Related papers: GMXPolymer: a generated polymerization algorithm b…
We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In…
Polymers are diverse and versatile materials that have met a wide range of material application demands. They come in several flavors and architectures, e.g., homopolymers, copolymers, polymer blends, and polymers with additives. Searching…
Functions of chemical composition are complex and discrete in nature making it impossible to optimize them with gradient methods. Genetic algorithms, which do not use derivative information, are used to maximize the thermal conductivity of…
Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
We present a detailed description of the generalized geometric cluster algorithm for the efficient simulation of continuum fluids. The connection with well-known cluster algorithms for lattice spin models is discussed, and an explicit full…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
Polymer composite performance depends significantly on the polymer matrix, additives, processing conditions, and measurement setups. Traditional physics-based optimization methods for these parameters can be slow, labor-intensive, and…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
Polymers play a crucial role in the development of engineering materials, with applications ranging from mechanical to biomedical fields. However, the limited polymerization processes constrain the variety of organic building blocks that…
A common task is the determination of system parameters from spectroscopy, where one compares the experimental spectrum with calculated spectra, that depend on the desired parameters. Here we discuss an approach based on a machine learning…
Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with different types of intrinsic stiffness. Important static observables of the single chain such as gyration radius or persistence length are…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Bottle brushes are polymeric macromolecules made of a linear polymeric backbone grafted with side chains. The choice of the grafting density {\sigma}g, the length ns the grafted side chains and their chemical nature fully determines the…
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerisation has been studied theoretically in a number of contexts, often by considering a Markov process in…
A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
The present research is dedicated to provide deeper understanding of the impact of complex architecture of branched polymers on their behaviour in solvents. The folding dynamics of macromolecules and hydrodynamics of polymer fluids are…
Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous…
Creating amorphous solid states by randomly bonding an ensemble of dense liquid monomers is a common procedure which is applied to create a variety of materials such as epoxy resins, colloidal gels, and vitrimers. The properties of the…
We develop a block-structured solver for high-fidelity simulation of flows in complex geometries, based on overlapping (Chimera) meshes. The key components of the algorithm are a baseline dissipation-free central discretization and…