[HTML][HTML] Multi-body effects in a coarse-grained protein force field

J Wang, N Charron, B Husic, S Olsson, F Noé… - The Journal of …, 2021 - pubs.aip.org
The use of coarse-grained (CG) models is a popular approach to study complex
biomolecular systems. By reducing the number of degrees of freedom, a CG model can …

[HTML][HTML] Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

AEP Durumeric, GA Voth - The Journal of chemical physics, 2019 - pubs.aip.org
We utilize connections between molecular coarse-graining (CG) approaches and implicit
generative models in machine learning to describe a new framework for systematic …

Understanding three-body contributions to coarse-grained force fields

C Scherer, D Andrienko - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
Coarse-graining is a systematic reduction of the number of degrees of freedom used to
describe a system of interest. Coarse-graining can be thought of as a projection on the …

Coarse-graining of polyisoprene melts using inverse Monte Carlo and local density potentials

N Shahidi, A Chazirakis, V Harmandaris… - The Journal of …, 2020 - pubs.aip.org
Bottom-up coarse-graining of polymers is commonly performed by matching structural order
parameters such as distribution of bond lengths, bending and dihedral angles, and pair …

Tables to LaTeX: structure and content extraction from scientific tables

P Kayal, M Anand, H Desai, M Singh - International Journal on Document …, 2023 - Springer
Scientific documents contain tables that list important information in a concise fashion.
Structure and content extraction from tables embedded within PDF research documents is a …

[HTML][HTML] Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability

KM Lebold, WG Noid - The Journal of Chemical Physics, 2019 - pubs.aip.org
The dual-potential approach promises coarse-grained (CG) models that accurately
reproduce both structural and energetic properties, while simultaneously providing …

[HTML][HTML] Systematic study of temperature and density variations in effective potentials for coarse-grained models of molecular liquids

KM Lebold, WG Noid - The Journal of Chemical Physics, 2019 - pubs.aip.org
Due to their computational efficiency, coarse-grained (CG) models are widely adopted for
modeling soft materials. As a consequence of averaging over atomistic details, the effective …

ICDAR 2021 competition on scientific table image recognition to LaTeX

P Kayal, M Anand, H Desai, M Singh - … 5–10, 2021, Proceedings, Part IV …, 2021 - Springer
Tables present important information concisely in many scientific documents. Visual features
like mathematical symbols, equations, and spanning cells make structure and content …

Insight into the Density-Dependence of Pair Potentials for Predictive Coarse-Grained Models

MC Lesniewski, WG Noid - The Journal of Physical Chemistry B, 2024 - ACS Publications
We investigate the temperature-and density-dependence of effective pair potentials for 1-site
coarse-grained (CG) models of two industrial solvents, 1, 4-dioxane and tetrahydrofuran. We …

Polybutadiene copolymers via atomistic and systematic coarse-grained simulations

A Rissanou, A Chazirakis, P Polinska, C Burkhart… - …, 2021 - ACS Publications
The systematic coarse graining of polymeric systems is a usual route in order to extend the
range of spatiotemporal scales and systems accessible to molecular simulations. Here, we …