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Subramaniam, Shankar

Publications and source records attributed to Subramaniam, Shankar.

Author Correction: A universal language for finding mass spectrometry data patterns

Correction to: Nature Methodshttps://doi.org/10.1038/s41592-025-02660-z, published online 12 May 2025. This article was originally published under standard Springer Nature license (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license, © The Author(s). The error has been corrected in the HTML and PDF versions of the article.

Damiani, Tito↗

A universal language for finding mass spectrometry data patterns

Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here, in this study, we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.

Damiani, Tito [Czech Academy of Sciences (CAS), Pr↗

A study on the scale dependence of mixing indices for Eulerian multiphase models

Abstract Mixing can vary based on the scale at which the system is observed, and a mixing index that can capture the features at different length scales is desirable. In this article, we analyze the scale dependence of the mixing indices developed for Eulerian multiphase models. Relevant length scales are distinguished by filtering solid fraction fields. The scale‐dependence study is first done on manufactured fields of solid fraction to assess the performance of the mixing indices. The study is extended to a two‐dimensional CFD simulation of the segregation of a bidisperse gas–solid mixture. The local mixing index performs well in capturing the spatial variation of mixing at different scales. The scale dependence of two global mixing indices is considered in the study, where the state of mixing is defined based on statistical measures. We demonstrate that the choice of measures influences the sensitivity of mixing indices to mixing at different scales.

Nagawkar, Barlev R.↗

Investigating the influence of particle distribution on force and torque statistics using hierarchical machine learning

An accurate representation of hydrodynamic force and torque experienced by every particle in a distribution can be obtained from particle resolved (PR) simulations. These unique quantities are influenced by the deterministic position of surrounding particles. However, systems simulated with this methodology are typically limited to particles due to the involved computational cost. This resource requirement is a major bottleneck in analyzing the effect of variations in particle distribution. Here, this article attempts to address this bottleneck by availing relatively inexpensive deep learning models. The surrogate models that we employ in this article use a physics‐based hierarchical framework and symmetry‐preserving neural networks to achieve robustness with limited training data. This article first performs additional generalizability tests on PR data of distinct distributions that are not involved in the training process. The models are then deployed on several different particle distributions. Impact of clustering and structure on the observed statistics are investigated.

42 ENGINEERING↗

An Open-Source Framework for the Computational Analysis and Design of Autothermal Chemical Processes

The main project object was to develop software tools for simulating non-equilibrium autothermal processes, improving the prospects for identifying and designing such systems. The project demonstrates the use of these tools to simulate autothermal pyrolysis, a process recently developed at the pilot-plant scale at Iowa State University. In such process, instead of externally heating a reactor to pro-vide the enthalpy of pyrolysis, sufficient oxygen in the form of air is introduced into the reactor to support partial oxidation of reactants and products with the exothermic energy released supporting endothermic pyrolysis reactions. A fluidized bed is used to assure good mixing of biomass and oxidant and provide an isothermal reaction environment. The amount of oxygen required depends upon the kind of biomass being pyrolyzed and parasitic heat losses from the reactor. For example, for woody biomass pyrolyzed under conditions that simulate adiabatic operation, equivalence ratios can be as low as 0.06, compared to 0.20 or higher for autothermal gasifiers. By removing the heat transfer bottleneck of conventional pyrolysis, operation in autothermal mode allowed a significant increase in reactor throughput process, approaching five times the throughput of the conventionally operated pyrolyzer. Different simulation strategies were considered and developed: a zero-dimensional chemistry model was used to verify the applicability of kinetic schemes to predict biomass fast pyrolysis in autothermal conditions. Conventional chemical reactor models such as the plug flow reactor and the partially stirred reactor were used to investigate the role of mixing in the fluidized bed pyrolyzer and to establish the impact of mixing time on the gas-phase reactions. A comprehensive multiphase computational fluid dynamics (mCFD) framework, including polydisperse granular phase modeling and detailed chemical kinetics was formulated and used to model the experimental setup for autothermal biomass fast pyrolysis at ISU. Multiphase CFD was also used to investigate the role of biomass feed positioning on the mixing of biomass in the pyrolizer. Finally, a reduced order model (ROM), suitable to be implemented in process simulators was obtained. Both the mCFD and the ROM were validated against experiments.

09 BIOMASS FUELS↗

An index to characterize gas‐solid and solid‐solid mixing from average volume fraction fields

Abstract A mixing index based on solid volume fraction fields is developed for gas‐solid flows. Conventional mixing indices are based on particle realizations of granular mixing and are applicable to experimental data or discrete element method simulations. However, these indices cannot be used as‐is for multifluid models, and an index for characterizing mixing in gas‐solid flows from continuous fields is needed. The performance of the new mixing index is tested in two applications. The first is a 3D simulation of the mixing of biomass and sand in a fluidized bed reactor, and the second is a 2D simulation of binary particle segregation in a fluidized bed. The simulations are performed using OpenFOAM®. The mixing index is used to quantify gas‐solid mixing using solid volume fractions and solid‐solid mixing using solid fractions. The formulation of conventional mixing indices is extended to be used with solid volume fractions fields, and methods for performance improvement are presented.

09 BIOMASS FUELS↗

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

59 BASIC BIOLOGICAL SCIENCES↗

Machine Learning Reduced Order Model for Cost and Emission Assessment of a Pyrolysis System

Biomass pyrolysis is a promising approach for producing economic and environmentally-friendly fuels and bioproducts. Biomass pyrolysis experiments show that feedstock properties have a significant impact on product yields and composition. Scientists are developing detailed chemical reaction mechanisms to capture the relationships between biomass composition and pyrolysis yields. These mechanisms can be computationally intensive. In this study, we investigate the use of a machine learning reduced order model (ROM) for assessing the costs and emissions of a pyrolysis biorefinery. Here, we developed a Kriging-based ROM to predict pyrolysis yields of 314 feedstock samples based on the results of a detailed chemical kinetic pyrolysis mechanism. The ROM is integrated into a chemical process model for calculating mass and energy yields in a commercial-scale (2000 tonne/day) biorefinery. The ROM estimated biofuel yields of 65 to 130 gallons per ton of dry biomass. This results in biofuel minimum fuel-selling prices of $2.62 to $5.43 per gallon and emissions of -13.62 to 145 kg of CO 2 per MJ. The ROM achieved an average mean square error of 1.8e-20 and a mean absolute error of 0.53%. These results suggest that ROMs can facilitate rapid feedstock screening for biorefinery systems.

09 BIOMASS FUELS↗

Acoustic radiation from lifting airfoils in compressible subsonic flow

The far field acoustic radiation from a lifting airfoil in a three-dimensional gust is studied. The acoustic pressure is calculated using the Kirchhoff method, instead of using the classical acoustic analogy approach due to Lighthill. The pressure on the Kirchhoff surface is calculated using an existing numerical solution of the unsteady flow field. The far field acoustic pressure is calculated in terms of these values using Kirchhoff's formula. The method is validated against existing semi-analytical results for a flat plate. The method is then used to study the problem of an airfoil in a harmonic three-dimensional gust, for a wide range of Mach numbers. The effect of variation of the airfoil thickness and angle of attack on the acoustic far field is studied. The changes in the mechanism of sound generation and propagation due to the presence of steady loading and non-uniform mean flow are also studied.

Atassi, Hafiz M.↗

Acoustic radiation from lifting airfoils in compressible subsonic flow

The far field acoustic radiation from a lifting airfoil in a three-dimensional gust is studied. The acoustic pressure is calculated using the Kirchhoff method, instead of using the classical acoustic analogy approach due to Lighthill. The pressure on the Kirchhoff surface is calculated using an existing numerical solution of the unsteady flow field. The far field acoustic pressure is calculated in terms of these values using Kirchhoff's formula. The method is validated against existing semi-analytical results for a flat plate. The method is then used to study the problem of an airfoil in a harmonic three-dimensional gust, for a wide range of Mach numbers. The effect of variation of the airfoil thickness and angle of attack on the acoustic far field is studied. The changes in the mechanism of sound generation and propagation due to the presence of steady loading and nonuniform mean flow are also studied.

Atassi, Hafiz M.↗