Related papers: Towards Open Boundary Molecular Dynamics Simulatio…
A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic…
In conventional molecular simulation, metastable structures often survive over considerable computational time, resulting in difficulties in simulating equilibrium states. In order to overcome this difficulty, here we propose a newly…
We present the IAMReX, an adaptive and parallel solver for particle-resolved simulations on the multi-level grid. The fluid equations are solved using a finite-volume scheme on the block-structured semi-staggered grids with both subcycling…
We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution…
Hypothesis:Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to…
Metastable structures in macromolecular and colloidal systems are non-equilibrium states that often have long lifetimes and cause difficulties in simulating equilibrium. In order to escape from the long-lived metastable states, we propose a…
In this work we study the dynamic behaviour of compound shells of revolution partially filled with an ideal incompressible fluid based on boundary-value problems. New analytical mathematical model with corresponding discrete scheme for the…
Imidazolium-based ionic liquids are widely used in conjunction with molecular liquids for various applications. Solvation, miscibility and similar properties are of fundamental importance for successful implementation of theoretical…
openCOSMO-RS is an open-source predictive thermodynamic model that can be applied to a broad range of systems in various chemical and biochemical engineering domains. This study focuses on improving openCOSMO-RS by introducing a new…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Large-scale first principles molecular dynamics are crucial for simulating complex processes in chemical, biomedical, and materials sciences. However, the unfavorable time complexity with respect to system sizes leads to prohibitive…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
We develop an immersed-boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a…
We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
The evolution of an initially prepared distribution of micron sized colloidal particles, trapped at a fluid interface and under the action of their mutual capillary attraction, is analyzed by using Brownian dynamics simulations. At a…