arXiv subjects

Luca Monticelli

Publications and source records attributed to Luca Monticelli.

4 recordsLinked to original sources

arXiv2021

Polyply: a python suite for facilitating simulations of (bio-)macromolecules and nanomaterials

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that leverages 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating melt simulations of six different polymers using two force-fields with different resolution. We further demonstrate the power of our approach by setting up a multi lamellar microphase-separated block copolymer system for next generation batteries, and by generating a liquid-liquid phase separated polyethylene oxide-dextran system inside a lipid vesicle, featuring both branching and molecular weight distribution of the dextran component.

cond-mat.mtrl-sci↗

arXiv2019

Role of Ligand Conformation on Nanoparticle-Protein Interactions

Engineered biomedical nanoparticles (NP) administered via intravenous routes are prone to associate to serum proteins. The protein corona can mask the NP surface functionalization and hamper the delivery of the NP to its biological target. The design of corona-free NPs relies on our understanding of the chemical-physical features of the NP surface driving the interaction with serum proteins. Here we address, by computational means, the interaction between human serum albumin (HSA) and a prototypical monolayer-protected Au nanoparticle. We show that both the chemical composition (charge, hydrophobicity) and the conformational preferences of the ligands decorating the NP surface affect the NP propensity to bind HSA.

physics.comp-ph↗

arXiv2019

Transferable MARTINI Model of Poly(ethylene Oxide)

Motivated by the deficiencies of the previous MARTINI models of poly(ethylene oxide) (PEO), we present a new model featuring a high degree of transferability. The model is parametrized on (a) a set of 8 free energies of transfer of dimethoxyethane (PEO dimer) from water to solvents of varying polarity; (b) the radius of gyration in water at high dilution; and (c) matching angle and dihedral distributions from atomistic simulations. We demonstrate that our model behaves well in five different areas of application: (1) it produces accurate densities and phase behavior or small PEO oligomers and water mixtures; (2) it yields chain dimensions in good agreement with the experiment in three different solvents (water, diglyme, and benzene) over a broad range of molecular weights (1.2 kg/mol to 21 kg/mol); (3) it reproduces qualitatively the structural features of lipid bilayers containing PEGylated lipids in the brush and mushroom regime; (4) it is able to reproduce the phase behavior of several PEO-based nonionic surfactants in water; and (5) it can be combined with the existing MARTINI PS to model PS/PEO block copolymers. Overall, the new PEO model outperforms previous models and features a high degree of transferability.

physics.comp-ph↗

arXiv2015

Towards atomistic resolution structure of phosphatidylcholine glycerol backbone and choline headgroup at different ambient conditions

Phospholipids are essential building blocks of biological membranes. Despite of vast amount of accurate experimental data the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulation model would automatically resolve the structures giving an interpretation of experimental results, if the model would reproduce the experimental data. In this work we compare the C-H bond vector order parameters for glycerol backbone and choline headgroup between 14 different atomistic resolution models and experiments in fully hydrated lipid bilayer. The current models are not accurately enough to resolve the structure. However, closer inspection of three best performing models (CHARMM36, GAFFlipid and MacRog) suggest that improvements in the sampled dihedral angle distributions would potentilly lead to the model which would resolve the structure. Despite of the inaccuracy in the fully hydrated structures, the response to the dehydration, i.e. P-N vector tilting more parallel to membrane normal, is qualitatively correct in all models. The CHARMM36 and MacRog models describe the interactions between lipids and cholesterol better than Berger/Höltje model. This work has been, and continues to be, progressed and discussed through the blog: nmrlipids.blogspot.fi. Everyone is invited to join the discussion and make contributions through the blog. The manuscript will be eventually submitted to an appropriate scientific journal. Everyone who has contributed to the work through the blog will be offered coauthorship. For more details see: nmrlipids.blogspot.fi.

physics.bio-ph↗