Related papers: Mapping atomistic to coarse-grained polymer models…
In this paper we present a new machine learning workflow with unsupervised learning techniques to identify domains within atomic force microscopy images obtained from polymer films. The goal of the workflow is to identify the spatial…
In this work we used dissipative particle dynamics simulations to study the copolymerization process in the presence of spatial heterogeneities caused by incompatibility between polymerizing monomers. The polymer sequence details as well as…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We systematically studied the validity and transferability of effective, coarse-grained, pair potentials in ultrasoft colloidal systems. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping…
In this article we introduce the MARTINI model of a widely used thermoresponsive polymer, Poly(N-isopropylacrylamide). Importantly, our model takes into account polymer's stereoregularity (i.e. tacticity). We highlight the effect of…
We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…
The statistical mechanics of a linear non-interacting polymer chain with a large number of monomers is considered with fixed angular momentum. The radius of gyration for a linear polymer is derived exactly by functional integration. This…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…
Through extensive molecular simulations we determine a phase diagram of attractive, flexible polymer chains in two and three dimensions. A surprisingly rich collection of distinct crystal morphologies appear, which can be finely tuned…
Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for…
The enormous structural and chemical diversity of metal-organic frameworks (MOFs) forces researchers to actively use simulation techniques on an equal footing with experiments. MOFs are widely known for outstanding adsorption properties, so…
Coarse-graining (CG) enables molecular dynamics (MD) simulations of larger systems and longer timescales that are otherwise infeasible with atomistic models. Machine learning potentials (MLPs), with their capacity to capture many-body…
Decoding the self-assembly mechanism of metal-organic frameworks is a crucial step in reducing trial-and-error tests in their synthesis protocols. Atomistic simulations have proven essential in revealing molecular-level features of MOF…
Glassy polymers are central to engineering applications, yet their viscoelastic response over broad frequency and temperature ranges remains difficult to characterize. We extend non-affine deformation theory by incorporating a…
The polymer model framework is a classical tool from statistical mechanics that has recently been used to obtain approximation algorithms for spin systems on classes of bounded-degree graphs; examples include the ferromagnetic Potts model…
Multiscale simulations facilitate the efficient exploration of large spatiotemporal scales in chemical and physical systems, yet particle-based simulations become prohibitively expensive at time and length scales beyond the molecular level.…
We present an extension to the iterative Boltzmann inversion method to generate coarse-grained models with three-body intramolecular potentials that can reproduce correlations in structural distribution functions. The coarse-grained…
We propose a new scheme to parameterize effective potentials that can be used to simulate atomic systems such as oxide glasses. As input data for the optimization, we use the radial distribution functions of the liquid and the vibrational…
Polyhalogenated compounds are common in industrial, agricultural, and environmental applications. These compounds contain more halogen bonds than monohalogenated compounds. The presence of coupled {\sigma}-holes in the covalent halogen…