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For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are…
Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…
The mechanics of single-chain stretching and rupture are central to understanding the resilience of biological polymers and designing strong and tough soft materials such as double-network gels and multi-network elastomers. In this work, we…
In this work, we develop a two-component coarse-grained molecular dynamics (CGMD) model for simulating the erythrocyte membrane. This proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton,…
Highly stretchable and self-healable supramolecular elastomers are promising materials for future soft electronics, biomimetic systems, and smart textiles, due to their dynamic cross-linking bonds. The dynamic or reversible nature of the…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…
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…
Elastomers are used in a wide range of applications because of their large strain to failure, low density, and tailorable stiffness and toughness. The mechanical behavior of elastomers derives mainly from the entropic elasticity of the…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Condense phase molecular systems organize in wide range of distinct molecular configurations, including amorphous melt and glass as well as crystals often exhibiting polymorphism, that originate from their intricate intra- and…
Materials with network-like microstructure, including polymers, are the backbone for many natural and human-made materials such as gels, biological tissues, metamaterials, and rubbers. Fracture processes in these networked materials are…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
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…
Experiments have long shown that a polymer network of covalent bonds commonly ruptures at a stress that is orders of magnitude lower than the strength of the covalent bonds. Here we investigate this large reduction in strength by…
In this paper, we show how kernel-based models for the Koopman generator -- the gEDMD method -- can be used to identify coarse-grained dynamics on reduced variables, which retain the slowest transition timescales of the original dynamics.…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
This study demonstrates that the apparent complexity of fracture in phantom-chain polymer networks is fully decoupled into two universal master curves: (i) macroscopic softening governed by the absolute stretch, and (ii) microscopic…
Molecular dynamics (MD) has served as a powerful tool for designing materials with reduced reliance on laboratory testing. However, the use of MD directly to treat the deformation and failure of materials at the mesoscale is still largely…
We propose a coarse-grained model for polymer chains and polymer networks based on the meso-scale dynamics. The model takes the internal degrees of freedom of the constituent polymer chains into account using memory functions and colored…