Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userA new configurational bias scheme for sampling supramolecular structures
197
0
0.0
(
0
)
Added by
Bortolo Matteo Mognetti
Publication date
2014
fields
Physics
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular we compute the density of states of adsorbed polymers as a function of the number of ligand-receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking.
rate research
Read More
A simple model was constructed to describe the polar ordering of non-centrosymmetric supramolecular aggregates formed by self assembling triblock rodcoil polymers. The aggregates are modeled as dipoles in a lattice with an Ising-like penalty associated with reversing the orientation of nearest neighbor dipoles. The choice of the potentials is based on experimental results and structural features of the supramolecular objects. For films of finite thickness, we find a periodic structure along an arbitrary direction perpendicular to the substrate normal, where the repeat unit is composed of two equal width domains with dipole up and dipole down configuration. When a short range interaction between the surface and the dipoles is included the balance between the up and down dipole domains is broken. Our results suggest that due to surface effects, films of finite thickness have a none zero macroscopic polarization, and that the polarization per unit volume appears to be a function of film thickness.
The speculated presence of monomolecular lamellae of antagonistic salts in oil-water mixtures has left several open questions besides their hypothetical existence, including their microscopic structure and stabilization mechanism. Here, we simulate the spontaneous formation of supramolecular aggregates of the antagonistic salt sodium tetraphenylborate (NaBPh$_4$) in water and 3-methylpyridine (3-MP) at the atomistic level. We show that, indeed, the lamellae are formed by a monomolecular layer of the anion, enveloped by 3-MP and hydrated sodium counterions. To understand which thermodynamic forces drive the aggregation, we compare the full-atomistic model with a simplified one for the salt and show that the strong hydrophobic effect granted by the large excluded volume of the anion, together with electrostatic repulsion, suffice to explain the stability of the monomolecular lamellae.
Theory is presented for the phase stability of mixtures containing nanospheres and non-adsorbing reversible supramolecular polymers. This was made possible by incorporating the depletion thickness and osmotic pressure of reversible supramolecular polymer chains into generalized free-volume theory, recently developed for investigating the phase behaviour of colloidal spheres mixed with interacting polymers [Adv. Colloid Interface Sci. 143 (2008) 1-47]. It follows that the fluidfluid phase stability region where reversible supramolecular polymer chains can be mixed with nanospheres is sensitive to the energy of scission between the monomers and to the nanoparticle radius. One can then expect the fluidfluid coexistence curves to have a strong dependence on temperature and that shifting of phase boundaries within a single experimental system should be possible by varying the temperature. The calculations reveal the width of the stability region to be rather small. This implies that phase homogeneity of product formulations containing reversible supramolecular polymers is only possible at low nanoparticle concentrations.
We report Monte Carlo simulations of the self-assembly of supramolecular polymers based on a model of patchy particles. We find a first-order phase transition, characterized by hysteresis and nucleation, toward a solid bundle of polymers, of length much greater than the average gas phase length. We argue that the bundling transition is the supramolecular equivalent of the sublimation transition, that results from a weak chain-chain interaction. We provide a qualitative equation of state that gives physical insight beyond the specific values of the parameters used in our simulations.
We propose a new generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multi-dimensional, energy-overlap space and explores widely in the configurational space including specific configurations, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We apply the multicanonical-multioverlap molecular dynamics method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap molecular dynamics methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap molecular dynamics method realizes effective sampling in the configurational space including specific configurations more than the other two methods. From the results of the multicanonical-multioverlap molecular dynamics simulation, furthermore, we obtain a new local-minimum state of the Met-enkephalin system.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
