Related papers: Force probe simulations using an adaptive resoluti…
In recent years, constant applied potential molecular dynamics has allowed to study the structure and dynamics of the electrochemical double-layer of a large variety of nanoscale capacitors. Nevertheless it remained impossible to simulate…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
In a single molecule assay, the motion of a molecular motor is often inferred from measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic set-up taking into account…
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…
Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The non-matching properties of…
Aerosol injectors applied in single-particle diffractive imaging experiments demonstrated their potential in efficiently delivering nanoparticles with high density. Continuous optimization of injector design is crucial for achieving…
Partial differential equations (PDEs) with near singular solutions pose significant challenges for traditional numerical methods, particularly in complex geometries where mesh generation and adaptive refinement become computationally…
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Molecular Dynamics simulations can help scientists to gather valuable insights for physical processes on an atomic scale. This work explores various techniques for SIMD vectorization to improve the pairwise force calculation between…
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…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…