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Using the perturbation-response scanning (PRS) technique, we study a set of 23 proteins that display a variety of conformational motions upon ligand binding (e.g. shear, hinge, allosteric). In most cases, PRS determines residues that may be…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…
Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
The high-pressure compaction of three dimensional granular packings is simulated using a bonded particle model (BPM) to capture linear elastic deformation. In the model, grains are represented by a collection of point particles connected by…
We present a GPU-native mesh adaptation procedure that incorporates a complex geometry represented with a triangle mesh within a primary Cartesian computational grid organized as a forest of octrees. A C++/CUDA program implements the…
Adaptive gradient methods are typically used for training over-parameterized models. To better understand their behaviour, we study a simplistic setting -- smooth, convex losses with models over-parameterized enough to interpolate the data.…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
Accelerated coarse-graining (CG) algorithms for simulating heterogeneous chemical reactions on surface systems have recently gained much attention. In the present paper, we consider such an issue by investigating the oscillation behavior of…
Simulations have acted as a cornerstone to understand MOF/polymer interface structure, however, no molecular-level simulation has yet been performed at the nanoparticle scale. In this work, a hybrid MARTINI/Force Matching (FM) force field…
Model order reduction encompasses mathematical techniques aimed at reducing the complexity of mathematical models in simulations while retaining the essential characteristics and behaviors of the original model. This is particularly useful…
Stochastic models of chemical systems are often analysed by solving the corresponding Fokker-Planck equation which is a drift-diffusion partial differential equation for the probability distribution function. Efficient numerical solution of…
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…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to…
Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this paper in the context of multiscale factorization methods for molecular…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
Multiphase flows are an important class of fluid flow and their study facilitates the development of diverse applications in industrial, natural, and biomedical systems. We consider a model that uses a continuum description of both phases…
Computationally solving the equations of elasticity is a key component in many materials science and mechanics simulations. Phenomena such as deformation-induced microstructure evolution, microfracture, and microvoid nucleation are examples…
Free-energy-based adaptive biasing methods, such as Metadynamics, the Adaptive Biasing Force (ABF) and their variants, are enhanced sampling algorithms widely used in molecular simulations. Although their efficiency has been empirically…