoplasmic accumulation of the ARE-binding protein HuR through activation of the p38/MK2 pathway. Moreover, HuR binds to and stabilizes PROX1 mRNA through its ARE and is necessary for KSHV-mediated PROX1 mRNA stabilization. Together, our study demonstrates that kaposin-B plays a key role in PROX1 upregulation during lymphatic reprogramming of blood vascular endothelial cells by KSHV.
Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients
Guanggan Hu, Joyce Wang, Jaehyuk Choi, Won Jung, Iris Liu, Anastasia P Litvintseva, Tihana Bicanic, Rajeev Aurora, Thomas G Mitchell, John R Perfect, James W Kronstad
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-526
Abstract: In an initial set of strains, melanin production was correlated with monosomy at chromosome 13, and disomic variants were less melanized and attenuated for virulence in mice. After growth in culture or passage through mice, subsequent strains were identified that varied in melanin formation and exhibited copy number changes for other chromosomes. The correlation between melanin and disomy at chromosome 13 was observed for some but not all strains. A survey of environmental and clinical isolates maintained in culture revealed few occurrences of disomic chromosomes. However, an examination of isolates that were freshly collected from the cerebrospinal fluid of AIDS patients and minimally cultured provided evidence for infections with multiple strains and copy number variation.Overall, these results suggest that the genome of C. neoformans exhibits a greater degree of plasticity than previously appreciated. Furthermore, the expression of an essential virulence factor and the severity of disease are associated with genome variation. The occurrence of chromosomal variation in isolates from AIDS patients, combined with the observed influence of disomy on virulence, indicates that genome plasticity may have clinical relevance.The adaptation of pathogens to the host environment is a critical determinant of the outcome of disease. Well-documented examples include antigenic variation in parasites and fungi to evade adaptive immune responses, viral evasion of immune detection, and phase variation in bacterial pathogens [1-5]. For fungi that attack humans, accumulating evidence indicates that genomic plasticity also contributes to adaptation to the host. For example, surveys of clinical isolates of Candida albicans reveal extensive variation in karyotypes and chromosome copy number, and genomic changes have been shown to arise during infection [6-11]. Furthermore, aneuploidy is common in laboratory strains of C. albicans, and this trait, along with isochromosome formation, is a
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