相关论文: Broad chemical transferability in structure-based …
Atomic-scale engineering typically involves bottom-up approaches, leveraging parameters such as temperature, partial pressures, and chemical affinity to promote spontaneous arrangement of atoms. These parameters are applied globally,…
Particle-based shape modeling (PSM) is a family of approaches that automatically quantifies shape variability across anatomical cohorts by positioning particles (pseudo landmarks) on shape surfaces in a consistent configuration. Recent…
A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach groups of monomers are mapped onto a single pseudoatom (a blob) and the…
Room-temperature ionic liquids (RTILs) stand out among molecular liquids for their rich physicochemical characteristics, including structural and dynamic heterogeneity. The significance of electrostatic interactions in RTILs results in long…
The objective of graph coarsening is to generate smaller, more manageable graphs while preserving key information of the original graph. Previous work were mainly based on the perspective of spectrum-preserving, using some predefined…
Coarse-grained (CG) models are simplified representations of soft matter systems that are commonly employed to overcome size and time limitations in computational studies. Many approaches have been developed to construct and parametrise…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
Exercising direct control over the unusual electronic structures arising from quantum confinement effects in graphene nanoribbons (GNRs) - atomically defined quasi one-dimensional (1D) strips of graphene - is intimately linked to geometric…
We introduce a framework for model reduction of chain models for dissipative particle dynamics (DPD) simulations, where the characteristic size of the chain, pressure, density, and temperature are preserved. The proposed methodology reduces…
A challenging topic in materials engineering is the development of numerical models that can accurately predict material properties with atomistic accuracy, matching the scale and level of detail achieved by experiments. In this regard,…
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…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
This paper introduces a new representation method that is mainly based on chemical bonds among atoms in materials. Each chemical bond and its surrounded atoms are considered as a unified unit or a local structure that is expected to reflect…
Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…
A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific…
Reticular materials, including metal-organic frameworks and covalent organic frameworks, combine relative ease of synthesis and an impressive range of applications in various fields, from gas storage to biomedicine. Diverse properties arise…
An accurate force field is the key to the success of all molecular mechanics simulations on organic polymers and biomolecules. Accuracy beyond density functional theory is often needed to describe the intermolecular interactions, while most…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its…