Related papers: Multiscale virtual particle based elastic network …
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…
To quantify the complexity of a system, entropy-based methods have received considerable critical attentions in real-world data analysis. Among numerous entropy algorithms, amplitude-based formulas, represented by Sample Entropy, suffer…
Gaussian network model(GNM) and anisotropic network model(ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM(gGNM) and ANM methods and show that the…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…
This paper introduces the multivariate beta mixture model (MBMM), a new probabilistic model for soft clustering. MBMM adapts to diverse cluster shapes because of the flexible probability density function of the multivariate beta…
Membrane proteins typically deform the surrounding lipid bilayer membrane, which can play an important role in the function, regulation, and organization of membrane proteins. Membrane elasticity theory provides a beautiful description of…
Molecular dynamics simulations are a central computational methodology in materials design for relating atomic composition to mechanical properties. However, simulating materials with atomic-level resolution on a macroscopic scale is…
We review the computation models for biofilm and bacteria cells, providing perspectives on biofilm's various properties and potential serving as engineering living materials (ELMs), considering the omnipresence of such biological matter.…
We propose a simple, but efficient and accurate machine learning (ML) model for developing high-dimensional potential energy surface. This so-called embedded atom neural network (EANN) approach is inspired by the well-known empirical…
The concept bottleneck model (CBM), as a technique improving interpretability via linking predictions to human-understandable concepts, makes high-risk and life-critical medical image classification credible. Typically, existing CBM methods…
We propose a novel method, basis vector model material indexing (BVM-MI), for predicting atomic composition and mass density from two independent basis vector model weights derived from dual-energy CT (DECT) for Monte Carlo (MC) dose…
Multiple Kernel Learning (MKL) models combine several kernels in supervised and unsupervised settings to integrate multiple data representations or sources, each represented by a different kernel. MKL seeks an optimal linear combination of…
A class of analog computers built from large numbers of microscopic probabilistic machines is discussed. It is postulated that such computers are implemented in biological systems as ensembles of protein molecules. The formalism is based on…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…
Objective: Due to the non-linearity of numerous biomedical signals, non-linear analysis of multi-channel time series, notably multivariate multiscale entropy (mvMSE), has been extensively used in biomedical signal processing. However, mvMSE…
Distributed parameter identification for large-scale multi-agent networks encounters challenges due to nonlinear dynamics and partial observations. Simultaneously, ensuring the stability is crucial for the robust identification of dynamic…
The modelling of empirically observed data is commonly done using mixtures of probability distributions. In order to model angular data, directional probability distributions such as the bivariate von Mises (BVM) is typically used. The…
Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…