1. Characterizing the Three-Dimensional Structure of Block Copolymers via Sequential Infiltration Synthesis and Scanning Transmission Electron Tomography.

    ACS Nano 9(5):5333 (2015) PMID 25919347

    Understanding and controlling the three-dimensional structure of block copolymer (BCP) thin films is critical for utilizing these materials for sub-20 nm nanopatterning in semiconductor devices, as well as in membranes and solar cell applications. Combining an atomic layer deposition (ALD)-based...
  2. S-7 : A new cytokine receptor activation paradigm: Activation of JAK2 by the growth hormone receptor

    Cytokine 70(1):22 (2014)

    The conformational changes required to transmit the GH binding signal from the extracellular domain of the GH receptor to its intracellular domain resulting in activation of JAK2 has been enigmatic. We have recently defined the first complete mechanistic model for JAK2 activation based...
  3. Multiscale modeling of polyisoprene on graphite.

    Journal of Chemical Physics 140(5):054908 (2014) PMID 24511980

    The local dynamics and the conformational properties of polyisoprene next to a smooth graphite surface constructed by graphene layers are studied by a multiscale methodology. First, fully atomistic molecular dynamics simulations of oligomers next to the surface are performed. Subsequently, Monte...
  4. Molecular dynamics of polyisoprene/polystyrene oligomer blends: the role of self-concentration and fluctuations on blend dynamics.

    Journal of Chemical Physics 139(3):034904 (2013) PMID 23883054

    The effect of self-concentration and intermolecular packing on the dynamics of polyisoprene (PI)/polystyrene (PS) blends is examined by extensive atomistic simulations. Direct information on local structure of the blend system allows a quantitative calculation of self- and effective composition ...
  5. Detailed atomistic Monte Carlo simulations of a polymer melt on a solid surface and around a nanoparticle.

    Journal of Chemical Physics 136(9):094901 (2012) PMID 22401467

    The molecular factors that govern interfacial interactions between a polymer melt and a solid surface remain largely unclear despite significant progress made in the last years. Simulations are increasingly employed to elucidate these features, however, equilibration and sampling with models of ...
  6. Self-Association of Transmembrane Domains of ErbB2 Receptors in Cholesterol-Containing Membranes

    Biophysical Journal 102(3):470a (2012)

  7. GxxxG motifs, phenylalanine, and cholesterol guide the self-association of transmembrane domains of ErbB2 receptors.

    Biophysical Journal 101(8):1949 (2011) PMID 22004749 PMCID PMC3192960

    GxxxG motifs are common in transmembrane domains of membrane proteins and are often introduced to artificial peptides to inhibit or promote association to stable structures. The transmembrane domain of ErbB2 presents two separate such motifs that are proposed to be connected to stability and act...
  8. Molecular Simulations of Sequence-Specific Association of Transmembrane Proteins in Lipid Bilayers

    Biophysical Journal 100(3):614a (2011)

  9. Self-association of models of transmembrane domains of ErbB receptors in a lipid bilayer.

    Biophysical Journal 99(11):3657 (2010) PMID 21112290 PMCID PMC2998631

    Association of transmembrane (TM) helices is facilitated by the close packing of small residues present along the amino-acid sequence. Extensive studies have established the role of such small residue motifs (GxxxG) in the dimerization of Glycophorin A (GpA) and helped to elucidate the associati...
  10. Lipid-modulated sequence-specific association of glycophorin A in membranes.

    Biophysical Journal 99(1):284 (2010) PMID 20655857 PMCID PMC2895386

    Protein association in lipid membranes is a complex process with thermodynamics directed by a multitude of different factors. Amino-acid sequence is a molecular parameter that affects dimerization as shown by limited directed mutations along the transmembrane domains. Membrane-mediated interacti...
  11. Accelerating flat-histogram methods for potential of mean force calculations.

    Journal of Chemical Physics 131(5):054105 (2009) PMID 19673549

    Potential of mean force calculations along a reaction coordinate (RC) demand exhaustive sampling, which often leads to prohibitively long computational times. The expanded ensemble density of states (EXEDOS) [E. B. Kim, R. Faller, Q. Yan et al., J. Chem. Phys. 117, 7781 (2002)] is a simple flat-...
  12. Calculation of local mechanical properties of filled polymers.

    Physical Review E 75(3 Pt 1):031803 (2007) PMID 17500718

    A study is presented on the effects of smooth nanoparticles on the structure and elastic moduli of a polymer matrix. Structural changes between the unfilled polymer matrix and the nanocomposite give rise to the formation of a glassy layer that surrounds the nanoparticles. Results for the effects...
  13. Local mechanical properties of polymeric nanocomposites.

    Physical Review E 72(3 Pt 1):031801 (2005) PMID 16241467

    The inclusion of a nanoparticle into a polymer matrix is studied by efficient Monte Carlo simulations. The resulting structural changes in the melt and glass exhibit a strong dependence on the strength of the polymer attraction to the surface of the filler. The mechanical properties of the nanoc...
  14. Large scale atomistic polymer simulations using Monte Carlo methods for parallel vector processors

    Computer Physics Communications 144(1):1 (2002)

    In this paper we discuss the implementation of advanced variable connectivity Monte Carlo (MC) simulation methods for studying large (>10 5 atom) polymer systems at the atomic level. Such codes are intrinsically difficult to optimize since they involve a mixture of many different elem...