相关论文: Force Matching and Iterative Boltzmann Inversion C…
Designing metal-organic frameworks (MOFs) synthesis protocols is currently largely driven by trial-and-error, since we lack fundamental understanding of the molecular level mechanisms that underlie their self-assembly processes. Previous…
An increasing interest in molecular structures whose long term dynamics resemble those of bistable mechanical systems promotes the search of possible candidates that may operate as two-state switching units. Of particular interest are the…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
Generative models offer a direct way of modeling complex data. Energy-based models attempt to encode the statistical correlations observed in the data at the level of the Boltzmann weight associated with an energy function in the form of a…
This paper presents an extended coarse-grained investigation of the elastic properties of polystyrene. In particular, we employ the well-known MARTINI force field and its modifications to perform extended molecular dynamics simulations at…
Iterative Fast Fourier Transform methods are useful for calculating the fields in composite materials and their macroscopic response. By iterating back and forth until convergence, the differential constraints are satisfied in Fourier…
Coarse-graining (CG) reduces molecular details to extend the time and length scales of molecular dynamics simulations to microseconds and micrometers. However, the CG approaches have long been limited by the difficulty of constructing both…
Bio-inspired composites are a great promise for mimicking the extraordinary and highly efficient properties of natural materials. Recent developments in voxel-by-voxel 3D printing have enabled extreme levels of control over the material…
Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta \Delta G$ data,…
The zeolitic imidazolate frameworks (ZIF) have emerged as a promising candidate for catalysis, carbon-dioxide (CO$_{2}$) capture and storage as well as flue gas separation due to their tunable porosity and chemical stability. ZIFs consists…
Machine-learned (ML) coarse-grained (CG) models are a promising tool for significantly enhancing the efficiency of molecular simulations by systematically removing degrees of freedom while retaining fidelity to the underlying fine-grained…
The study of the underlying physics of soft flowing materials depends heavily on numerical simulations, due to the complex structure of the governing equations reflecting the competition of concurrent mechanisms acting at widely disparate…
We derive and introduce anisotropic effective pair potentials to coarse-grain solutions of semiflexible rings polymers of various lengths. The system has been recently investigated by means of full monomer-resolved computer simulations,…
Understanding how structural flexibility affects the properties of metal-organic frameworks (MOFs) is crucial for the design of better MOFs for targeted applications. Flexible MOFs can be studied with molecular dynamics simulations, whose…
Accelerated coarse-graining (CG) algorithms for simulating heterogeneous chemical reactions on surface systems have recently gained much attention. In the present paper, we consider such an issue by investigating the oscillation behavior of…
Zeolitic Imidazolate Frameworks (ZIFs) are a family of metal--organic frameworks that feature metal centers tetrahedrally linked to imidazole-based ligands and adopt zeolite-like topologies. ZIFs formed by Zinc cations and imidazolate…
We review the recent development of machine-learning (ML) force-field frameworks for Landau-Lifshitz-Gilbert (LLG) dynamics simulations of itinerant electron magnets, focusing on the general theory and implementations of symmetry-invariant…
Finding suitable features has been an essential problem in computer vision. We focus on Restricted Boltzmann Machines (RBMs), which, despite their versatility, cannot accommodate transformations that may occur in the scene. As a result,…
Coherent surface scattering imaging (CSSI) is an emerging experimental technique uniquely suited to probing the structure of thin nanostructures. In these experiments, a specimen is placed on a substrate, and a series of X-ray diffraction…
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…