Related papers: MARTINI-based Coarse-grained Model for Poly(alpha-…
Development of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo…
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…
We report a simulation study for bottle-brush polymers grafted on a rigid backbone. Using a standard coarse-grained bead-spring model extensive molecular dynamics simulations for such macromolecules under good solvent conditions are…
Given that the physical properties of polymeric liquids extend on a wide range of lengthscales, it is computationally convenient to represent them by coarse-grained (CG) descriptions at various granularities to investigate local and global…
The hierarchical graphene model is a simple toy model which is useful to understand the mechanics of renormalization group flows in super-renormalizable systems. It is based on a model of interacting electrons in graphene, for which the…
A novel fully bio-based Poly (Glycerol-Itaconic acid) (PGI) was designed and highly efficiently synthesized by solvent-free polycondensation. The Poly (ethylene glycol) (PEG) was used as the phase change materials (PCM) working substance…
We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to…
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…
Even though atomistic and coarse-grained (CG) models have been used to simulate liquid nanodroplets in vapor, very few rigorous studies of the liquid-liquid interface structure are available, and most of them are limited to planar…
We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional…
The characterization of protein-nanoparticle assemblies in solution remains a challenge. We demonstrate a technique based on a graphene microelectrode for structural-functional analysis of model systems composed of nanoparticles enclosed in…
Multifidelity models integrate data from multiple sources to produce a single approximator for the underlying process. Dense low-fidelity samples are used to reduce interpolation error, while sparse high-fidelity samples are used to…
We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarse-grained bead. The new force fields are designed to match structural properties such as…
We introduce a powerful Monte Carlo (MC) algorithm for the atomistic simulation of bulk models of oligo- and poly-thiophenes by redesigning MC moves originally developed for considerably simpler polymer structures and architectures, such as…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight…
We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules.…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
A novel self-assembly strategy for polypeptide nanostructure design was presented in [Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments, Nature Chemical Biology 9 (2013) 362--366]. The first mathematical…