相关论文: Implementing Dimer Metadynamics using GROMACS
Progressive dimensionality reduction algorithms allow for visually investigating intermediate results, especially for large data sets. While different algorithms exist that progressively increase the number of data points, we propose an…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
Numerical hydrodynamical simulations have proven a successful means of reproducing many of the statistical properties of the Lyman-Alpha forest as measured in high redshift quasar spectra. Pseudo-hydrodynamical methods based only on…
Prioritizing methane for near-term climate action is crucial due to its significant impact on global warming. Previous work used columnwise matched filter products from the airborne AVIRIS-NG imaging spectrometer to detect methane plume…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
The underlying mechanisms and physics of catalytic Janus microswimmers is highly complex, requiring details of the associated phoretic fields and the physiochemical properties of catalyst, particle, boundaries, and the fuel used. Therefore,…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
We report on the latest additions to our open-source, block-grid adaptive framework MPI-AMRVAC, which is a general toolkit for especially hyperbolic/parabolic partial differential equations (PDEs). Applications traditionally focused on…
Molecular dynamics simulations have emerged as a fundamental instrument for studying biomolecules. At the same time, it is desirable to perform simulations of a collection of particles under various conditions in which the molecules can…
We develop and implement a parallel flatPERM algorithm \cite{G97,PK04} with mutually interacting parallel flatPERM sequences and use it to sample self-avoiding walks in 2 and 3 dimensions. Our data show that the parallel implementation…
We present a new polynomial-free prolongation scheme for Adaptive Mesh Refinement (AMR) simulations of compressible and incompressible computational fluid dynamics. The new method is constructed using a multi-dimensional kernel-based…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…
We adapt the Gradient Discretisation Method (GDM), originally designed for elliptic and parabolic partial differential equations, to the case of a linear scalar hyperbolic equations. This enables the simultaneous design and convergence…
When a liquid drop spreads on an adaptive substrate the latter changes its properties what may result in an intricate coupled dynamics of drop and substrate. Here we present a generic mesoscale hydrodynamic model for such processes that is…
Coarse-grain Lagrangian methods, such as Dissipative Particle Dynamics ( Hoogerbrugge et al., EPL, 1992), are suitable for describing mesoscopic fluid systems that include thermal fluctuations. However, the realistic simulation of liquids…
3D Gaussian Splatting (3DGS) has made significant strides in scene representation and neural rendering, with intense efforts focused on adapting it for dynamic scenes. Despite delivering remarkable rendering quality and speed, existing…