Multi-Phenotypic Breast Cancer Post-Radiotherapy for Hodgkin Lymphoma: A Case of Secondary Malignancy

Morbidity and mortality associated with radiation-induced secondary malignancies (RISMs) have shifted treatment paradigms to minimize or eliminate radiation from treatment regimens. In this case, a 48-year-old woman was diagnosed with Hodgkin lymphoma (HL) and treated with radiotherapy in 2000. In 2018, she was diagnosed with ductal carcinoma in situ (DCIS) of the right breast and treated with a mastectomy. Soon after, she developed triple-negative invasive ductal carcinoma (IDC) in her reconstructed breast. The patient underwent a left lumpectomy, and pathology showed ER-/PR-/HER2+ IDC. This patient's multi-phenotypic DCIS and IDC presentation are suspected to be RISM due to her previous HL treatment regimen.

Structure and thermodynamics of a 2D Lennard-Jones hexagonal fluid

The thermodynamic and structural properties of the 2D hexagonal soft-sites fluid are examined by integral equation theory benchmarked against extensive Monte Carlo simulations. Hexamers are built of six equal Lennard-Jones segments. Site-site integral equation theory is used to compute site-site correlation functions, excess internal energies and isotherms over a wide range of conditions and compared with results obtained from Monte Carlo simulations. Various approaches for computing the pressure are discussed as well. Satisfactory qualitative agreement between theory and simulations is found with details depending on the applied closure relation.

Comment on "Density functional theory and 3D-RISM-KH molecular theory of solvation studies of CO2 reduction on Cu-, Cu2O-, Fe-, and Fe3O4-based nanocatalysts"

Recently, A. Kovalenko et al. reported the computational study of molecular structure and energetics of CO₂ + H₂ reduction reaction on Cu-, Cu₂O-, Fe-, and Fe₃O₄-based nanocatalysts in the J. Mol. Model., 26, 267 (2020). The authors claim that they developed and tested the multiscale modeling description of this process by combining the periodical boundary condition density functional theory (PBC DFT) and molecular theory of solvation. However, due to inappropriate selection of intermediate strictures, in particular, the unfavorite structure of CO* adsorbed on Cu-, Cu₂O-, Fe-, and Fe₃O₄-nanoparticles, and some inconsistency in preparation of initial structures by DFT approach, there are serious concerns about the correctness and quality of the presented results. In addition, by this comment, I would like to help other researchers working on the development of new catalysts for electrochemical reduction of CO₂ to avoid further misunderstandings following this study.

A simple model of planar membrane: An integral equation investigation

A simple model of a lipid membrane, a binary mixture of saturated lipids and unsaturated lipids, was studied using an integral equation theory. The planar membrane is modeled as mixture of linear and bent molecules in two-dimensional space, and site-site radial distribution function, Kirkwood-Buff (KB) integral and related quantities were computed over the whole range of the molar fraction to understand their mixing behavior. We found that a close packing of linear molecules is enhanced as the fraction of bent molecules increases, but a long range correlation between the linear molecules is weakened. A high concentration of linear molecules promotes the demixing of linear molecules and bent molecules, and enhances the long range correlation between molecules. This implies that, the higher the concentration of linear molecules, the larger clusters tend to be formed. © 2018 Wiley Periodicals, Inc.

coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study

The non-Watson-Crick (non-WC) base pairs of Escherichia coli loop E of 5S rRNA are stabilized by Mg²⁺ ions through water-mediated interaction. It is important to know the synergic role of Mg²⁺ and the water network surrounding Mg²⁺ in stabilizing the non-WC base pairs of RNA. For this purpose, free energy change of the system is calculated using molecular dynamics (MD) simulation as Mg²⁺ is pulled from RNA, which causes disturbance of the water network. It was found that Mg²⁺ remains hexahydrated unless it is close to or far from RNA. In the pentahydrated form, Mg²⁺ interacts directly with RNA. Water network has been identified by two complimentary methods; MD followed by a density-based clustering algorithm and three-dimensional-reference interaction site model. These two methods gave similar results. Identification of water network around Mg²⁺ and non-WC base pairs gives a clue to the strong effect of water network on the stability of this RNA. Based on sequence analysis of all Eubacteria 5s rRNA, we propose that hexahydrated Mg²⁺ is an integral part of this RNA and geometry of base pairs surrounding it adjust to accommodate the [Formula: see text]. Overall the findings from this work can help in understanding the basis of the complex structure and stability of RNA with non-WC base pairs.

The Effect of Molecular Structure and Environment on the Miscibility and Diffusivity in Polythiophene-Methanofullerene Bulk Heterojunctions: Theory and Modeling with the RISM Approach

Although better means to model the properties of bulk heterojunction molecular blends are much needed in the field of organic optoelectronics, only a small subset of methods based on molecular dynamics- and Monte Carlo-based approaches have been hitherto employed to guide or replace empirical characterization and testing. Here, we present the first use of the integral equation theory of molecular liquids in modelling the structural properties of blends of phenyl-C61-butyric acid methyl ester (PCBM) with poly(3-hexylthiophene) (P3HT) and a carboxylated poly(3-butylthiophene) (P3BT), respectively. For this, we use the Reference Interaction Site Model (RISM) with the Universal Force Field (UFF) to compute the microscopic structure of blends and obtain insight into the miscibility of its components. Input parameters for RISM, such as optimized molecular geometries and charge distribution of interaction sites, are derived by the Density Functional Theory (DFT) methods. We also run Molecular Dynamics (MD) simulation to compare the diffusivity of the PCBM in binary blends with P3HT and P3BT, respectively. A remarkably good agreement with available experimental data and results of alternative modelling/simulation is observed for PCBM in the P3HT system. We interpret this as a step in the validation of the use of our approach for organic photovoltaics and support of its results for new systems that do not have reference data for comparison or calibration. In particular, for the less-studied P3BT, our results show that expectations about its performance in binary blends with PCBM may be overestimated, as it does not demonstrate the required level of miscibility and short-range structural organization. In addition, the simulated mobility of PCBM in P3BT is somewhat higher than what is expected for polymer blends and falls into a range typical for fluids. The significance of our predictive multi-scale modelling lies in the insights it offers into nanoscale morphology and charge transport behaviour in multi-component organic semiconductor blends.

Fast and General Method To Predict the Physicochemical Properties of Druglike Molecules Using the Integral Equation Theory of Molecular Liquids

We report a method to predict physicochemical properties of druglike molecules using a classical statistical mechanics based solvent model combined with machine learning. The RISM-MOL-INF method introduced here provides an accurate technique to characterize solvation and desolvation processes based on solute-solvent correlation functions computed by the 1D reference interaction site model of the integral equation theory of molecular liquids. These functions can be obtained in a matter of minutes for most small organic and druglike molecules using existing software (RISM-MOL) (Sergiievskyi, V. P.; Hackbusch, W.; Fedorov, M. V. J. Comput. Chem. 2011, 32, 1982-1992). Predictions of caco-2 cell permeability and hydration free energy obtained using the RISM-MOL-INF method are shown to be more accurate than the state-of-the-art tools for benchmark data sets. Due to the importance of solvation and desolvation effects in biological systems, it is anticipated that the RISM-MOL-INF approach will find many applications in biophysical and biomedical property prediction.