Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Models

Machine learning has recently entered into the mainstream of coarse-grained (CG) molecular modeling and simulation. While a variety of methods for incorporating deep learning into these models exist, many of them involve training neural networks to act directly as the CG force field. This has several benefits, the most significant of which is accuracy. Neural networks can inherently incorporate multi-body effects during the calculation of CG forces, and a well-trained neural network force field outperforms pairwise basis sets generated from essentially any methodology. However, this comes at a significant cost. First, these models are typically slower than pairwise force fields even when accounting for specialized hardware which accelerates the training and integration of such networks. The second, and the focus of this paper, is the need for the considerable amount of data needed to train such force fields. It is common to use tens of microseconds of molecular dynamics data to train a single CG model, which approaches the point of eliminating the CG models usefulness in the first place. As we investigate in this work, it is apparent that this data-hunger trap from neural networks for predicting molecular energies and forces is caused in large part by the difficulty in learning force equivariance, i.e., the fact that force vectors should rotate while maintaining their magnitude in response to an equivalent rotation of the system. We demonstrate that for CG water, networks that inherently incorporate this equivariance into their embedding can produce functional models using datasets as small as a single frame of reference data, which networks without inherent symmetry equivariance cannot

Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models Through Virtual Particles

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 models of biomolecules remains challenging. We demonstrate in this work how virtual particles, CG sites with no atomistic correspondence, can be incorporated into CG models within the context of relative entropy minimization (REM) as latent variables. The methodology presented, variational derivative relative entropy minimization (VD-REM), enables optimization of virtual particle interactions through a gradient descent algorithm aided by machine learning. We apply this methodology to the challenging case of a solvent-free CG model of a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer and demonstrate that introduction of virtual particles captures solvent-mediated behavior and higher-order correlations which REM alone cannot capture in a more standard CG model based only on the mapping of collections of atoms to the CG sites.Comment: 35 pages, 9 figure

OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining

The “bottom-up” approach to coarse-graining, for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes, is an important approach in computational chemistry, biophysics, and materials science. As one example, the Multiscale Coarse-Graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure, such as MS-CG modeling, is particularly valuable. Here, we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (EDCG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS, and NAMD. OpenMSCG is modularized in the Python programming framework, which allows users to create and customize modeling “recipes” for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications

Healthcare-associated infections (HAIs) during the coronavirus disease 2019 (COVID-19) pandemic: A time-series analysis

OBJECTIVE: To use interrupted time-series analyses to investigate the impact of the coronavirus disease 2019 (COVID-19) pandemic on healthcare-associated infections (HAIs). We hypothesized that the pandemic would be associated with higher rates of HAIs after adjustment for confounders. DESIGN: We conducted a cross-sectional study of HAIs in 3 hospitals in Missouri from January 1, 2017, through August 31, 2020, using interrupted time-series analysis with 2 counterfactual scenarios. SETTING: The study was conducted at 1 large quaternary-care referral hospital and 2 community hospitals. PARTICIPANTS: All adults ≥18 years of age hospitalized at a study hospital for ≥48 hours were included in the study. RESULTS: In total, 254,792 admissions for ≥48 hours occurred during the study period. The average age of these patients was 57.6 (±19.0) years, and 141,107 (55.6%) were female. At hospital 1, 78 CLABSIs, 33 CAUTIs, and 88 VAEs were documented during the pandemic period. Hospital 2 had 13 CLABSIs, 6 CAUTIs, and 17 VAEs. Hospital 3 recorded 11 CLABSIs, 8 CAUTIs, and 11 VAEs. Point estimates for hypothetical excess HAIs suggested an increase in all infection types across facilities, except for CLABSIs and CAUTIs at hospital 1 under the no pandemic scenario. CONCLUSIONS: The COVID-19 era was associated with increases in CLABSIs, CAUTIs, and VAEs at 3 hospitals in Missouri, with variations in significance by hospital and infection type. Continued vigilance in maintaining optimal infection prevention practices to minimize HAIs is warranted

OpenMSCG: A Software Tool for Bottom-up Coarse-graining

The “bottom-up” approach to coarse-graining – for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes – is an important approach in computational chemistry, biophysics, and materials science. As one example, the multiscale coarse-graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure such as MS-CG modeling is particularly valuable. Here we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (ED-CG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS and NAMD. OpenMSCG is modulized in the Python programming framework, which allows users to create and customize modeling “recipes” for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications

In vitro evaluation of the oxidation efficacy of transgingival photodynamic therapy

OBJECTIVE: To evaluate the capability of soft laser light to penetrate blood, serum, gingival connective tissue and pure collagen type I. MATERIALS AND METHODS: A 1:1 mixture of methylene blue (MB) and diphenylisobenzofuran (DPBF) was irradiated for 60 s with a diode laser (670 nm, 0.3 W) through blood, serum, gingival connective tissue and collagen type I (2 mm transillumination thickness). The oxidation of DPBF by MB was determined spectrophotometrically by measuring the optical density (oD) at 410 nm. The absorption spectra of DPBF/MB irradiated through MB (1%) and strawberry red solution (3%) served as control. RESULTS: The mean oD of non-irradiated DPBF/MB was 1.98 ± 0.04. Irradiation through MB showed no oxidation of DPBF (1.98 ± 0.02; p > 0.05), while interposition of strawberry red and serum resulted in almost complete oxidation of DPBF (0.13 ± 0.09, 0.06 ± 0.03; p ≤ 0.0001). Irradiation through gingiva and collagen reduced the oxidation of DPBF significantly (1.0 ± 0.04, 0.7 ± 0.04; p ≤ 0.0001), accounting for 50% to 35% of the non-irradiated DPBF/MB solution. CONCLUSION: Red light from a diode laser can penetrate blood and gingival tissues. However, light absorption for collagen and connective tissue can hamper the oxidation process