Related papers: Adaptive resolution molecular dynamics simulation …
Molecular dynamics in pure water and aqueous salt solutions remain incompletely understood, partly due to the apparent contradictions between results from different spectroscopic techniques. In this work, we demonstrate, by detailed…
A new gradient-based adaptive sampling method is proposed for design of experiments applications which balances space filling, local refinement, and error minimization objectives while reducing reliance on delicate tuning parameters. High…
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…
Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the convergence settings of electronic structure calculations…
We employ the Grand Canonical Adaptive Resolution Molecular Dynamics Technique (GC-AdResS) to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS atomistic details are kept only in an open sub-region…
Speckle photography can be used to monitor deformations of solid surfaces. The measuring characteristics, such as range or lateral resolution depend heavily on the optical recording and illumination set-up. This paper shows how, by the…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
A new computational method is presented to resolve hydrodynamic interactions acting on solid particles immersed in incompressible host fluids. In this method, boundaries between solid particles and host fluids are replaced with a continuous…
Cosmic structure simulations have improved enormously over the past decade, both in terms of the resolution which can be achieved, and with the addition of hydrodynamic and other techniques to formerly purely gravitational methods. This is…
A technique used to accelerate an adaptive optics simulation platform using reconfigurable logic is described. The performance of parts of this simulation have been improved by up to 600 times (reducing computation times by this factor) by…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting…
We discuss in detail a recently proposed hybrid particle-continuum scheme for complex fluids and evaluate it at the example of a confined homopolymer solution in slit geometry. The hybrid scheme treats polymer chains near the impenetrable…
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…
A technique is presented for producing synthetic images from numerical simulations whereby the image resolution is adapted around prominent features. In so doing, adaptive image ray-tracing (AIR) improves the efficiency of a calculation by…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
A brief review is presented of the scaling of complex fluids, polymers and polyelectrolytes in solution and in confined geometry, in thermodynamical, structural and rheology properties using equilibrium and nonequilibrium dissipative…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Reservoir computing is a machine learning algorithm that excels at predicting the evolution of time series, in particular, dynamical systems. Moreover, it has also shown superb performance at solving partial differential equations. In this…
We consider a lattice model for amphiphiles in a solvent with molecules chemically similar to one part of the amphiphilic molecule. The dependence of the interaction potential on orientation of the amphiphilic molecules is taken into…