相关论文: Current MD forcefields fail to capture key feature…

The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…

Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…

Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…

The particle contact model is important for powder simulations. Although several contact models have been proposed, their validity has not yet been well established. Therefore, we perform molecular dynamics (MD) simulations to clarify the…

The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…

The dilute fluid phase of model globular proteins is studied. The model possesses a fluid-fluid transition buried within the fluid-crystal coexistence region, as do some globular proteins. If this fluid-fluid transition is not buried deep…

Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods have focused on the use of internal coordinates due to the…

Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this,…

In computer simulations performed in constant number of particles ensembles, although the total number of particles N contained in the simulation box does not fluctuate, hence giving a zero apparent compressibility, there are still local…

While nuclear magnetic resonance (NMR) provides valuable insights into the local environment of many nuclei, the unambiguous interpretation of the signal in terms of microscopic dynamics is often difficult, particularly when the quadrupolar…

Generating molecular dynamics (MD) trajectories using deep generative models has attracted increasing attention, yet remains inherently challenging due to the limited availability of MD data and the complexities involved in modeling…

Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…

The control of biofilm formation is a challenging goal that has not been reached yet in many aspects. One is the role of van der Waals forces and another the importance of mutual interactions between the adsorbing and the adsorbed…

Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…

Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…

Extensively exploring protein conformational landscapes remains a major challenge in computational biology due to the high computational cost involved in dynamic physics-based simulations. In this work, we propose a novel pipeline, MoDyGAN,…

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…

Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…

Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…