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We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…
The quantum-to-classical transition of a quantum state is a topic of great interest in fundamental and practical aspects. A coarse-graining in quantum measurement has recently been suggested as its possible account in addition to the usual…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
Nuclear quantum effects (NQEs) remain a major challenge for molecular simulations, as rigorous treatment requires imaginary-time path-integral methods with heavy computational overhead. Neglecting NQEs leads to systematic errors in…
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are…
Inspired by holographic Wilsonian renormalization, we consider coarse graining a quantum system divided between short distance and long distance degrees of freedom, coupled via the Hamiltonian. Observations using purely long distance…
Machine learning has proven to be a valuable tool to approximate functions in high-dimensional spaces. Unfortunately, analysis of these models to extract the relevant physics is never as easy as applying machine learning to a large dataset…
Physics-based, atom-centered machine learning (ML) representations have been instrumental to the effective integration of ML within the atomistic simulation community. Many of these representations build off the idea of atoms as having…
In molecular dynamics and sampling of high dimensional Gibbs measures coarse-graining is an important technique to reduce the dimensionality of the problem. We will study and quantify the coarse-graining error between the coarse-grained…
Years ago Edwards proposed a thermodynamic description of dense granular matter, in which the grains (the `atoms' of the system) interact with inelastic forces. The approach is intriguing but is not justified from first principles, and…
We propose to employ the hierarchical coarse-grained structure in the artificial neural networks explicitly to improve the interpretability without degrading performance. The idea has been applied in two situations. One is a neural network…
The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of…
Variational quantum algorithms (VQAs) are increasingly being applied in simulations of strongly-bound (covalently bonded) systems using full molecular orbital basis representations. The application of quantum computers to the weakly-bound…
Quantum geometrical molecular dynamics provides a quantum geometric picture for understanding reactive dynamics, especially excited-state conical intersection dynamics, and also a numerically exact method for strongly correlated…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
We develop a rigorous error analysis for coarse-graining of defect-formation free energy. For a one-dimensional constrained atomistic system, we establish the thermodynamic limit of the defect-formation free energy and obtain explicitly the…