1,721,007 research outputs found
How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships from Coarse-Grained Simulations
No full textThe rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in a controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at an experimental level. Here we show coarse-grained molecular dynamics simulations (<5 Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers. As a representative case, we focus on a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers, experimentally seen to undergo dynamic clustering following the superselective binding to a multivalent recruiter. Our simulations show that the dynamic reorganization of the supramolecular structure proceeds via monomer diffusion on the dynamic fiber surface (exchange within the fiber). Rationally changing the structure of the monomers to make the fiber surface more or less dynamic allows tuning the rate of response to the stimulus and of supramolecular reconfiguration. Simple in silico experiments draw a structure-dynamics-property relationship revealing the key factors underpinning the dynamic adaptivity and stimuli-responsiveness of these supramolecular polymers. We come out with clear evidence that to master the bioinspired properties of these fibers, it is necessary to control their intrinsic dynamics, while the high-resolution of our molecular models permits us to show how
Effect of Concentration on the Supramolecular Polymerization Mechanism via Implicit-Solvent Coarse-Grained Simulations of Water-Soluble 1,3,5-Benzenetricarboxamide
Full text linkWe report an implicit-solvent coarse-grained (CG) model for a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer. The technical advances guaranteed by this CG model allow simulation of the self-assembly of 1000 BTA monomers and easy variation of the BTA concentration into the system down to experimental dilute conditions. In this way, we can monitor the mechanism of supramolecular polymerization as a function of the concentration at submolecular resolution exceeding the microsecond time scale. While increasing the concentration produces rapid formation of large disordered clusters that are then converted into BTA fibers, moving to very dilute concentrations favors early ordering of the oligomers in solution even at small sizes. Interestingly, we observe that below a certain concentration the oligomers that dynamically grow in solution during the self-assembly present the same level (and amplification) of order of prestacked equilibrated oligomers of the same size, meaning that concentration-dependent kinetic effects have disappeared from the polymerization mechanism
Molecular modelling of supramolecular polymers
Full text linkNature 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
Ephemeral ice-like local environments in classical rigid models of liquid water
Full text linkDespite great efforts over the past 50 years, the simulation of water still presents significant challenges and open questions. At room temperature and pressure, the collective molecular interactions and dynamics of water molecules may form local structural arrangements that are non-trivial to classify. Here, we employ a data-driven approach built on Smooth Overlap of Atomic Position (SOAP) that allows us to compare and classify how widely used classical models represent liquid water. Macroscopically, the obtained results are rationalized based on water thermodynamic observables. Microscopically, we directly observe how transient ice-like ordered environments may dynamically/statistically form in liquid water, even above freezing temperature, by comparing the SOAP spectra for different ice structures with those of the simulated liquid systems. This confirms recent ab initio-based calculations but also reveals how the emergence of ephemeral local ice-like environments in liquid water at room conditions can be captured by classical water models
From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations
Full text linkSupramolecular
polymers, formed via noncovalent
self-assembly of elementary monomers, are extremely interesting for
their dynamic bioinspired properties. In order to understand their
behavior, it is necessary to access their dynamics while maintaining
high resolution in the treatment of the monomer structure and monomer–monomer
interactions, which is typically a difficult task, especially in aqueous
solution. Focusing on 1,3,5-benzenetricarboxamide (BTA) water-soluble
supramolecular polymers, we have developed a transferable coarse-grained
model that allows studying BTA supramolecular polymerization in water,
while preserving remarkable consistency with the atomistic models
in the description of the key interactions between the monomers (hydrophobic,
H-bonding, etc.), self-assembly cooperativity, and
amplification of order into the growing fibers. This permitted us
to monitor the amplification of the key interactions between the monomers
(including H-bonding) in the BTA fibers during the dynamic polymerization
process. Our molecular dynamics simulations provide a picture of a
stepwise cooperative polymerization mechanism, where initial fast
hydrophobic aggregation of the BTA monomers in water is followed by
the slower reorganization of these disordered aggregates into ordered
directional oligomers. Supramolecular polymer growth then proceeds
on a slower time scale. We challenged our models via comparison with the experimental evidence, capturing the effect
of temperature variations and subtle changes in the monomer structure
on the polymerization and on the properties of the fibers seen in
the real systems. This work provides a multiscale spatiotemporal characterization
of BTA self-assembly in water and a useful platform to study a variety
of BTA-based supramolecular polymers toward structure–property
relationships
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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