Related papers: GMXPolymer: a generated polymerization algorithm b…
The glass transition is a long-standing unsolved problem in materials science. For polymers, our understanding of glass-formation is particularly poor due to the added complexity of chain connectivity and flexibility; structural relaxation…
GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes.…
Understanding and predicting polymer solubility in various solvents is critical for applications ranging from recycling to pharmaceutical formulation. This work presents a deep learning framework that predicts polymer solubility, expressed…
Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
Accurately modeling and predicting complex dynamical systems, particularly those involving force exchange and dissipation, is crucial for applications ranging from fluid dynamics to robotics, but presents significant challenges due to the…
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…
The mesoscopic modeling of three polysiloxanes in solution is reported in this work, with the purpose of predicting their physicochemical properties as functions of the quality of the solvent, so that a judicious choice of polymer/solvent…
Data-driven models of robot motion constructed using principles from Geometric Mechanics have been shown to produce useful predictions of robot motion for a variety of robots. For robots with a useful number of DoF, these geometric…
Computation of (approximate) polynomials common factors is an important problem in several fields of science, like control theory and signal processing. While the problem has been widely studied for scalar polynomials, the scientific…
We present a new method that successfully predicts the glass transition temperature $T_{\! \textrm{g}}$ of polymers based on their monomer structure. The model combines ideas from Group Additive Properties (GAP) and Quantitative Structure…
In this paper we study the shape characteristics of star-like polymers in various solvent quality using a mesoscopic level of modeling. The dissipative particle dynamics simulations are performed for the homogeneous and four different…
Understanding the nature of glass transition, as well as precise estimation of the glass transition temperature for polymeric materials, remain open questions in both experimental and theoretical polymer sciences. We propose a data-driven…
Glassy polymer melts such as the plastics used in pipes, structural materials, and medical devices are ubiquitous in daily life. They accumulate damage over time due to their use, which limits their functionalities and demands periodic…
A variational formulation for non-equilibrium thermodynamics was developed by Gay-Balmaz and Yoshimura. In a recent article, the first two authors of the present paper introduced partially cosymplectic structures as a geometric framework…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Some recent results on the rotational dynamics of polymers are reviewed and extended. We focus here on the relaxation of a polymer, either flexible or semiflexible, initially wrapped around a rigid rod. We also study the steady polymer…
Industrial polymeric materials often rely on antioxidants to achieve long-term reliability. Previous studies have frequently discussed the stabilization effect in the presence of macroscopic additive migration. However, the micro- to…
In the last two decades, significant effort has been put in understanding and designing so-called structure-preserving numerical methods for the simulation of mechanical systems. Geometric integrators attempt to preserve the geometry…