Related papers: Hierarchical Framework for Predicting Entropies in…
Applying an excess entropy scaling formalism to the coarse-grained (CG) dynamics of liquids, we discovered that missing rotational motions during the CG process are responsible for artificially accelerated CG dynamics. In the context of the…
Coarse-grained (CG) models are often parametrized to reproduce one-dimensional structural correlation functions of an atomically-detailed model along the degrees of freedom governing each interaction potential. While cross correlations…
We develop the framework of classical Observational entropy, which is a mathematically rigorous and precise framework for non-equilibrium thermodynamics, explicitly defined in terms of a set of observables. Observational entropy can be seen…
Multiscale simulations facilitate the efficient exploration of large spatiotemporal scales in chemical and physical systems, yet particle-based simulations become prohibitively expensive at time and length scales beyond the molecular level.…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
Additive Gaussian process (GP) models offer flexible tools for modelling complex non-linear relationships and interaction effects among covariates. While most studies have focused on predictive performance, relatively little attention has…
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly…
In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output, while removing the degrees of…
We introduce a definition of coarse-grained entropy that unifies measurement-based (observational entropy) and max-entropy-based (Jaynes) approaches to coarse-graining, by identifying physical constraints with information theoretic priors.…
We present a systematic coarse-graining (CG) strategy for many particle molecular systems based on cluster expansion techniques. We construct a hierarchy of coarse-grained Hamiltonians with interaction potentials consisting of two, three…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a…
These notes provide a brief primer on the basic aspects of "observational entropy" (also known as "quantum coarse-grained entropy"), a general framework for applying the concept of coarse-graining to quantum systems. We review the basic…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
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…
Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately describe classical molecular dynamics at a…
At the nanoscale, random effects govern not only the dynamics of a physical system but may also affect its observation. This work introduces a novel paradigm for coarse graining that eschews the assignment of a unique coarse-grained…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
In a recent paper, J. Chem. Phys. 162, 214101 (2025), a novel approach for the rigidification of a molecular cluster was proposed, in which starting with an all-atom (AA) potential, a coarse-grained (CG) potential for the associated cluster…