Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

doi:10.1063/1.4966265

Cited by 54 publications

(101 citation statements)

References 33 publications

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“…Various computational approaches have been used to study rare events in complex molecular systems 32 – 36 , 38 – 43 . Well suited for our case, the group of Parrinello recently used WT-MetaD simulations to study, for example, drug unbinding from protein binding pockets 33 , or the condensation of Argon droplets from supersaturated vapour 34 . We adapted this approach to study monomer exchange in BTA supramolecular polymers.…”

Section: Resultsmentioning

confidence: 99%

“…Among the various methods used to study rare events in complex molecular systems 32 – 36 , 38 – 43 , recently it has been reported that the real (unbiased) dynamics of an event (e.g., drug-protein unbinding 33 , etc. 34 ) is related to the transition time associated to events activated by infrequent WT-MetaD simulations (biased dynamics) 32 , 35 . This approach is particularly convenient as it allows to directly extract information on the kinetics of the activated transition from the biased WT-MetaD simulations.…”

Section: Methodsmentioning

confidence: 99%

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Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution

2017

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To rationally design supramolecular polymers capable of self-healing or reconfiguring their structure in a dynamically controlled way, it is imperative to gain access into the intrinsic dynamics of the supramolecular polymer (dynamic exchange of monomers) while maintaining a high-resolution description of the monomer structure. But this is prohibitively difficult at experimental level. Here we show atomistic, coarse-grained modelling combined with advanced simulation approaches to characterize the molecular mechanisms and relative kinetics of monomer exchange in structural variants of a synthetic supramolecular polymer in different conditions. We can capture differences in supramolecular dynamics consistent with the experimental observations, revealing that monomer exchange in and out the fibres originates from the defects present in their supramolecular structure. At the same time, the submolecular resolution of this approach offers a molecular-level insight into the dynamics of these bioinspired materials, and a flexible tool to obtain structure-dynamics relationships for a variety of polymeric assemblies.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution

2017

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“…For computational efficiency, the potential is cutoff at r c =2.5 σ and shifted by − V LJ ( r c ). System sizes range up to N =2,048, which is competitive with state-of-the-art Molecular Dynamics simulations such as well-tempered metadynamics 52 . For the chosen density ρ =10 −2 , a system with 2,048 particles requires a box of linear dimension L ′≈59 =59 × 2 1/6 σ ′.…”

Section: Methodsmentioning

confidence: 99%

Canonical free-energy barrier of particle and polymer cluster formation

2017

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A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with a proper definition of the cluster boundary. Here we demonstrate a shape-free determination of the free energy for temperature-driven cluster formation in particle as well as polymer systems. Combined with rigorous results on equilibrium droplet formation, this allows for a well-defined finite-size scaling analysis of the effective interfacial free energy at a fixed density. We first verify the theoretical predictions for the formation of a liquid droplet in a supersaturated particle gas by generalized-ensemble Monte Carlo simulations of a Lennard-Jones system. Going one step further, we then generalize this approach to cluster formation in a dilute polymer solution. Our results suggest an analogy with particle condensation, when the macromolecules are interpreted as extended particles.

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“…Particularly interesting, infrequent well-tempered metadynamics (WT-MetaD) [81] simulations were recently proven an efficient tool to explore rare exchange events, providing information on the pathway, rate limiting steps and their relative kinetics in once [82]. For example, the group of Parrinello used WT-MetaD simulations to study drug unbinding from protein binding pockets [87], or the condensation of Argon droplets from supersaturated vapour [88]. Recently, it was demonstrated that similar approaches combined with atomistic and coarse-grained models also allow investigating the intrinsic dynamics of supramolecular polymers [30].…”

Section: Supramolecular Dynamics At Submolecular Resolutionmentioning

confidence: 99%

Molecular modelling of supramolecular polymers

Bochicchio

Pavan

2018

Advances in Physics: X

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Nature uses self-assembly for building supramolecular materials possessing fascinating properties (self-healing, adaptive, reconfigurable and responsive) that are fundamental for many complex biological functions. Artificial supramolecular polymers, composed of monomers that self-assemble via non-covalent interactions, are attracting increasing interest as platforms for building innovative materials, as these possess similar bioinspired dynamic properties. However, their design still relies on an inefficient/expensive trial-and-error approach. A key question is how to design the monomers to control the properties of the supramolecular polymer. Most often, obtaining from the experiments molecular-level information on how to control these assemblies is prohibitively difficult. Molecular modelling is a fundamental support in this field, allowing investigation of the supramolecular polymer from a privileged point of view and at high-resolution. Such a 'virtual microscope' can provide information on the factors that control supramolecular polymer structure and dynamics, on the monomer-monomer interactions and their cooperativity that are precluded to the experiments, paving the way to structure-property relationships useful to advance the rational design of such materials. This review discusses the state of the art of molecular modelling and simulation of supramolecular polymers. The field is advancing quickly. But the detailed insight that can be reached and the continuous technical developments promise that this is only the beginning.

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Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

Cited by 54 publications

References 33 publications

Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution

Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution

Canonical free-energy barrier of particle and polymer cluster formation

Molecular modelling of supramolecular polymers

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