Browsing Kjemisk institutt by Author "Cascella, Michele"

Now showing items 1-20 of 32

  • A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase 
    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 ...
  • Accelerating Lipid Flip-Flop at Low Concentrations: A General Mechanism for Membrane Binding Peptides 
    Carrer, Manuel; Nielsen, Josefine Eilsø; Musseli Cezar, Henrique; Lund, Reidar; Cascella, Michele; Soares da Silva, Thereza Amelia (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    We report a physicochemical investigation of the lipid transport properties of model lipid membranes in the presence of the antimicrobial peptide indolicidin through comparisons of experimental SANS/SAXS scattering techniques ...
  • Aggregation of Lipid A Variants: A Hybrid Particle-Field Model 
    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 ...
  • Automated determination of hybrid particle-field parameters by machine learning 
    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 ...
  • Bias Amplification in Gender, Gender Identity, and Geographical Affiliation 
    Cascella, Michele; Soares, Thereza A. (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    In the quest for greater equity in science, individual attitudes and institutional policies should also embrace greater diversity and inclusion of minority groups. This viewpoint calls for a broader definition of gender ...
  • Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents? 
    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 ...
  • Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions 
    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 ...
  • Engineering of a functional γ-tocopherol transfer protein 
    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 ...
  • First-Principles Calculation of 1H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics 
    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 ...
  • Four-component relativistic 31P NMR calculations for: Trans -platinum(ii) complexes: Importance of the solvent and dynamics in spectral simulations 
    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 ...
  • Hamiltonian and alias-free hybrid particle-field molecular dynamics 
    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. ...
  • How Solvent Dynamics Controls the Schlenk Equilibrium of Grignard Reagents: A Computational Study of CH3MgCl in Tetrahydrofuran 
    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 ...
  • Hybrid particle-field model for conformational dynamics of peptide chains 
    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 ...
  • Hybrid particle-field molecular dynamics simulations of charged amphiphiles in an aqueous environment 
    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 ...
  • Hybrid Particle-Field Molecular Dynamics Under Constant Pressure 
    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 ...
  • HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter 
    Ledum, Morten; Sen, Samiran; Li, Xinmeng; Carrer, Manuel; Feng, Yu; Cascella, Michele; Bore, Sigbjørn Løland (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics. The methodology is based on a tunable, grid-independent length-scale ...
  • HylleraasMD: Massively parallel hybrid particle-field molecular dynamics in Python 
    Ledum, Morten; Carrer, Manuel; Sen, Samiran; Li, Xinmeng; Cascella, Michele; Bore, Sigbjørn Løland (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    Molecular dynamics (MD) is a computational methodology in which the dynamical behavior of systems of interacting atoms and molecules is investigated by integrating the corresponding classical equations of motion. The ...
  • Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers 
    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 ...
  • Mechanisms of recognition and binding of α-TTP to the plasma membrane by multi-scale molecular dynamics simulations 
    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 ...
  • Mechanistic insights into formic acid dehydrogenation promoted by Cu-amino based systems 
    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. ...