相关论文: Current MD forcefields fail to capture key feature…
Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…
The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
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…
High-resolution structural information on membrane proteins is essential for understanding cell biology and for structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide {\AA}ngstrom-level…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
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…
The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of computational predictions of NMR chemical shieldings of candidate structures, which are usually taken to be local minima…
Traditional approaches to elucidation of protein structures by NMR spectroscopy rely on distance restraints also known as nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…