Now showing items 1-19 of 19

  • Sommer, Theis; Bjerregaard-Andersen, Kaare; Uribe, Lalita; Etzerodt, Michael; Diezemann, Gregor; Gauss, Jürgen; Cascella, Michele; Morth, Jens Preben (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2018)
    The catalytic mechanism of the cyclic amidohydrolase isatin hydrolase depends on a catalytically active manganese in the substrate-binding pocket. The Mn2+ ion is bound by a motif also present in other metal dependent ...
  • De Nicola, Antonio; Soares, Thereza; Santos, Denys ES; Bore, Sigbjørn Løland; Sevink, G J Agur; Cascella, Michele; Milano, Giuseppe (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2021)
    Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of ...
  • Ledum, Morten; Bore, Sigbjørn Løland; Cascella, Michele (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    The hybrid particle-field molecular dynamics method is an efficient alternative to standard particle-based coarse grained approaches. In this work, we propose an automated protocol for optimisation of the effective parameters ...
  • Carrer, Manuel; Skrbic, Tatjana; Bore, Sigbjørn Løland; Milano, Giuseppe; Cascella, Michele; Giacometti, Achille (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    We investigate the self-assembly process of a surfactant with inverted polarity in water and cyclohexane using both all-atom and coarse-grained hybrid particle-field molecular dynamics simulations. Unlike conventional ...
  • Franco-Ulloa, Sebastian; Tatulli, Giuseppina; Bore, Sigbjørn Løland; Moglianetti, Mauro; Pompa, Pier Paolo; Cascella, Michele; De Vivo, Marco (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    Abstract The fundamental interactions underlying citrate-mediated chemical stability of metal nanoparticles, and their surface characteristics dictating particle dispersion/aggregation in aqueous solutions, are ...
  • Aeschimann, Walter; Kammer, Stephan; Staats, Stefanie; Schneider, Petra; Schneider, Gisbert; Rimbach, Gerald; Cascella, Michele; Stocker, Achim (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    α-tocopherol transfer protein (TTP) was previously reported to self-aggregate into 24-meric spheres (α-TTPS) and to possess transcytotic potency across mono-layers of human umbilical vein endothelial cells (HUVECs). In ...
  • Castro, Abril C; Balcells, David; Repisky, Michal; Helgaker, Trygve; Cascella, Michele (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    1H NMR spectroscopy has become an important technique for the characterization of transition-metal hydride complexes, whose metal-bound hydrides are often difficult to locate by X-ray diffraction. In this regard, the ...
  • Castro, Abril C.; Fliegl, Heike; Cascella, Michele; Helgaker, Trygve; Repisky, Michal; Komorovsky, Stanislav; Medrano, María Ángeles; Quiroga, Adoración G.; Swart, Marcel (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2019)
    We report a combined experimental–theoretical study on the 31P NMR chemical shift for a number of trans-platinum(II) complexes. Validity and reliability of the 31P NMR chemical shift calculations are examined by comparing ...
  • Bore, Sigbjørn Løland; Cascella, Michele (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2020)
    Hybrid particle–field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. ...
  • Peltzer, Raphael Mathias; Eisenstein, Odile; Nova, Ainara; Cascella, Michele (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
    The Schlenk equilibrium is a complex reaction governing the presence of multiple chemical species in solution of Grignard reagents. The full characterization at the molecular level of the transformation of CH3MgCl into ...
  • Bore, Sigbjørn Løland; Milano, Giuseppe; Cascella, Michele (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2018)
    We propose the first model of a polypeptide chain based on a hybrid-particle field approach. The intramolecular potential is built on a two-bead coarse grain mapping for each amino acid. We employ a combined potential for ...
  • Kolli, Hima Bindu; De Nicola, Antonio; Bore, Sigbjørn Løland; Schäfer, Ken; Diezemann, Gregor; Gauss, Jürgen; Kawakatsu, Toshihiro; Lu, Zhong-Yuan; Zhu, You-Liang; Milano, Giuseppe; Cascella, Michele (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2018)
    We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in an aqueous environment, to ...
  • Bore, Sigbjørn Løland; Kolli, Hima Bindu; De Nicola, Antonio; Byshkin, Maksym; Kawakatsu, Toshihiro; Milano, Giuseppe; Cascella, Michele (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2020)
    Hybrid particle-field methods are computationally efficient approaches for modeling soft matter systems. So far, applications of these methodologies have been limited to constant volume conditions. Here, we reformulate ...
  • Jaschonek, Stefan; Cascella, Michele; Gauss, Jurgen; Diezemann, Gregor; Milano, Giuseppe (Journal article / Tidsskriftartikkel / SubmittedVersion, 2018)
    The capability of coarse-grained models based on the MARTINI mapping to reproduce the gel-liquid phase transition in saturated and unsaturated model lipids was investigated. We found that the model is able to reproduce a ...
  • Lamprakis, Christos; Stocker, Achim; Cascella, Michele (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2015)
    We used multiple sets of simulations both at the atomistic and coarse-grained level of resolution to investigate interaction and binding of α-tochoperol transfer protein (α-TTP) to phosphatidylinositol phosphate lipids ...
  • Correa, Andrea; Cascella, Michele; Scotti, Nicola; Zaccheria, Federica; Ravasio, Nicoletta; Psaro, Rinaldo (Journal article / Tidsskriftartikkel / SubmittedVersion, 2018)
    A computational study on the molecular mechanism of formic acid dehydrogenation in the presence of Cu-amine complex has been carried out in order to shed light on the role of the amine in determining the catalyst activity. ...
  • Peltzer, Raphael Mathias; Kolli, Hima Bindu; Stocker, Achim; Cascella, Michele (Journal article / Tidsskriftartikkel / AcceptedVersion; Peer reviewed, 2018)
    We describe the mechanism of self-aggregation of α-tocopherol transfer protein into a spherical nanocage employing Monte Carlo simulations. The protein is modeled by a patchy coarse-grained representation, where the ...
  • Schäfer, Ken; Kolli, Hima Bindu; Christensen, Mikkel Killingmoe; Bore, Sigbjørn Løland; Diezemann, Gregor; Gauss, Jürgen; Milano, Giuseppe; Lund, Reidar; Cascella, Michele (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    The shape and size of self‐assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long‐range interactions. Combining small‐angle X‐ray/neutron scattering data, ...
  • Peltzer, Raphael Mathias; Gauss, Jürgen; Eisenstein, Odile; Cascella, Michele (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    More than 100 years since its discovery, the mechanism of the Grignard reaction remains unresolved. Ambiguities arise from the concomitant presence of multiple organomagnesium species and the competing mechanisms involving ...