Related papers: Modeling of polymer-enzyme conjugates formation: T…
We present an application of Wertheim's Thermodynamic Perturbation Theory (TPT1) to a simple coarse grained model made of flexibly bonded Lennard-Jones monomers. We use both the Reference Hyper-Netted-Chain (RHNC) and Mean Spherical…
In the development of equations of state for polyatomic molecules, thermodynamic perturbation theory (TPT) is widely used to calculate the change in free energy due to chain formation. TPT is a simplification of a more general and exact…
We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear…
In this work we extend Wertheim's thermodynamic perturbation theory (TPT) to binary mixtures (species A and species B) of patchy colloids where each species has a single patch which can bond a maximum of twice (divalent). Colloids are…
We critically discuss the application of the Wertheim's theory to classes of complex associating fluids that can be today engineered in the laboratory as patchy colloids and to the prediction of their peculiar gas-liquid phase diagrams. Our…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
We show that the formalism of Wertheim's first order thermodynamic perturbation theory can be generalised for the fluid of rotating sticky particles with anisotropic hard core confined to a quasi-one-dimensional channel. Using the transfer…
We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…
Colloidal patchy particles with divalent attractive interaction can self-assemble into linear polymer chains. Their equilibrium properties in 2D and 3D are well described by Wertheim's thermodynamic perturbation theory which predicts a…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
Despite the long-recognized fact that chemical structure and specific interactions greatly influence the thermodynamic properties of polymer systems, a predictive molecular theory that enables systematically addressing the role of chemical…
Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are…
We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions…
In this paper a new theory is developed for the self - assembly of associating molecules confined to a single spatial dimension, but allowed to explore all orientation angles. The interplay of the anisotropy of the pair potential and the…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
First steps towards developing a new perturbation theory for molecular liquids are taken. By choosing a new form of splitting the site-site potential functions between molecules, we will get a set of atomic fluids as the reference system…
Entropy alone can self-assemble hard particles into colloidal crystals of remarkable complexity whose structures are the same as atomic and molecular crystals, but with larger lattice spacings. Although particle-based molecular simulation…