Related papers: Practical Classical Molecular Dynamics Simulations…
This work establishes a protocol to study via Molecular Dynamics simulation the degradation of Per-and Polyfluoroalkyl Substances (PFAS) in water by hydroxyl radical. To achieve this, molecular dynamics simulations are carried out, using…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
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…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
Over the past decade, tremendous progress has been made to extend the tools of laser cooling and trapping to molecules. Those same tools have recently been applied to polyatomic molecules (molecules containing three or more atoms). In this…
Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in…
A recent expansion of cold and ultracold molecule applications has led to renewed focus on molecular species preparation under ultrahigh vacuum conditions. Meanwhile, molecular beams have been used to study gas phase chemical reactions for…
Understanding the quantum dynamics of strongly coupled molecule-cavity systems remains a significant challenge in molecular polaritonics. This work develops a comprehensive self-consistent model simulating electromagnetic interactions of…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Spectral line profiles are powerful diagnostic tools for both laboratory and astrophysical plasmas, as their shape is sensitive to the plasma environment. The low-frequency component of the electric microfield is an important input 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…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…
Numerical simulation of quantum systems is crucial to further our understanding of natural phenomena. Many systems of key interest and importance, in areas such as superconducting materials and quantum chemistry, are thought to be described…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
Dense suspensions are widespread in nature, manufacturing and process engineering. Particle-based simulations have proven to be an invaluable complement to experimental rheological characterisation, serving as a virtual rheometer that…