We present Swarm-CG, a versatile software for the automatic iterative parametrization of bonded parameters in coarse-grained (CG) models, ideal in 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 parametrization of bonded terms in CG models composed of up to 200 pseudo atoms within 4–24 h on standard desktop machines, using default settings. The software benefits from a user-friendly interface and two different usage modes (default and advanced). We particularly expect Swarm-CG to support and facilitate the development of new CG models for the study of complex molecular systems interesting for bio- and nanotechnology. Excellent performances are demonstrated using a benchmark of 9 molecules of diverse nature, structural complexity, and size. Swarm-CG is available with all its dependencies via the Python Package Index (PIP package: swarm-cg). Demonstration data are available at: www.github.com/GMPavanLab/SwarmCG.
Unlike molecular crystals, soft self-assembled fibers, micelles, vesicles, etc., exhibit a certain order in the arrangement of their constitutive monomers but also high structural dynamicity and ...variability. Defects and disordered local domains that continuously form-and-repair in their structures impart to such materials unique adaptive and dynamical properties, which make them, e.g., capable to communicate with each other. However, objective criteria to compare such complex dynamical features and to classify soft supramolecular materials are non-trivial to attain. Here we show a data-driven workflow allowing us to achieve this goal. Building on unsupervised clustering of Smooth Overlap of Atomic Position (SOAP) data obtained from equilibrium molecular dynamics simulations, we can compare a variety of soft supramolecular assemblies via a robust SOAP metric. This provides us with a data-driven "defectometer" to classify different types of supramolecular materials based on the structural dynamics of the ordered/disordered local molecular environments that statistically emerge within them.
The conformational behavior of o-phenylene 8-mers and 10-mers solvated in a series of linear alkane solvents by means of classical molecular dynamics and first-principles calculations was studied. ...Irrespective of the solvent used, we find that at ambient pressure the molecule sits in the well-defined close-helical arrangement previously observed in light polar solvents. However, for pressures greater than 50 atm, and for tetradecane or larger solvent molecules, our simulations predict that o-phenylene undergoes a conformational transition to an uncoiled, extended geometry with a 35% longer head-to-tail distance and a much larger overlap between its lateral aromatic ring groups. The free energy barrier for the transition was studied as a function of pressure and temperature for both solute molecules in butane and hexadecane. Gas-phase density functional theory-based nudged elastic band calculations on 8-mer and 10-mer o-phenylene were used to estimate how the pressure-induced transition energy barrier changes with solute length. Our results indicate that a sufficiently large solvent molecule size is the key factor enabling a configuration transition upon pressure changes and that longer solute molecules associate with higher conformation transition energy barriers. This suggests the possibility of designing systems in which a solute molecule can be selectively “activated” by a controlled conformation transition achieved at a predefined set of pressure and temperature conditions.
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain useful insights for understanding the structural dynamics of these assemblies. In ...this context, one crucial point concerns the comparison of the performance and accuracy of classical force fields (FFs), which sometimes remains elusive. To date, the assessments performed on different classical potentials are mostly based on the comparison with experimental observables, which typically regard average properties. However, local differences of the structure and dynamics, which are poorly captured by average measurements, can make a difference, but these are nontrivial to catch. Here, we propose an agnostic way to compare different FFs at different resolutions (atomistic, united-atom, and coarse-grained), by means of a high-dimensional similarity metrics built on the framework of Smooth Overlap of Atomic Position (SOAP). We compare and classify a set of 13 FFs, modeling 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Our SOAP kernel-based metrics allows us to compare, discriminate, and correlate different FFs at different model resolutions in an unbiased, high-dimensional way. This also captures differences between FFs in modeling nonaverage events (originating from local transitions), for example, the liquid-to-gel phase transition in dipalmitoylphosphatidylcholine (DPPC) bilayers, for which our metrics allows us to identify nucleation centers for the phase transition, highlighting some intrinsic resolution limitations in implicit versus explicit solvent FFs.
Supramolecular fibers composed of monomers that self-assemble directionally via noncovalent interactions are ubiquitous in nature, and of great interest in chemistry. In these structures, the ...constitutive monomers continuously exchange in-and-out the assembly according to a well-defined supramolecular equilibrium. However, unraveling the exchange pathways and their molecular determinants constitutes a nontrivial challenge. Here, we combine coarse-grained modeling, enhanced sampling, and machine learning to investigate the key factors controlling the monomer exchange pathways in synthetic supramolecular polymers having an intrinsic dynamic behavior. We demonstrate how the competition of directional vs. nondirectional interactions between the monomers controls the creation/annihilation of defects in the supramolecular polymers, from where monomers exchange proceeds. This competition determines the exchange pathway, dictating whether a fiber statistically swaps monomers from the tips or from all along its length. Finally, thanks to their generality, our models allow the investigation of molecular approaches to control the exchange pathways in these dynamic assemblies.
In this work molecular dynamics simulation identifies a clear link between the dendron−virus multivalent molecular recognition and the nature of the consequent self-assembly. Data demonstrate how a ...weak hydrophobic association is transformed in an electrostatic self-assembly, orders of magnitude stronger, depending on the dendron generation used to assemble the viruses. This opens a new frontier in the engineering of hierarchical self-assemblies, potentially enabling the control of the supramolecular properties by acting at the single-molecule level.
Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular ...to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.
Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular ...to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.
DNA substrate conformation strongly affects the accessibility of restriction sites, consequently hindering/favouring the enzymatic restriction reaction in a programmable way.
Upon reduction with sodium borohydride, diazonium tetrachloroaurate salts of triazine dendrons yield dendron-coated gold nanoparticles connected by a gold-carbon bond. These robust nanoparticles are ...stable in water and toluene solutions for longer than one year and present surface groups that can be reacted to change surface chemistry and manipulate solubility. Molecular modeling was used to provide insight on the hydration of the nanoparticles and their observed solubilties.
PDF
