Related papers: Molecular Dynamics Analysis of Biomolecular System…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
With recent advances in structural biology, including experimental techniques and deep learning-enabled high-precision structure predictions, molecular dynamics methods that scale up to large biomolecular systems are required. Current…
Over recent years, molecular simulations have provided invaluable insights into the microscopic processes governing the initial stages of crystal nucleation and growth. A key aspect that has been observed in many different systems is the…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
Droplet formation has emerged as an essential concept for the spatiotemporal organisation of biomolecules in cells. However, classical descriptions of droplet dynamics based on passive liquid-liquid phase separation cannot capture the…
Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…
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…
Quantum molecular dynamics is applied to study the ground state properties of nuclear matter at subsaturation densities. Clustering effects are observed as to soften the equation of state at these densities. The structure of nuclear matter…
The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…