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Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics (2018)
Journal Article
Paulo, S., Khandelia, H., Orsi, M., & Dias, L. G. (2018). Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics. Journal of Computer-Aided Molecular Design, 32(11), 1259-1271. https://doi.org/10.1007/s10822-018-0164-4

© 2018, Springer Nature Switzerland AG. We present a new coarse-grained (CG) model of cholesterol (CHOL) for the electrostatic-based ELBA force field. A distinguishing feature of our CHOL model is that the electrostatics is modeled by an explicit poi... Read More about Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics.

Effects of lipid composition on membrane permeation (2018)
Journal Article
Palaiokostas, M., Ding, W., Shahane, G., & Orsi, M. (2018). Effects of lipid composition on membrane permeation. Soft Matter, 14(42), 8496-8508. https://doi.org/10.1039/c8sm01262h

© 2018 The Royal Society of Chemistry. Passive permeation through lipid membranes is an essential process in biology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterized by their tende... Read More about Effects of lipid composition on membrane permeation.

Molecular simulation of self-assembly (2018)
Book Chapter
Orsi, M. (2018). Molecular simulation of self-assembly. In H. Azevedo, & R. da Silva (Eds.), Self-Assembling Biomaterials, 305-318. Elsevier

Molecular simulation is a powerful tool for studying self-assembly, as it can provide unprecedented access into a range of physical properties at the intra-, inter- and supra-molecular scales. The self-assembly of biological molecules, a ubiquitous p... Read More about Molecular simulation of self-assembly.

Effects of High Pressure on Phospholipid Bilayers (2017)
Journal Article
Ding, W., Wei, D., Palaiokostas, M., Shahane, G., Wang, W., & Orsi, M. (2017). Effects of High Pressure on Phospholipid Bilayers. Journal of Physical Chemistry B, 121(41), 9597-9606. https://doi.org/10.1021/acs.jpcb.7b07119

© 2017 American Chemical Society. The response of lipid membranes to changes in external pressure is important for many biological processes, and it can also be exploited for technological applications. In this work, we employ all-atom molecular dyna... Read More about Effects of High Pressure on Phospholipid Bilayers.

Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics (2015)
Journal Article
Ding, W., Palaiokostas, M., Wang, W., & Orsi, M. (2015). Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics. Journal of Physical Chemistry B, 119(49), 15263-15274. https://doi.org/10.1021/acs.jpcb.5b06604

© 2015 American Chemical Society. Biological bilayer membranes typically contain varying amounts of lamellar and nonlamellar lipids. Lamellar lipids, such as dioleoylphosphatidylcholine (DOPC), are defined by their tendency to form the lamellar phase... Read More about Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics.

Stress testing the ELBA water model (2015)
Journal Article
Ding, W., Palaiokostas, M., & Orsi, M. (2016). Stress testing the ELBA water model. Molecular Simulation, 42(4), 337-346. https://doi.org/10.1080/08927022.2015.1047367

© 2015 © 2015 The Author(s). Published by Taylor & Francis. The ELBA coarse-grained model describes a water molecule as a single-site Lennard-Jones particle embedded with a point dipole. ELBA was previously reported to capture several properties of... Read More about Stress testing the ELBA water model.

Direct mixing of atomistic solutes and coarse-grained water (2014)
Journal Article
Orsi, M., Ding, W., & Palaiokostas, M. (2014). Direct mixing of atomistic solutes and coarse-grained water. Journal of Chemical Theory and Computation, 10(10), 4684-4693. https://doi.org/10.1021/ct500065k

© 2014 American Chemical Society. We present a new dual-resolution approach for coupling atomistic and coarse-grained models in molecular dynamics simulations of hydrated systems. In particular, a coarse-grained point dipolar water model is used to s... Read More about Direct mixing of atomistic solutes and coarse-grained water.

Molecular dynamics simulation of humic substances (2014)
Journal Article
Orsi, M. (2014). Molecular dynamics simulation of humic substances. Chemical and Biological Technologies in Agriculture, 1(1), https://doi.org/10.1186/s40538-014-0010-4

© 2014, Orsi. Humic substances (HS) are complex mixtures of natural organic material which are found almost everywhere in the environment, and particularly in soils, sediments, and natural water. HS play key roles in many processes of paramount impor... Read More about Molecular dynamics simulation of humic substances.

Comparative assessment of the ELBA coarse-grained model for water (2013)
Journal Article
Orsi, M. (2014). Comparative assessment of the ELBA coarse-grained model for water. Molecular Physics, 112(11), 1566-1576. https://doi.org/10.1080/00268976.2013.844373

The ELBA force field for water consists of a single spherical site embedded with a point dipole. This coarse-grained model is assessed here through the calculation of fundamental properties of bulk liquid water and the water-vapour interface. Accurac... Read More about Comparative assessment of the ELBA coarse-grained model for water.


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