Hwankyu Lee

Dankook University, Yŏng-dong, North Chungcheong, South Korea

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Publications (22)107.88 Total impact

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    ABSTRACT: Lipid bilayers, which consist of dipalmitoylglycerophosphocholines (DPPCs), PEGylated lipids, cholesterols, and elastin-like polypeptides (ELPs; [VPGVG]3) at different molar ratios, were simulated. Simulations were carried out for 2 μs using the coarse-grained (CG) model that had captured the experimentally observed phase behavior of PEGylated lipids and lateral diffusivity of DPPC bilayers. Starting with the initial position of ELPs on the bilayer surface, ELPs insert into the hydrophobic region of the bilayer because of their interaction with lipid tails, consistent with previous all-atom simulations. Lateral diffusion coefficients of DPPCs significantly increase in the bilayer composed of more ELPs and less cholesterols, showing their opposite effects on the bilayer dynamics. In particular, ELPs modulate the dynamics and phase for the disordered liquid bilayer, but not for the ordered gel bilayer, indicating that ELPs can destabilize only the disordered bilayer. In the ordered bilayer, ELP chains tend to have a spherical shape and slowly diffuse, while they are extended and diffuse faster in the disordered bilayer, indicating the effect of the bilayer phase on the conformation and diffusivity of ELPs. These findings explain the experimental observation that the ELP-conjugated liposomes are stable at 310 K (ordered phase) but become unstable and release the encapsulated drugs at 315 K (disordered phase), which suggests the effects of ELPs and cholesterols. Since the cholesterol-stabilized bilayer can be destabilized by the extended shaped ELPs only in the disordered phase (not in the ordered phase), the inclusion of cholesterols is required to safely shield drugs at 310 K as well as allow ELPs to disrupt lipids and destabilize the liposomes at 315 K.
    Physical Chemistry Chemical Physics 01/2014; · 3.83 Impact Factor
  • Eol Han, Hwankyu Lee
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    ABSTRACT: Bax-α5 and Bcl-xL-α5, which are shorter versions of apoptosis-regulating proteins Bax and Bcl-xL, were simulated with lipid bilayers composed of pure dioleoylglycerophosphocholine (DOPC) lipids or a mixture of DOPCs and cholesterols. Starting with the initial peptide position near the bilayer surface, both Bax-α5 and Bcl-xL-α5 bind to the bilayer because of their charge interactions with lipid head groups. After binding to the bilayer surface, Bax-α5 inserts into the pure DOPC bilayer, but not into the DOPC-cholesterol bilayer, showing the effect of cholesterols on the peptide-bilayer interaction. Despite the similar peptide structure, Bcl-xL-α5 does not insert into the bilayer, in contrast to the interaction of Bax-α5 with the bilayer. Bcl-xL-α5 predominantly has the random-coil structure in both aqueous and membrane environments, while Bax-α5 shows a higher extent of α-helical structure in the bilayer than in water, in quantitative agreement with experiment. In particular, although Bax-α5 and Bcl-xL-α5 have the same extent of the electrostatic interaction with lipid head groups, Bax-α5 has stronger hydrophobic interaction with lipid tails than does Bcl-xL-α5. These indicate that Bax-α5 retains α-helical structure, where hydrophobic residues on one side of the α-helix interact with lipid tails and thus can easily attract the peptide into the lipid-tail region, while Bcl-xL-α5 forms a random coil that tends to spread on the bilayer surface and thus has weaker hydrophobic interaction with lipid tails. Our findings help explain the experimental observation that showed that Bax-α5 disorders lipids and induces pore formation, but Bcl-xL-α5 does not.
    Physical Chemistry Chemical Physics 11/2013; · 3.83 Impact Factor
  • Eol Han, Hwankyu Lee
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    ABSTRACT: Polyethylene glycol (PEG)-grafted magainin 2 and tachyplesin I were simulated with lipid bilayers. In the simulations of PEGylated magainin 2 and tachyplesin I in water, both peptides are wrapped by PEG chains. The α-helical structure of PEGylated magainin 2 is broken in water, while β-sheet of PEGylated tachyplesin I keeps stable, similar to the structural behavior of unPEGylated peptides, in agreement with experiments. Simulations of PEGylated peptides with lipid bilayers show that PEG chains block the electrostatic interaction between cationic residues of peptides and anionic phosphates of lipids, leading to the less binding of the peptide to the bilayer surface, which is observed more significantly for magainin 2 than for tachyplesin I. Since the random-coiled magainin 2 can be more completely covered by PEGs than does the β-sheet tachyplesin I, the PEGylation effect on the decreased binding is larger for magainin 2, showing the dependence of PEGylation on the peptide structure. These simulation findings qualitatively support the experimental observation of the different extents of the reduced membrane-permeabilizing activity for PEGylated magainin 2 and tachyplesin I.
    Langmuir 10/2013; · 4.19 Impact Factor
  • Hwankyu Lee
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    ABSTRACT: We performed coarse-grained (CG) molecular dynamics (MD) simulations of single-walled carbon nanotubes (SWNTs) with lipid bilayers to understand the effect of the SWNT diameter, length, and concentration on membrane curvature and penetration. Starting with different orientations of multiple SWNTs near lipid bilayers, simulations show that SWNTs insert into the bilayer and induce membrane curvature, which is much larger than that observed from previous simulations of a single SWNT. Longer and thicker SWNTs at higher concentration cause larger membrane curvature, indicating the effect of the SWNT size and concentration, in qualitative agreement with experiments. In particular, thicker SWNTs significantly increase the bilayer height and the difference of the projected and contour bilayer areas, decrease the area compressibility, and disorder lipids. When inserted into the bilayer, thinner SWNTs mainly contact the entire tails of lipids, while thicker SWNTs are wrapped mainly by the ending tail-carbons, leading to the larger membrane curvature. This indicates the effect of SWNT diameter on the SWNT-lipid interaction, yielding different extents of membrane curvature. These findings imply that the SWNT-induced membrane penetration and curvature are modulated by a combination of SWNT length, diameter, and concentration.
    Physical Chemistry Chemical Physics 09/2013; · 3.83 Impact Factor
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    ABSTRACT: Heparin decomplexation experiments, as well as all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations were performed to determine the effect of the size of arginine(Arg)-rich peptides on the structure and binding strength of the siRNA-peptide complex. At a fixed peptide/siRNA mole ratio of 5:1 or 10:1, the siRNA complexes with peptides longer than 9 Arg residues are more easily decomplexed by heparin than are those with 9 Arg residues. At these mole ratios, peptides longer than 9 Arg residues have cationic/anionic charge ratios in excess of unity, and produce more weakly bound complexes than 9-Arg residue ones do. AA simulations of mixtures of peptides with a single siRNA show formation of an electrostatically-induced complex, and the longer peptides produce a larger complex, but with no significant increase in the number of Arg residues bound to the siRNA. Larger-scale CG-MD simulations show that multiple siRNAs can be linked together by peptides into a large complex, as observed in the experiments. The peptides longer than 9 residues, which at mole ratio 5:1 yield a peptide/siRNA charge ratio in excess of unity, include many non-interacting Arg residues, which repel each other electrostatically. This leads to a less dense complex than for 9-residue peptides, which can explain why these longer complexes are more easily decomplexed by heparin molecules, as observed in the experiments. The key role of the charge ratio is supported by simulations that show that at a mole ratio of 2.5 peptides per siRNA, the longer 18-residue peptide has a charge ratio of roughly unity, and also shows a tight complex, just as the 9-residue peptide does at a 5:1 mole ratio, where its charge ratio is also unity.
    The Journal of Physical Chemistry B 05/2013; · 3.61 Impact Factor
  • Macromolecules 09/2012; 45(17):7304-7312. · 5.52 Impact Factor
  • Macromolecules 11/2011; 44(21):8681-8686. · 5.52 Impact Factor
  • Source
    Hwankyu Lee, Richard W Pastor
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    ABSTRACT: Self-assembly of polyethylene glycol (PEG)-grafted lipids at different sizes and concentrations was simulated using the MARTINI coarse-grained (CG) force field. The interactions between CG PEG and CG dipalmitoylglycerophosphocholine (DPPC)-lipids were parametrized by matching densities of 19-mers of PEG and polyethylene oxide (PEO) grafted to the bilayer from all-atom simulations. Mixtures of lipids and PEG-grafted (M(w) = 550, 1250, and 2000) lipids in water self-assembled to liposomes, bicelles, and micelles at different ratios of lipids and PEGylated lipids. Average aggregate sizes decrease with increasing PEGylated-lipid concentration, in qualitative agreement with experiment. PEGylated lipids concentrate at the rims of bicelles, rather than at the planar surfaces; this also agrees with experiment, though the degree of segregation is less than that assumed in previous modeling of the experimental data. Charged lipids without PEG evenly distribute at the rim and planar surfaces of the bicelle. The average end-to-end distances of the PEG on the PEGylated lipids are comparable in liposomes, bicelles (edge or planar surface), and micelles and only slightly larger than for an isolated PEG in solution. The ability of PEGylated lipids to induce the membrane curvature by the bulky headgroup with larger PEG, and thereby modulate the phase behavior and size of lipid assemblies, arises from their relative concentration.
    The Journal of Physical Chemistry B 06/2011; 115(24):7830-7. · 3.61 Impact Factor
  • Hwankyu Lee, Ronald G. Larson
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    ABSTRACT: G4 PAMAM dendrimers grafted with poly(ethylene glycol) (PEG) of different sizes (Mw = 550 and 5000) and grafting densities (12−94% of surface terminals) were simulated using the coarse-grained (CG) force fields previously developed and reparametrized in this work. Simulations are carried out for G4, G5, and G7 un-PEGylated dendrimers that are either unprotonated, terminally protonated, or protonated on both terminals and interior sites, corresponding to pH values of >10, 7, and <5, respectively. As protonation increases, simulations show only a small (6% for G4 and G5) change of dendrimer radius of gyration Rg and show a structural transition from dense-core to dense-shell structure, both of which are in agreement with recent scattering experiments and all-atom simulations. For the PEGylated dendrimers, the Rg of the fully PEG(Mw = 5000)-grafted dendrimer also agrees well with experiment. Longer PEG chains with higher grafting density yield PEG−PEG crowding, which stretches dendrimer terminals toward water more strongly, leading to larger size and a dense-shell structure of the dendrimer. Long PEG chains at high grafting densities also penetrate into the dendrimer core, while short ones do not, which might help explain the reduced encapsulation of hydrophobic compounds seen experimentally in dendrimers that are 75%-grafted with long PEG’s (Mw = 5000). This reduced encapsulation for dendrimers with long grafted PEG’s has previously been attributed to PEG-induced dendrimer aggregation, but this explanation is not consistent with our previous simulations which showed no aggregation even with long PEG’s but is consistent with the new simulations reported here that show PEG penetration into the core of the dendrimer to which the PEG is attached.
    Macromolecules. 03/2011;
  • Hwankyu Lee, Ronald G. Larson
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    ABSTRACT: We performed molecular dynamics (MD) simu-lations of 36 copies of unmodified (charged), acetylated, and polyethylene glycol (PEG)-conjugated G4 dendrimers in dimyristoylphosphatidylcholine (DMPC) bilayers with explicit water using coarse-grained (CG) lipid and PEG force fields (FF). Attachment of small PEG chains to the dendrimer leads to the same reduction in membrane permeability as does attachment of acetyl groups, while a larger PEG size or a higher degree of PEGylation induces even fewer pores. This indicates that PEGylation is more efficient than acetylation in reducing membrane permeability and cytotoxicity, in qualitative agreement with experimental findings (Kim et al. Bioconjugate Chem. 2008, 19, 1660). Attachment of larger PEG chains makes the dendrimer−PEG complex larger and more spherical. Although a larger size and a more spherical shape are usually conducive to pore formation, a thick PEG layer on the dendrimer surface blocks the charge interaction between cationic dendrimer terminals and anionic lipid phosphate groups, and thus inhibits pore formation, despite the increased dendrimer size. Large PEG chains also keep the dendrimer−PEG complexes far from each other, suppressing interparticle aggregation.
    03/2011;
  • Hwankyu Lee, Richard W. Pastor
    Biophysical Journal 01/2010; 98(3). · 3.67 Impact Factor
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    ABSTRACT: A coarse-grained (CG) model for polyethylene oxide (PEO) and polyethylene glycol (PEG) developed within the framework of the MARTINI CG force field (FF) using the distributions of bonds, angles, and dihedrals from the CHARMM all-atom FF is presented. Densities of neat low molecular weight PEO agree with experiment, and the radius of gyration R(g) = 19.1 A +/- 0.7 for 76-mers of PEO (M(w) approximately 3400), in excellent agreement with neutron scattering results for an equal sized PEG. Simulations of 9, 18, 27, 36, 44, 67, 76, 90, 112, 135, and 158-mers of the CG PEO (442 < M(w) < 6998) at low concentration in water show the experimentally observed transition from ideal chain to real chain behavior at 1600 < M(w) < 2000, in excellent agreement with the dependence of experimentally observed hydrodynamic radii of PEG. Hydrodynamic radii of PEO calculated from diffusion coefficients of the higher M(w) PEO also agree well with experiment. R(g) calculated from both all-atom and CG simulations of PEO76 at 21 and 148 mg/cm(3) are found to be nearly equal. This lack of concentration dependence implies that apparent R(g) from scattering experiments at high concentration should not be taken to be the chain dimension. Simulations of PEO grafted to a nonadsorbing surface yield a mushroom to brush transition that is well described by the Alexander-de Gennes formalism.
    The Journal of Physical Chemistry B 09/2009; 113(40):13186-94. · 3.61 Impact Factor
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    Hwankyu Lee, Ronald G Larson
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    ABSTRACT: We performed molecular dynamics (MD) simulations of one or two copies of polyethylene glycol of molecular weight 550 (PEG550) and 5000 (PEG5000) daltons, conjugated to generation 3 (G3) to 5 (G5) polyamidoamine (PAMAM) dendrimers with explicit water using a coarse-grained model. We found the radii of gyration of these dendrimer-PEG molecules to be close to those measured in experiments by Hedden and Bauer (Hedden , R. C. ; Bauer , B. J. Macromolecules 2003 , 36 , 1829.). Densely grafted PEG ligands (>50% of the dendrimer surface) extend like brushes, with layer thickness in agreement with theory for starlike polymers. Two dendrimer-PEG complexes in the box drift away from each other, indicating that no aggregation is induced by either short or long PEG chains, conflicting with a recent view that the cytotoxicity of some PEGylated particles might be due to particle aggregation for long PEG lengths.
    The Journal of Physical Chemistry B 09/2009; 113(40):13202-7. · 3.61 Impact Factor
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    Hwankyu Lee, Ronald G Larson
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    ABSTRACT: Recent advances in molecular dynamics simulation methodologies and computational power have allowed accurate predictions of dendrimer size, shape, and interactions with bilayers and polyelectrolytes with modest computational effort. Atomistic and coarse-grained (CG) models show strong interactions of cationic dendrimers with lipid bilayers. The CG simulations with explicit lipid and water capture bilayer penetration and pore formation, showing that pore formation is enhanced at high dendrimer concentration, but suppressed at low temperature and high salt concentration, in agreement with experiments. Cationic linear polymers have also been simulated, but do not perforate membranes, evidently because by deforming into a pancake, the charges on a linear polymer achieve intimate contact with a single bilayer leaflet. The relatively rigid dendrimers, on the other hand, penetrate the bilayer, because only by interacting with both leaflets can they achieve a similar degree of contact between charged groups. Also, a "dendrimer-filled vesicle" structure for the dendrimer-membrane interaction is predicted by mesoscale thermodynamic simulations, in agreement with a picture derived from experimental observations. In simulations of complexes of dendrimer and polyelectrolyte, anionic linear chains wrap around the cationic dendrimer and penetrate inside it. Overall, these new results indicate that simulations can now provide predictions in excellent agreement with experimental observations, and provide atomic-scale insights into dendrimer structure and dynamics.
    Molecules 02/2009; 14(1):423-38. · 2.43 Impact Factor
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    ABSTRACT: Bin/Amphiphysin/Rvs-homology (BAR) domains generate and sense membrane curvature by binding the negatively charged membrane to their positively charged concave surfaces. N-BAR domains contain an N-terminal extension (helix-0) predicted to form an amphipathic helix upon membrane binding. We determined the NMR structure and nano-to-picosecond dynamics of helix-0 of the human Bin1/Amphiphysin II BAR domain in sodium dodecyl sulfate and dodecylphosphocholine micelles. Molecular dynamics simulations of this 34-amino acid peptide revealed electrostatic and hydrophobic interactions with the detergent molecules that induce helical structure formation from residues 8-10 toward the C-terminus. The orientation in the micelles was experimentally confirmed by backbone amide proton exchange. The simulation and the experiment indicated that the N-terminal region is disordered, and the peptide curves to adopted the micelle shape. Deletion of helix-0 reduced tubulation of liposomes by the BAR domain, whereas the helix-0 peptide itself was fusogenic. These findings support models for membrane curving by BAR domains in which helix-0 increases the binding affinity to the membrane and enhances curvature generation.
    Biophysical Journal 11/2008; 95(9):4315-23. · 3.67 Impact Factor
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    Hwankyu Lee, Ronald G Larson
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    ABSTRACT: We performed molecular dynamics (MD) simulations of multiple copies of poly- l-lysine (PLL) and charged polyamidoamine (PAMAM) dendrimers in dimyristoylphosphatidylcholine (DMPC) bilayers with explicit water using the coarse-grained model developed by Marrink et al. ( J. Chem. Theory Comput. 2008, 4, 819 ). Membrane disruption is enhanced at higher concentrations and charge densities of both spheroidally shaped dendrimers and linear PLL polymers, in qualitatively agreement with experimental studies by Hong et al. (Bioconjugate Chem. 2006, 17, 728 ). However, larger molecular size enhances membrane disruption and pore formation only for dendrimers and not for the linear PLL. Despite more intimate electrostatic interactions of linear molecules than are possible for spheroidal dendrimers, only the dendrimers were found to perforate membranes, apparently because they cannot spread onto a single leaflet, and so must penetrate the bilayer to get favorable electrostatic interactions with head groups on the opposite leaflet. These results indicate that a relatively rigid spheroidal shape is more efficient than a flexible linear shape in increasing membrane permeability. These results compare favorably with experimental findings.
    The Journal of Physical Chemistry B 10/2008; 112(39):12279-85. · 3.61 Impact Factor
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    Hwankyu Lee, Ronald G Larson
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    ABSTRACT: We have performed molecular dynamics (MD) simulations of multiple copies of unacetylated G5 and G7 and acetylated G5 dendrimers in dimyristoylphosphatidylcholine bilayers with explicit water using the coarse-grained model developed by Marrink et al. (J. Phys. Chem. B 2007, 111, 7812) with the inclusion of long-range electrostatics. When initially clustered together near the bilayer, neutral acetylated dendrimers aggregate, whereas cationic unacetylated dendrimers do not aggregate, but separate from each other, similar to the observations from atomic force microscopy by Mecke et al. (Chem. Phys. Lipids 2004, 132, 3). The bilayers interacting with unacetylated dendrimers of higher concentration are significantly deformed and show pore formation on the positively curved portions, while acetylated dendrimers are unable to form pores. Unacetylated G7 dendrimers bring more water molecules into the pores than do unacetylated G5 dendrimers. These results agree qualitatively with experimental results showing that significant cytoplasmic-protein leakage is produced by unacetylated G7 dendrimers at concentrations as low as 10 nM, but only at a much higher concentration of 400 nM for unacetylated G5 dendrimers (Bioconjugate Chem. 2004, 15, 774). This good qualitative agreement indicates that the effect on pore formation of the concentration and size of large nanoparticles can be studied through coarse-grained MD simulations, provided that long-range electrostatic interactions are included.
    The Journal of Physical Chemistry B 08/2008; 112(26):7778-84. · 3.61 Impact Factor
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    ABSTRACT: A revision (C35r) to the CHARMM ether force field is shown to reproduce experimentally observed conformational populations of dimethoxyethane. Molecular dynamics simulations of 9, 18, 27, and 36-mers of polyethylene oxide (PEO) and 27-mers of polyethylene glycol (PEG) in water based on C35r yield a persistence length lambda = 3.7 A, in quantitative agreement with experimentally obtained values of 3.7 A for PEO and 3.8 A for PEG; agreement with experimental values for hydrodynamic radii of comparably sized PEG is also excellent. The exponent upsilon relating the radius of gyration and molecular weight (R(g) proportional, variantM(w)(upsilon)) of PEO from the simulations equals 0.515 +/- 0.023, consistent with experimental observations that low molecular weight PEG behaves as an ideal chain. The shape anisotropy of hydrated PEO is 2.59:1.44:1.00. The dimension of the middle length for each of the polymers nearly equals the hydrodynamic radius R(h)obtained from diffusion measurements in solution. This explains the correspondence of R(h) and R(p), the pore radius of membrane channels: a polymer such as PEG diffuses with its long axis parallel to the membrane channel, and passes through the channel without substantial distortion.
    Biophysical Journal 06/2008; 95(4):1590-9. · 3.67 Impact Factor
  • Hwankyu Lee, Ronald G Larson
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    ABSTRACT: We have performed 0.5-micros-long molecular dynamics (MD) simulations of 0%, 50%, and 100% acetylated third- (G3) and fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in dipalmitoylphosphatidylcholine (DPPC) bilayers with explicit water using the coarse-grained (CG) model developed by Marrink et al. (J.Phys. Chem. B 2004, 108, 750-760), but with long-range electrostatic interactions included. Radii of gyration of the CG G5 dendrimers are 1.99-2.32 nm, close to those measured in the experiments by Prosa et al. (J. Polym. Sci. 1997, 35, 2913-2924) and atomistic simulations by Lee et al. (J. Phys. Chem. B 2006, 110, 4014-4019). Starting with the dendrimer initially positioned near the bilayer, we find that positively charged un-acetylated G3 and 50%-acetylated and un-acetylated G5 dendrimers insert themselves into the bilayer, and only un-acetylated G5 dendrimer induces hole formation at 310 K, but not at 277 K, which agrees qualitatively with experimental observations of Hong et al. (Bioconj. Chem. 2004, 15, 774-782) and Mecke et al. (Langmuir 2005, 21, 10348-10354). At higher salt concentration (approximately 500 mM NaCl), un-acetylated G5 dendrimer does not insert into the bilayer. The results suggest that with inclusion of long-range electrostatic interactions into coarse-grained models, realistic MD simulation of membrane-disrupting effects of nanoparticles at the microsecond time scale is now possible.
    The Journal of Physical Chemistry B 10/2006; 110(37):18204-11. · 3.61 Impact Factor
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    ABSTRACT: The molecular basis of nephronophthisis, the most frequent genetic cause of renal failure in children and young adults, and its association with retinal degeneration and cerebellar vermis aplasia in Joubert syndrome are poorly understood. Using positional cloning, we here identify mutations in the gene CEP290 as causing nephronophthisis. It encodes a protein with several domains also present in CENPF, a protein involved in chromosome segregation. CEP290 (also known as NPHP6) interacts with and modulates the activity of ATF4, a transcription factor implicated in cAMP-dependent renal cyst formation. NPHP6 is found at centrosomes and in the nucleus of renal epithelial cells in a cell cycle-dependent manner and in connecting cilia of photoreceptors. Abrogation of its function in zebrafish recapitulates the renal, retinal and cerebellar phenotypes of Joubert syndrome. Our findings help establish the link between centrosome function, tissue architecture and transcriptional control in the pathogenesis of cystic kidney disease, retinal degeneration, and central nervous system development.
    Nature Genetics 07/2006; 38(6):674-81. · 35.21 Impact Factor

Publication Stats

537 Citations
107.88 Total Impact Points

Institutions

  • 2011–2013
    • Dankook University
      • Department of Chemical Engineering
      Yŏng-dong, North Chungcheong, South Korea
  • 2008–2009
    • National Heart, Lung, and Blood Institute
      Maryland, United States
  • 2006
    • University of Michigan
      • Department of Biomedical Engineering
      Ann Arbor, MI, United States