相关论文: Multiscale Computational Modeling of Biofilm

Recent breakthroughs in high-resolution imaging of biomolecules in solution with cryo-electron microscopy (cryo-EM) have unlocked new doors for the reconstruction of molecular volumes, thereby promising further advances in biology,…

Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…

MRChem is a code for molecular electronic structure calculations, based on a multiwavelet adaptive basis representation. We provide a description of our implementation strategy and several benchmark calculations. Systems comprising more…

This work presents strategies to learn an Energy-Based Model (EBM) according to the desired length of its MCMC sampling trajectories. MCMC trajectories of different lengths correspond to models with different purposes. Our experiments cover…

Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…

Motivation: In systems biology, modelling strategies aim to decode how molecular components interact to generate dynamical behaviour. Boolean modelling is more and more used, but the description of the dynamics from two-levels components…

Machine Learning tools are nowadays widely applied extensively to the prediction of the properties of molecular materials, using datasets extracted from high-throughput computational models. In several cases of scientific and technological…

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…

Single particle cryo-electron microscopy has become a critical tool in structural biology over the last decade, able to achieve atomic scale resolution in three dimensional models from hundreds of thousands of (noisy) two-dimensional…

A multi-timescale hybrid model is proposed to study microscopically the degraded performance of electronic devices, covering three individual stages of radiation effects studies, including ultrafast displacement cascade, intermediate defect…

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…

Recently, advancements in deep learning-based superpixel segmentation methods have brought about improvements in both the efficiency and the performance of segmentation. However, a significant challenge remains in generating superpixels…

Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique in biomedical research that uses the fluorophore decay rate to provide additional contrast in fluorescence microscopy. However, at present, the calculation, analysis,…

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the…

Processes of mixing and segregation in a packed bed of granular material stirred by a periodically moving rectangular bar are simulated by the discrete element method (DEM). Influence of mechanical properties of the particle material…

The study of macro continuous flow has a long history. Simultaneously, the exploration of heat and mass transfer in small systems with a particle number of several hundred or less has gained significant interest in the fields of statistical…

In this work we to develop a general statistical mechanic formalism to study systems restricted to surfaces of revolution, these are a very well model to study the termodinamical properties of microbiological systems and macromolecules lies…

In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…

In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of…

Polyelectrolyte gels are a very attractive class of actuation materials with remarkable electronic and mechanical properties with a great similarity to biological contractile tissues. They consist of a polymer network with ionizable groups…