Himanshu Khandelia

University of Southern Denmark, Kolding, South Denmark, Denmark

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Publications (32)134.92 Total impact

  • Wojciech Kopec, Himanshu Khandelia
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    ABSTRACT: Thioridazine is a well-known dopamine-antagonist drug with a wide range of pharmacological properties ranging from neuroleptic to antimicrobial and even anticancer activity. Thioridazine is a critical component of a promising multi-drug therapy against M. tuberculosis. Amongst the various proposed mechanisms of action, the cell membrane-mediated one is peculiarly tempting due to the distinctive feature of phenothiazine drug family to accumulate in selected body tissues. In this study, we employ long-scale molecular dynamics simulations to investigate the interactions of three different concentrations of thioridazine with zwitterionic and negatively charged model lipid membranes. Thioridazine partitions into the interfacial region of membranes and modifies their structural and dynamic properties, however dissimilarly so at the highest membrane-occurring concentration, that appears to be obtainable only for the negatively charged bilayer. We show that the origin of such changes is the drug induced decrease of the interfacial tension, which ultimately leads to the significant membrane expansion. Our findings support the hypothesis that the phenothiazines therapeutic activity may arise from the drug-membrane interactions, and reinforce the wider, emerging view of action of many small, bioactive compounds.
    Journal of Computer-Aided Molecular Design 03/2014; · 3.17 Impact Factor
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    ABSTRACT: Mutations within ion transporting proteins may severely affect their ability to properly traffic ions and thus perturb the delicate balance of ion gradients. Somatic gain-of-function mutations of the Na+, K+-ATPase α1-subunit have been found in aldosterone-producing adenomas that are amongst the causes of hypertension. We use Molecular Dynamics simulations to investigate structural consequences of these mutations, namely Leu97 substitution by Arg (L97R), Val325 substitution by Gly (V325G), deletion of 93-97 residues (Del93-97) and deletion-substitution of 953-956 residues by Ser (EETA956S) that show inward leak currents under physiological conditions. First three mutations affect the structural context of the key ion binding residue Glu327 at binding site II, which leads to the loss of the ability to correctly bind ions and to occlude the pump. The mutated residue in L97K is more hydrated, which ultimately leads to the observed proton leak. V325G mimics the structural behavior of Leu97, however it does not promote the hydration of surrounding residues. In Del93-97, a broader opening is observed due to the rearrangement of the kinked trans-membrane helix 1, M1, which may explain the sodium leak measured with the mutant. The last mutant, EETA956S, opens an additional water pathway near the C-terminus, affecting the III sodium-specific binding site. The results are in excellent agreement with recent electrophysiology measurements and suggest how three mutations prevent the occlusion of the Na+, K+-ATPase, with a possibility of transforming the pump into a passive ion channel, while the fourth mutation provides an insight into the sodium binding in the E1 state.
    Biochemistry 01/2014; · 3.38 Impact Factor
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    ABSTRACT: Ladderanes, which are multiple fused cyclobutane rings, are unique structures available only in nature. Anammox bacteria produce ladderane phospholipids during their life cycle, but the synthesis mechanism still remains a mystery. The function of ladderane lipids in the membrane is unclear as well. According to previous speculations, ladderane moieties of the bilayer might decrease permeability for certain molecules, which should not diffuse out of the compartment enclosed by the ladderane-containing membrane. We report the first atomistic-precision molecular dynamics simulations of bilayers containing ladderane lipids. The structural and thermodynamics differences among (1) pure ladderane containing bilayer, (2) POPC bilayer, and (3) their equimolar mixture are discussed. Potentials of mean force are reported for the translocation of a hydrazine molecule through all investigated bilayers. All bilayers offer a potential energy barrier to hydrazine. Contrary to expectations, the presence of the ladderane lipids somewhat lowers the barrier for translocation of hydrazine. We conclude that the presence of ladderane phospholipids in anammox bacteria does not serve as a barrier to hydrazine. It may serve as a barrier to larger and noxious intermediates in the anammox reaction, or, the true mission of ladderane lipids must be located in a different plane.
    Chemistry and Physics of Lipids. 01/2014;
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    ABSTRACT: We investigate the effect of an applied electric potential on the mechanics of a coarse grained POPC bilayer under tension. The size and duration of our simulations allow for a detailed and accurate study of the fluctuations. Effects on the fluctuation spectrum, tension, bending rigidity, and bilayer thickness are investigated in detail. In particular, the least square fitting technique is used to calculate the fluctuation spectra. The simulations confirm a recently proposed theory that the effect of an applied electric potential on the membrane will be moderated by the elastic properties of the membrane. In agreement with the theory, we find that the larger the initial tension the larger the effect of the electric potential. Application of the electric potential increases the amplitude of the long wavelength part of the spectrum and the bending rigidity is deduced from the short wavelength fluctuations. The effect of the applied electric potential on the bending rigidity is non-existent within error bars. However, when the membrane is stretched there is a point where the bending rigidity is lowered due to a decrease of the thickness of the membrane. All these effects should prove important for mechanosensitive channels and biomembrane mechanics in general.
    The Journal of Chemical Physics 10/2013; 139(16):164902. · 3.16 Impact Factor
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    ABSTRACT: The compound 2,6-diisopropylphenol (Propofol, PRF) is widely used for inducing general anesthesia, but the mechanism of PRF action remains relatively poorly understood at the molecular level. This work examines the possibility that a potential mode of action of PRF is to modulate the lipid order in target membranes. The effect on monolayers and bilayers of dipalmitoyl-sn-glycero-3-phosphorylcholine (DPPC) was probed using Langmuir monolayer isotherms, differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD). Increasing amounts of PRF in a DPPC monolayer causes a decrease in isothermal compressibility modulus at the phase transition. A partition constant for PRF in DPPC liposomes on the order of K≈1500M(-1) was found, and the partitioning was found to be enthalpy-driven above the melting temperature (Tm). A decrease in Tm with PRF content was found whereas the bilayer melting enthalpy ΔHm remains almost constant. The last finding indicates that PRF incorporates into the membrane at a depth near the phosphatidylcholine headgroup, in agreement with our MD-simulations. The simulations also reveal that PRF partitions into the membrane on a timescale of 0.5 microsecond and has a cholesterol-like ordering effect on DPPC in the fluid phase. The vertical location of the PRF binding site in a bacterial ligand-gated ion channel coincides with the location found in our MD-simulations. Our results suggest that multiple physicochemical mechanisms may determine anesthetic potency of PRF, including effects on proteins that are mediated through the bilayer.
    Chemistry and physics of lipids 08/2013; · 2.15 Impact Factor
  • Wojciech Kopeć, Jelena Telenius, Himanshu Khandelia
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    ABSTRACT: Several small drugs and medicinal plant extracts such as the Indian spice extract curcumin have a wide range of useful pharmacological properties, which cannot be ascribed to binding to a single protein target alone. The lipid bilayer membrane is thought to mediate the effects of many such molecules directly via the perturbation of the plasma membrane structure and dynamics, or indirectly by modulating trans-membrane protein conformational equilibria. Furthermore, for bioavailability, drugs need to interact with and eventually permeate the lipid bilayer barrier on the surface of cells. Biophysical studies of the interactions of drugs and plant extracts is therefore of interest. Molecular dynamics (MD) simulations, which can access time and length scales not simultaneously accessible by other experimental methods, are often applied to obtain quantitative molecular and thermodynamic descriptions of these interactions, also often with complementary biophysical measurements. In this review, we survey recent MD simulations of small drug-like molecules with membranes, and provide a biophysical description of possible routes of membrane-mediated pharmacological effects of drugs. The review is not exhaustive, and in particular, we use molecules containing aromatic ring-like structures to develop our hypotheses. We also show that some drugs and anesthetics may have an effect on lipid bilayer analogous to cholesterol. This article is protected by copyright. All rights reserved.
    FEBS Journal 04/2013; · 4.25 Impact Factor
  • Albin Hermetter, Himanshu Khandelia
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    ABSTRACT: Products of phospholipid oxidation can produce lipids with a carbonyl moiety at the end of a shortened lipid acyl tail, such as 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine (POVPC). The carbonyl tail of POVPC can covalently bond to the free tertiary amine of a phosphatidylethanolamine lipid in a Schiff base reaction to form a conjugate lipid (SCH) with two head groups, and three acyl tails (Fig. 1). We investigate the conformations and properties of this unique class of adduct lipids using Molecular Dynamics Simulations, and show that their insertion into lipid bilayers of POPC increases the average cross-sectional area per lipid and decreases bilayer thickness. Significant increase in acyl tail fluidity is only observed at 25% SCH concentration. The SCH lipids occupy a larger area per lipid than expected for a lipid with three acyl tails, owing to the interfacial location of the long spacer between the two head groups of the SCH lipids. Schiff base formation of lipids can alter the concentration, homeostasis and localizations of phosphatidylserine and phosphatidylethanol lipids in membranes, and can therefore influence several membrane-associated processes including fusion and budding. The current work provides the first detailed structural model of this unique new class of lipids that may have important roles to play in modulating membrane properties and cell physiology.
    Biochimica et Biophysica Acta 04/2013; · 4.66 Impact Factor
  • Bastien Loubet, Michael A. Lomholt, Himanshu Khandelia
    Biophysical Journal 01/2013; 104(2):662-. · 3.67 Impact Factor
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    ABSTRACT: Lipid peroxidation plays a key role in the alteration of cell membrane's properties. Here we used as model systems multilamellar vesicles (MLVs) made of the first two products in the oxidative cascade of linoleoyl lecithin, namely 1-palmitoyl-2-(13-hydroperoxy-9,11-octadecanedienoyl)-lecithin (HpPLPC) and 1-palmitoyl-2-(13-hydroxy-9,11-octadecanedienoyl)-lecithin (OHPLPC), exhibiting a hydroperoxide or a hydroxy group at position 13, respectively. The two oxidized lipids were used either pure or in a 1:1 molar ratio mixture with untreated 1-palmitoyl-2-linoleoyl-lecithin (PLPC). The model membranes were doped with spin-labeled lipids to study bilayer alterations by electron paramagnetic resonance (EPR) spectroscopy. Two different spin-labeled lipids were used, bearing the doxyl ring at position (n) 5 or 16: γ-palmitoyl-β-(n-doxylstearoyl)-lecithin (n-DSPPC) and n-doxylstearic acid (n-DSA). Small changes in the acyl chain order in the sub-polar region and at the methyl-terminal induced by lipid peroxidation were detected by X-band EPR. Concomitantly, the polarity and proticity of the membrane bilayer in those regions were investigated at W band in frozen samples. Analysis of the g(xx) and A(zz) parameters revealed that OHPLPC, but mostly HpPLPC, induced a measurable increase in polarity and H-bonding propensity in the central region of the bilayer. Molecular dynamics simulation performed on 16-DSA in the PLPC-HpPLPC bilayer revealed that water molecules are statistically favored with respect to the hydroperoxide groups to interact with the nitroxide at the methyl-terminal, confirming that the H-bonds experimentally observed are due to increased water penetration in the bilayer. The EPR and MD data on model membranes demonstrate that cell membrane damage by oxidative stress cause alteration of water penetration in the bilayer.
    Biochimica et Biophysica Acta 10/2012; · 4.66 Impact Factor
  • Ole G Mouritsen, Himanshu Khandelia
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    ABSTRACT: The fifth taste quality, umami, arises from binding of glutamate to the umami receptor T1R1/T1R3. The umami taste is enhanced several-fold upon addition of free nucleotides such as guanosine-5'-monophosphate (GMP) to glutamate-containing food. GMP may operate via binding to the ligand-binding domain of the T1R1 part of the umami receptor at an allosteric site. Using molecular dynamics simulations, we show that GMP can stabilize the closed (active) state of T1R1 by binding to the outer vestibule of the so-called Venus flytrap domain of the receptor. The transition between the closed and open conformations was accessed in the simulations. Using principal component analysis, we show that the dynamics of the Venus flytrap domain along the hinge-bending motion that activates signaling is dampened significantly upon binding of glutamate, and further slows down upon binding of GMP at an allosteric site, thus suggesting a molecular mechanism of cooperativity between GMP and glutamate.
    FEBS Journal 07/2012; 279(17):3112-20. · 4.25 Impact Factor
  • Hanne Poulsen, Poul Nissen, Ole G Mouritsen, Himanshu Khandelia
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    ABSTRACT: Phosphorylation is one of the major mechanisms for posttranscriptional modification of proteins. The addition of a compact, negatively charged moiety to a protein can significantly change its function and localization by affecting its structure and interaction network. We have used all-atom Molecular Dynamics simulations to investigate the structural consequences of phosphorylating the Na(+)/K(+)-ATPase (NKA) residue Ser(936), which is the best characterized phosphorylation site in NKA, targeted in vivo by protein kinase A (PKA). The Molecular Dynamics simulations suggest that Ser(936) phosphorylation opens a C-terminal hydrated pathway leading to Asp(926), a transmembrane residue proposed to form part of the third sodium ion-binding site. Simulations of a S936E mutant form, for which only subtle effects are observed when expressed in Xenopus oocytes and studied with electrophysiology, does not mimic the effects of Ser(936) phosphorylation. The results establish a structural association of Ser(936) with the C terminus of NKA and indicate that phosphorylation of Ser(936) can modulate pumping activity by changing the accessibility to the ion-binding site.
    Journal of Biological Chemistry 03/2012; 287(19):15959-65. · 4.65 Impact Factor
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    Himanshu Khandelia, Sarah Witzke, Ole G Mouritsen
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    ABSTRACT: We investigate the effects of two structurally similar small cyclic molecules: salicylic acid and perillic acid on a zwitterionic model lipid bilayer, and show that both molecules might have biological activity related to membrane thinning. Salicylic acid is a nonsteroidal antiinflammatory drug, some of the pharmacological properties of which arise from its interaction with the lipid bilayer component of the plasma membrane. Prior simulations show that salicylate orders zwitterionic lipid membranes. However, this is in conflict with Raman scattering and vesicle fluctuation analysis data, which suggest the opposite. We show using extensive molecular dynamics simulations, cumulatively >2.5 μs, that salicylic acid indeed disorders membranes with concomitant membrane thinning and that the conflict arose because prior simulations suffered from artifacts related to the sodium-ion induced condensation of zwitterionic lipids modeled by the Berger force field. Perillic acid is a terpenoid plant extract that has antiinfective and anticancer properties, and is extensively used in eastern medicine. We found that perillic acid causes large-scale membrane thinning and could therefore exert its antimicrobial properties via a membrane-lytic mechanism reminiscent of antimicrobial peptides. Being more amphipathic, perillic acid is more potent in disrupting lipid headgroup packing, and significantly modifies headgroup dipole orientation. Like salicylate, the membrane thinning effect of perillic acid is masked by the presence of sodium ions. As an alternative to sodium cations, we advocate the straightforward solution of using larger countercations like potassium or tetra-methyl-ammonium that will maintain electroneutrality but not interact strongly with, and thus not condense, the lipid bilayer.
    Biophysical Journal 12/2010; 99(12):3887-94. · 3.67 Impact Factor
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    ABSTRACT: The plant Perilla frutescens is widely employed in Asian medicine. The active components of Perilla include cyclic terpenes, which have a diverse range of antimicrobial, anticancer, sedative, and anti-inflammatory properties, hinting at a membrane-mediated mechanism of action. We have used molecular dynamics (MD) simulations and isothermal titration calorimetry (ITC) to investigate the interaction of four terpenes with model lipid bilayers. The ITC and MD data are mostly in accordance. The terpenes partition into membranes, pack along the lipid tails, and alter bilayer structure and dynamics. Three of the four molecules could cross the bilayer. The carboxylate-group-containing terpene modifies headgroup repulsion and increases the area per lipid by more than 10%, in a manner reminiscent of membrane-thinning peptides and solvents such as DMSO. Our results support the possibility that at least some medicinal properties of volatile Perilla extracts might arise from interactions with the lipid bilayer component of biological membranes.
    The Journal of Physical Chemistry B 11/2010; 114(48):15825-31. · 3.61 Impact Factor
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    ABSTRACT: The Na(+)/K(+)-ATPase pumps three sodium ions out of and two potassium ions into the cell for each ATP molecule that is split, thereby generating the chemical and electrical gradients across the plasma membrane that are essential in, for example, signalling, secondary transport and volume regulation in animal cells. Crystal structures of the potassium-bound form of the pump revealed an intimate docking of the alpha-subunit carboxy terminus at the transmembrane domain. Here we show that this element is a key regulator of a previously unrecognized ion pathway. Current models of P-type ATPases operate with a single ion conduit through the pump, but our data suggest an additional pathway in the Na(+)/K(+)-ATPase between the ion-binding sites and the cytoplasm. The C-terminal pathway allows a cytoplasmic proton to enter and stabilize site III when empty in the potassium-bound state, and when potassium is released the proton will also return to the cytoplasm, thus allowing an overall asymmetric stoichiometry of the transported ions. The C terminus controls the gate to the pathway. Its structure is crucial for pump function, as demonstrated by at least eight mutations in the region that cause severe neurological diseases. This novel model for ion transport by the Na(+)/K(+)-ATPase is established by electrophysiological studies of C-terminal mutations in familial hemiplegic migraine 2 (FHM2) and is further substantiated by molecular dynamics simulations. A similar ion regulation is likely to apply to the H(+)/K(+)-ATPase and the Ca(2+)-ATPase.
    Nature 09/2010; 467(7311):99-102. · 38.60 Impact Factor
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    Himanshu Khandelia, Yiannis N. Kaznessis
    Biochimica Et Biophysica Acta-biomembranes - BBA-BIOMEMBRANES. 01/2010; 1798(8):1623-1623.
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    ABSTRACT: Triglycerides have a limited solubility, around 3%, in phosphatidylcholine lipid bilayers. Using millisecond-scale course grained molecular dynamics simulations, we show that the model lipid bilayer can accommodate a higher concentration of triolein (TO) than earlier anticipated, by sequestering triolein molecules to the bilayer center in the form of a disordered, isotropic, mobile neutral lipid aggregate, at least 17 nm in diameter, which forms spontaneously, and remains stable on at least the microsecond time scale. The results give credence to the hotly debated existence of mobile neutral lipid aggregates of unknown function present in malignant cells, and to the early biogenesis of lipid droplets accommodated between the two leaflets of the endoplasmic reticulum membrane. The TO aggregates give the bilayer a blister-like appearance, and will hinder the formation of multi-lamellar phases in model, and possibly living membranes. The blisters will result in anomalous membrane probe partitioning, which should be accounted for in the interpretation of probe-related measurements.
    PLoS ONE 01/2010; 5(9):e12811. · 3.73 Impact Factor
  • Himanshu Khandelia, Ole G. Mouritsen
    Biophysical Journal 01/2010; 98(3). · 3.67 Impact Factor
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    ABSTRACT: We present relative binding free energy calculations for six antimicrobial peptide-micelle systems, three peptides interacting with two types of micelles. The peptides are the scorpion derived antimicrobial peptide (AMP), IsCT and two of its analogues. The micelles are dodecylphosphatidylcholine (DPC) and sodium dodecylsulphate (SDS) micelles. The interfacial electrostatic properties of DPC and SDS micelles are assumed to be similar to those of zwitterionic mammalian and anionic bacterial membrane interfaces, respectively. We test the hypothesis that the binding strength between peptides and the anionic micelle SDS can provide information on peptide antimicrobial activity, since it is widely accepted that AMPs function by binding to and disrupting the predominantly anionic lipid bilayer of the bacterial cytoplasmic membrane. We also test the hypothesis that the binding strength between peptides and the zwitterionic micelle DPC can provide information on peptide haemolytic activities, since it is accepted that they also bind to and disrupt the zwitterionic membrane of mammalian cells. Equilibrium structures of the peptides, micelles and peptide-micelle complexes are obtained from more than 300 ns of molecular dynamics simulations. A thermodynamic cycle is introduced to compute the binding free energy from electrostatic, non-electrostatic and entropic contributions. We find relative binding free energy strengths between peptides and SDS to correlate with the experimentally measured rankings for peptide antimicrobial activities, and relative free energy binding strengths between peptides and DPC to correlate with the observed rankings for peptide haemolytic toxicities. These findings point to the importance of peptide-membrane binding strength for antimicrobial activity and haemolytic activity.
    Molecular Simulation 09/2009; 35(10-11):986-997. · 1.06 Impact Factor
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    Himanshu Khandelia, Ole G Mouritsen
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    ABSTRACT: In oxidative environments, biomembranes contain oxidized lipids with short, polar acyl chains. Two stable lipid oxidation products are PoxnoPC and PazePC. PoxnoPC has a carbonyl group, and PazePC has an anionic carboxyl group pendant at the end of the short, oxidized acyl chain. We have used MD simulations to explore the possibility of complete chain reversal in OXPLs in POPC-OXPL mixtures. The polar AZ chain of PazePC undergoes chain reversal without compromising the lipid bilayer integrity at concentrations up to 25% OXPL, and the carboxyl group points into the aqueous phase. Counterintuitively, the perturbation of overall membrane structural and dynamic properties is stronger for PoxnoPC than for PazePC. This is because of the overall condensing and ordering effect of sodium ions bound strongly to the lipids in the PazePC simulations. The reorientation of AZ chain is similar for two different lipid force fields. This work provides the first molecular evidence of the "extended lipid conformation" in phospholipid membranes. The chain reversal of PazePC lipids decorates the membrane interface with reactive, negatively charged functional groups. Such chain reversal is likely to exert a profound influence on the structure and dynamics of biological membranes, and on membrane-associated biological processes.
    Biophysical Journal 05/2009; 96(7):2734-43. · 3.67 Impact Factor
  • Himanshu Khandelia, Morten Ø Jensen, Ole G Mouritsen
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    ABSTRACT: The spinach plant aquaporin SoPIP2;1 is a gated water channel, which switches between open and closed states depending on the conformation of a 20-residue cytoplasmic loop, the D-loop. Using fully atomistic molecular dynamics simulations, we have investigated the possibility of driving the conformational equilibrium of the protein toward a constitutively open state. We introduce two separate mutations in the D-loop, while being in the closed conformation. We show that the single channel permeability of both mutants is comparable to that of the open conformation. This Article provides new molecular insight into the gating mechanism of SoPIP2;1. It is proposed that residues Arg190, Asp191, and Ser36 might play important roles in the gating of the protein.
    The Journal of Physical Chemistry B 05/2009; 113(15):5239-44. · 3.61 Impact Factor

Publication Stats

286 Citations
134.92 Total Impact Points


  • 2008–2013
    • University of Southern Denmark
      • Center for Biomembrane Physics (MEMPHYS)
      Kolding, South Denmark, Denmark
  • 2012
    • Aarhus University
      • Centre for Membrane Pumps in Cells and Disease PUMPKIN
      Aars, Region North Jutland, Denmark
  • 2006–2010
    • University of Minnesota Duluth
      Duluth, Minnesota, United States
  • 2005–2009
    • University of Minnesota Twin Cities
      • Department of Chemical Engineering and Materials Science
      Minneapolis, MN, United States