相关论文: Simulation of a particle domain in a continuum/flu…
Fluid transport across nanometric channels induced by electric, pressure and concentration gradients is ubiquitous in biological systems and fosters various applications. In this context, computer simulation setups with well-defined…
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a…
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 adaptive resolution simulation (AdResS) technique couples regions with different molecular resolutions and allows the exchange of molecules between different regions in an adaptive fashion. The latest development of the technique allows…
We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle…
Many natural phenomena involve processes that happen simultaneously at different characteristic length- and timescales. Typically, the region where the process of interest happens is affected by fluctuations in its surroundings. Modeling…
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the…
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
We introduce a finite-volume numerical scheme for solving stochastic gradient-flow equations. Such equations are of crucial importance within the framework of fluctuating hydrodynamics and dynamic density functional theory. Our proposed…
The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar…
The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea…
Fluctuating hydrodynamics (FHD) provides a framework for modeling microscopic fluctuations in a manner consistent with statistical mechanics and nonequilibrium thermodynamics. This paper presents an FHD formulation for isothermal reactive…
In this work, we provide a detailed theoretical analysis, supported by numerical tests, of the reliability of the adaptive resolution simulation (AdResS) technique in sampling the Grand Canonical ensemble. We demonstrate that the correct…
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…
A good representation of mesoscopic fluids is required to combine with molecular simulations at larger length and time scales (De Fabritiis {\it et. al}, Phys. Rev. Lett. 97, 134501 (2006)). However, accurate computational models of the…
We formulate theoretical modeling approaches and develop practical computational simulation methods for investigating the non-equilibrium statistical mechanics of fluid interfaces with passive and active immersed particles. Our approaches…
Recent advances in high-resolution imaging techniques and particle-based simulation methods have enabled the precise microscopic characterization of collective dynamics in various biological and engineered active matter systems. In…