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We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
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…
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…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
This article is the updated version of the paper: "Combined 3D thinning and greedy algorithm to approximate realistic particles with corrected mechanical properties, Granular Matter (2019)" by the first author [58]. The main changes here…
In this paper, a predictive constraint-aware control scheme is formulated within the Command Governor (CG) framework for localized hydration management of a proton exchange membrane (PEM) fuel cell system. First, a comprehensive nonlinear…
The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in…
In this paper, we present a coarse-grained model of DNA based on the soft ellipsoid contact potential (ECP) to evaluate the base pairing interaction properly. We extend the ellipsoid contact like potential model (ECP), suitably modified and…
We address the problem of aligning real-world 3D data of garments, which benefits many applications such as texture learning, physical parameter estimation, generative modeling of garments, etc. Existing extrinsic methods typically perform…
Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions.…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
The physics of crystalline membranes, i.e. fixed-connectivity surfaces embedded in three dimensions and with an extrinsic curvature term, is very rich and of great theoretical interest. To understand their behavior, numerical simulations…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility…
Model Predictive Control (MPC) has become a popular framework in embedded control for high-performance autonomous systems. However, to achieve good control performance using MPC, an accurate dynamics model is key. To maintain real-time…
Phyllosilicate clays have diverse applications in packaging industries and are found highly suitable for formulation, including thermoplastic starch (TPS), polyethylene (PE), or their combination. We developed CG MARTINI-3 parameters of the…
Automated detection of grain boundaries (GBs) in electron microscope images of polycrystalline materials could help accelerate the nanoscale characterization of myriad engineering materials and novel materials under scientific research.…
We develop a polycrystal graph neural network (PGNN) model for predicting the effective properties of polycrystalline materials, using the Li7La3Zr2O12 ceramic as an example. A large-scale dataset with >5000 different three-dimensional…
We present a three-dimensional (3D) common-refinement method for non-matching meshes between discrete non-overlapping subdomains of incompressible fluid and nonlinear hyperelastic structure. To begin, we first investigate the accuracy of…
Nanophotonic devices excel at confining light into intense hot spots of the electromagnetic near fields, creating unprecedented opportunities for light-matter coupling and surface-enhanced sensing. Recently, all-dielectric metasurfaces with…