Related papers: Redox potential replica exchange molecular dynamic…
In this paper, we present the design and the analysis of an electrochemical circuit for measuring the concentrations of therapeutic drugs using structure-switching aptamers. Aptamers are single-stranded nucleic acids, whose sequence is…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
We compare the predicted phase behaviour of lead (Pb) using three different interatomic potential models, including an embedded atom method (EAM), a modified embedded atom method (MEAM), and a neural network-based machine-learned model in…
Presented is an algorithm based on dynamic mode decomposition (DMD) for acceleration of the power method (PM). The power method is a simple technique for determining the dominant eigenmode of an operator $\mathbf{A}$, and variants of the…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
Robust header compression (ROHC), critically positioned between the network and the MAC layers, plays an important role in modern wireless communication systems for improving data efficiency. This work investigates bi-directional ROHC…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
The capacity to predict and control bioprocesses is perhaps one of the most important objectives of biotechnology. Computational simulation is an established methodology for the design and optimization of bioprocesses, where the finite…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…
A novel embedded atom method (EAM) potential for the Xi-phases of Al-Pd-Mn has been determined with the force-matching method. Different combinations of analytic functions were tested for the pair and transfer part. The best results are…
Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…
We propose a new quantum dynamics method called the effective potential analytic continuation (EPAC) to calculate the real time quantum correlation functions at finite temperature. The method is based on the effective action formalism which…
Constant potential molecular dynamics simulation plays important role for applications of electrochemical systems, yet the calculation of charge fluctuation on electrodes remains a computational bottleneck. We propose a highly scalable,…
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…
Activation barriers associated with ion diffusion and chemical reactions are vital to understand and predict a wide range of phenomena, such as material growth, ion transport, and catalysis. In the calculation of activation barriers for…
We propose a simple model of cytochrome c oxidase, including four redox centers and four protonable sites, to study the time evolution of electrostatically coupled electron and proton transfers initiated by the injection of a single…