Related papers: Automatic Multi-Objective Optimization of Coarse-G…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
Image reconstruction by Algebraic Methods (AM) outperforms the transform methods in situations where the data collection procedure is constrained by time, space, and radiation dose. AM algorithms can also be applied for the cases where…
Meshfree simulation methods are emerging as compelling alternatives to conventional mesh-based approaches, particularly in the fields of Computational Fluid Dynamics (CFD) and continuum mechanics. In this publication, we provide a…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
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…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Fine-tuning large language models (LLMs) for downstream tasks has become increasingly crucial due to their widespread use and the growing availability of open-source models. However, the high memory costs associated with fine-tuning remain…
To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
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…
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.…
Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…
We present a fast and accurate method to select an optimal set of parameters in semi-analytic models of galaxy formation and evolution (SAMs). Our approach compares the results of a model against a set of observables applying a stochastic…
Coarse-graining (CG) reduces molecular details to extend the time and length scales of molecular dynamics simulations to microseconds and micrometers. However, the CG approaches have long been limited by the difficulty of constructing both…
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.…
Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…
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…
The study of convex optimization has historically been concerned with worst-case convergence rates. The development of the Optimized Gradient Method (OGM), due to \citet{drori2012PerformanceOF,Kim2016optimal}, marked a major milestone in…
Classical molecular dynamics (MD) simulations enable modeling of materials and examination of microscopic details that are not accessible experimentally. The predictive capability of MD relies on the force field (FF) used to describe…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…