A5090015240- Protein Structure and Dynamics
- Lipid Membrane Structure and Behavior
- Metabolomics and Mass Spectrometry Studies
- Enzyme Structure and Function
- Supramolecular Self-Assembly in Materials
- Advanced Polymer Synthesis and Characterization
- Machine Learning in Materials Science
- Advanced Mathematical Modeling in Engineering
- Computational Drug Discovery Methods
- Groundwater flow and contamination studies
- Enhanced Oil Recovery Techniques
- thermodynamics and calorimetric analyses
- Block Copolymer Self-Assembly
- biodegradable polymer synthesis and properties
- Surface Chemistry and Catalysis
- Spectroscopy and Quantum Chemical Studies
- Chemical Synthesis and Analysis
- Polyoxometalates: Synthesis and Applications
- Microbial Natural Products and Biosynthesis
- Healthcare Systems and Public Health
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Nanopore and Nanochannel Transport Studies
- Genetic Neurodegenerative Diseases
University of Applied Sciences and Arts of Southern Switzerland
2019-2024
Polytechnic University of Turin
2021
Weizmann Institute of Science
2017-2020
Conservatoire National des Arts et Métiers
2015-2017
Génomique Bioinformatique et Applications
2016-2017
Délégation Paris 7
2013
Sorbonne Paris Cité
2013
Laboratoire de Biochimie Théorique
2013
Université Paris Cité
2013
Centre National de la Recherche Scientifique
2013
The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple use tools design new games. In the molecular sciences, only a small number experts with specialized know-how are able interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons learned from games? Could technology help us explore graphics ideas render...
Multicomponent supramolecular copolymerization promises to construct complex nanostructures with emergent properties. However, even two monomeric components, various possible outcomes such as self-sorted homopolymers, a random (statistical) copolymer, an alternate or block copolymer can occur, determined by their intermolecular interactions and monomer exchange dynamics hence structural prediction is extremely challenging. Herein, we target this challenge demonstrate unprecedented...
Supramolecular block copolymerzation with optically or electronically complementary monomers provides an attractive bottom-up approach for the non-covalent synthesis of nascent axial organic heterostructures, which promises to deliver useful applications in energy conversion, optoelectronics, and catalysis. However, supramolecular copolymers (BCPs) constitutes a significant challenge due exchange dynamics non-covalently bound hence requires fine microstructure control. Furthermore, temporal...
In the present work, we aim to transfer field of virtual screening predictiveness curve, a metric that has been advocated in clinical epidemiology. The literature describes use curves evaluate performances biological markers formulate diagnoses, prognoses and assess disease risks, fit risk models, estimate utility model when applied population. Similarly, logistic regression models calculate activity probabilities related scores compounds obtained experiments. curve can provide an intuitive...
Screening Explorer is a web-based application that allows for an intuitive evaluation of the results screening experiments using complementary metrics in field. The usual implies separate generation and apprehension ROC, predictiveness, enrichment curves their global metrics. Similarly, partial need to be calculated repeatedly different fractions data set there exists no handy tool reading simultaneously on charts. For deeper understanding experiments, we rendered analysis straightforward by...
We present Swarm-CG, a versatile software for the automatic iterative parametrization of bonded parameters in coarse-grained (CG) models, ideal combination with popular CG force fields such as MARTINI. By coupling fuzzy self-tuning particle swarm optimization to Boltzmann inversion, Swarm-CG performs accurate bottom-up terms models composed up 200 pseudo atoms within 4–24 h on standard desktop machines, using default settings. The benefits from user-friendly interface and two different usage...
After two decades of continued development the Martini coarse-grained force field (CG FF), further refinment already rather accurate lipid models has become a demanding task that could benefit from integrative data-driven methods. Automatic approaches are increasingly used in molecular models, but they typically make use specifically designed interaction potentials transfer poorly to systems or conditions different than those for model calibration. As proof concept, here, we employ
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain useful insights for understanding the structural these assemblies. In this context, one crucial point concerns comparison performance accuracy classical force fields (FFs), which sometimes remains elusive. To date, assessments performed on different potentials mostly based with experimental observables, typically regard average properties. However, local differences structure...
Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used study membrane phenomena but faced limitations, particularly capturing realistic lipid phase behavior. Here, we present refined 3 models with mapping scheme that distinguishes tails...
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning parameters in order to have the approximated CG behave correctly and consistently with, e.g., available higher-resolution simulation data and/or experimental observables. Automatic data-driven approaches are increasingly used develop accurate for dynamics simulations. However, obtained via such automatic methods often make use specifically designed interaction potentials poorly...
After two decades of continued development the Martini coarse-grained force field (CG FF), further refining already rather accurate lipid models has become a demanding task that could benefit from integrative data-driven methods. Automatic approaches are increasingly used in molecular models, but they typically make use specifically-designed interaction potentials transfer poorly to systems or conditions different than those for model calibration. As proof concept here we employ SwarmCG, an...
The development of accurate water models is primary importance for molecular simulations. Despite their intrinsic approximations, three-site rigid are still ubiquitously used to simulate a variety systems. Automatic optimization approaches have been recently iteratively refine fit macroscopic (average) thermodynamic properties, providing state-of-the-art that present some deviations from the liquid properties. Here, we show results obtained by automatically optimizing combination microscopic...
Abstract Nuclear receptors (NRs) constitute an important class of therapeutic targets. During the last 4 years, we tackled pharmacological profile assessment NR ligands for which constructed NRLiSt BDB. We evaluated and compared performance different virtual screening approaches: mean molecular descriptor distribution values, docking 3D pharmacophore models. The simple comparison profiles 4885 descriptors between agonist antagonist datasets didn′t provide satisfying results. obtained overall...
Proteins can self-associate with copies of themselves to form symmetric complexes called homomers. Homomers are widespread in all kingdoms life and allow for unique geometric functional properties, as reflected viral capsids or allostery. Once a protein forms homomer, however, its internal symmetry compound the effect point mutations trigger uncontrolled self-assembly into high-order structures. We identified mutation hot spots supramolecular assembly, which predictable by geometry. Here, we...
We present Swarm-CG, a versatile software for the automatic parametrization of bonded parameters in coarse-grained (CG) models. By coupling state-of-the-art metaheuristics to Boltzmann inversion, Swarm-CG performs accurate terms CG models composed up 200 pseudoatoms within 4h-24h on standard desktop machines, using an AA trajectory as reference and default settings software. The benefits from user-friendly interface two different usage modes (default advanced). particularly expect support...
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain insights useful for understanding the structural these assemblies. In this context, one crucial point concerns comparison performance accuracy classical force fields (FFs), which sometimes remains elusive. To date, assessments performed on different potentials mostly based with experimental observables, typically regard average properties. However, local differences structure...
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain insights useful for understanding the structural these assemblies. In this context, one crucial point concerns comparison performance accuracy classical force fields (FFs), which sometimes remains elusive. To date, assessments performed on different potentials mostly based with experimental observables, typically regard average properties. However, local differences structure...
<div><div><div><p>Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain insights useful for understanding the structural these assemblies. In this context, one crucial point concerns comparison performance accuracy classical force fields (FFs), which sometimes remains elusive. To date, assessments performed on different potentials mostly based with experimental observables, typically regard average...
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain insights useful for understanding the structural these assemblies. In this context, one crucial point concerns comparison performance accuracy classical force fields (FFs), which sometimes remains elusive. To date, assessments performed on different potentials mostly based with experimental observables, typically regard average properties. However, local differences structure...
After two decades of continued development the Martini coarse-grain force field, further refining lipid models has become a demanding task that could benefit from integrative data-driven methods. Here we employ SwarmCG, an automatic multi-objective optimization approach facilitating fields, to calibrate exclusively bonded parameters in context finely tuned non-bonded interaction matrix available 3.0.0. We explore different CG representations molecules and evaluate their ability enhance...
The development of accurate water models is primary importance for molecular simulations. Despite their intrinsic approximations, three-site rigid are still ubiquitously used to simulate a variety systems. Automatic optimization approaches have been recently iteratively optimize fit macroscopic (average) thermodynamic properties, providing “state-of-the-art” that present some deviations from the liquid properties. Here we show results obtained by automatically optimizing combination...