相关论文: Molecular Dynamics-Based Strength Estimates of Bet…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
Predictive modeling of the phonon/thermal transport properties of materials is vital to rational design for a diverse spectrum of engineering applications. Classical Molecular Dynamics (MD) simulations serve as a tool to simulate the time…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Advanced modern technology and industrial sustainability theme have contributed implementing composite materials for various industrial applications. Green composites are among the desired alternatives for the green products. However, to…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
Machine-learning force fields (MLFFs) have emerged as a promising solution for speeding up ab initio molecular dynamics (MD) simulations, where accurate force predictions are critical but often computationally expensive. In this work, we…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Epoxy resins are used extensively in composite materials for a wide range of engineering applications, including structural components of aircraft and spacecraft. The processing of fiber-reinforced epoxy composite structures requires…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Computational biomechanical analysis plays a pivotal role in understanding and improving human movements and physical functions. Although physics-based modeling methods can interpret the dynamic interaction between the neural drive to…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Predicting the functional impact of single amino acid substitutions (SAVs) is central to understanding genetic disease and engineering therapeutic proteins. While protein language models and structure-based methods have achieved strong…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
Modelling of single cellulose fibres is usually performed by assuming homogenous properties, such as strength and Young s modulus, for the whole fibre. Additionally, the inhomogeneity in size and swelling behaviour along the fibre is often…
We use three-dimensional numerical simulations to study self-organization in supersonic turbulence in molecular clouds. Our numerical experiments describe decaying and driven turbulent flows with an isothermal equation of state, sonic Mach…