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| PID (if applicable): doi:[https://dx.doi.org/10.1007/s10910-020-01201-7 10.1007/s10910-020-01201-7]
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| ==Problem Statement==
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| Crystallization of Paracetamol in Ethanol
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| ===Object of Research and Objective===
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| Determination of Intermediate States and their Kinetics along the Crystallization of Paracetamol in Ethanol using Raman Spectroscopy.
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| ===Procedure===
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| [[File:Workflow Figure.png|thumb|Workflow Illustration]]
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|
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| <b>1. Data Acquisition</b>
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|
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| Time-resolved Raman Spectroscopy to follow the crystallization of Paracetamol in accoustically-levitated Ethanol droplets. Surface, temperature (22.0 +/- 1.0 °C), and relative humidity (17.5 +/- 2.5 %) of the environment are controlled by Nitrogen stream.
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|
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| <b>2. Data Extraction</b>
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|
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| Extract the spectroscopic measurement matrix <math> \mathbf{M} \in \mathbb{R}_+^{n \times m} </math> (<math> m </math> measurements of <math> n </math> non-negative intensities) from measurement file containing spectroscopic data and metadata.
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|
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| <b>3. Data Analysis</b>
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|
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| Factorize <math> \mathbf{M} </math> such that <math> \mathbf{M} = \mathbf{W} \cdot \mathbf{H} </math> (<math> \mathbf{W} \in \mathbb{R}_+^{n \times r}, \mathbf{H} \in \mathbb{R}_+^{r \times m} </math> with <math> r </math> the rank of factorization or <i>expected</i> number of components) using a novel non-negative matrix factorization (NMF) approach:
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|
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| <b><u>Pre-proceesing</u></b>
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|
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| Singular Value Decomposition (SVD) for primary factorization <math> \mathbf{M^{T}} =</math> '''U''' <math> \mathbf \Sigma \mathbf{V^{T}} </math>.
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|
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| Generate <math> \mathbf{U} </math> from '''U''' with <math> \mathbf{U}[:,0] = [ 1 , 1 , ... , 1 , 1 ]^T </math> and <math> \mathbf{U}[ : , 1 : ] = </math> '''U''' <math> [ : , : r - 1 ] </math>.
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|
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| Ensure orthogonality among columns of <math> \mathbf{U} </math>.
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|
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| <b><u>Initializing</u></b>
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|
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| Apply PCCA+ to <math> \mathbf{U} </math> to obtain the transformation matrix <math> \mathbf{A} </math> to initialize <math> \mathbf{H} </math>, <math> \mathbf{W} </math>, and <math> \mathbf{P} </math>.
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|
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| <math> \widetilde{\mathbf{H}} = (\mathbf{UA})^{T} </math>
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|
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| <math> \widetilde{\mathbf{W }}= \mathbf{M}(\mathbf{A^{T}U^{T}})^{\#} </math> (<math>\#</math> the pseudoinverse of singular / non-square matrices)
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|
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| <math> \widetilde{\mathbf{P}} = \mathbf{A^{-1}}(\mathbf{U_{-}^{\#}U_{+}})\mathbf{A} </math> (<math> \mathbf{U_{+/-}} </math> defined as <math> \mathbf{U} </math> without the first / last row)
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|
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| <b><u>Minimizing</u></b>
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|
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| Objective function <math> \Psi^2 </math> maintains positivity (1,2,4), column (3) and row stochastics (5), depending on <math> \mathbf{M} </math>, <math> \mathbf{U} </math>, and <math> \mathbf{A} </math>.
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|
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| Minimization of <math> \Psi^2 </math> with respect to <math> \mathbf{A} </math> adjusts <math> \widetilde{\mathbf{W}} </math> and <math> \widetilde{\mathbf{H}} </math> numerically to the claimed structural properties.
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|
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| <math> \Psi = \alpha ( \underset{i,j}{\min} \widetilde{W_{i,j}} ) + \beta ( \underset{i,j}{\min} \widetilde{H_{i,j}} ) + \gamma ( \underset{j}{\max} | \sum\limits_{i=1}^r \widetilde{H_{i,j}} - 1 | ) + \delta ( \underset{i,j}{\min} \widetilde{P_{i,j}} ) + \mu ( \underset{j}{\max} | \sum\limits_{j=1}^r \widetilde{P_{i,j}} - 1 | ) </math>
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|
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| <b><u>Recovering</u></b>
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|
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| Minimization returns <math> \mathbf{A_{opt}} </math>, which allows to recover <math> \mathbf{H_{rec}} </math>, <math> \mathbf{W_{rec}} </math>, and <math> \mathbf{P_{rec}} </math>.
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|
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| <math> \mathbf{H_{rec}} = (\mathbf{UA_{opt}})^{T} </math>
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|
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| <math> \mathbf{W_{rec}} = \mathbf{M}(\mathbf{A_{opt}^{T}{U}^{T}}) ^{\#} </math>
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|
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| <math> \mathbf{P_{rec}} = \mathbf{A_{opt}^{-1}}(\mathbf{U^{\#}_{-} U_{+}})\mathbf{A_{opt}} </math>
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|
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| <b>4. Data Interpretation</b>
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|
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| <math> \mathbf{W_{rec}} </math> contains the spectra of the substances involved in the crystallization process, while <math> \mathbf{H_{rec}} </math> allows an inference on the kinetics. Interpretation of both matrices leads to the identification of intermediate states and the underlying kinetics.
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|
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| ===Involved Disciplines===
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| NFDI4Chem (wikidata:[[wikidata:Q96678459|Q96678459]])
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|
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| <math> \Rightarrow </math> Raman Spectroscopy (wikidata:[[wikidata:Q862228|Q862228]])
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|
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| MaRDI (wikidata:[[wikidata:Q108327788|Q108327788]])
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|
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| <math> \Rightarrow </math> Numerical Analysis (wikidata:[[wikidata:Q11216|Q11216]])
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|
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| <math> \Rightarrow </math> Mathematical Optimization (wikidata:[[wikidata:Q141495|Q141495]])
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|
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| <math> \Rightarrow </math> Linear Algebra (wikidata:[[wikidata:Q82571|Q82571]])
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| ===Data Streams===
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| NFDI4Chem <math> \Rightarrow </math> MaRDI (.txt File containing measurement matrix <math> \mathbf{M} </math>)
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|
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| MaRDI <math> \Rightarrow </math> NFDI4Chem (.png Files containing component spectra <math> \mathbf{W} </math> and relative concentration profiles <math> \mathbf{H} </math>)
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| ==Model==
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| <math> \mathbf{M}=\mathbf{WH} </math>
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|
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| A measurement matrix <math> \mathbf{M} </math> is factorized in a matrix <math> \mathbf{W} </math>, containing the spectra of the substances involved, and a matrix <math> \mathbf{H} </math>, which allows an inference on the kinetics.
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| ===Discretization===
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| *Time: Time-resolution of Raman Spectroscopy
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| *Space: -
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| ===Variables===
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|
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| {| class="wikitable"
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| |-
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| !Name !! Unit !! Symbol !! dependent (measured) / independent (controlled)
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| |-
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| |Time || s || t || independent
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| |-
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| |Wavelength || cm<sup>-1</sup> || <math> \lambda </math> || independent
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| |-
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| |Intensity || - ||I ||dependent (measured)
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| |-
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| |Substance Matrix || - ||<math> \mathbf{W} </math> || dependent (calculated)
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| |-
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| |Kinetic Matrix || - ||<math> \mathbf{H} </math> ||dependent (calculated)
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| |}
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| <br/>
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| ===Parameter===
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|
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| {| class="wikitable"
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| !Name
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| !Unit
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| !Symbol
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| |-
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| |Temperature
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| |°C
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| |T
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| |-
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| |Relative Humidity
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| | %
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| |RH
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| |-
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| |Rank of Factorization
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| | -
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| |<math> r </math>
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| |-
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| |Number of Singular Values
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| | -
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| |<math> k </math>
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| |-
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| |Singular Value Tolerance
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| | -
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| |<math> tol </math>
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| |-
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| |Objective Function Parameter
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| | -
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| |<math> \alpha, \beta, \gamma, \delta, \mu </math>
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| |-
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| |Maximum Number of Iterations
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| | -
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| |<math> MAXITER </math>
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| |}
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| <br/>
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| ==Process Informationen==
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|
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| ===Process Steps===
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|
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| {| class="wikitable"
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| !Name
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| !Description
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| !Input
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| !Output
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| !Method
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| !Parameter
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| !Environment
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| !Mathematical Area
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| |-
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| |Data Acquisition
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| |Measurement
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| | -
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| |.icraman
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| |Time-resolved Raman Spectroscopy
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| |T, RH
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| |RXN1™
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| | -
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| |-
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| |Data Extraction
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| |Extract Spectroscopic Data
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| |.icraman
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| |.txt
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| | -
| |
| | -
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| |iC Raman™
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| | -
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| |-
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| |Data Analysis
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| |Determine Component Spectra & Concentration Profiles
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| |.txt
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| |.png
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| |NMF algorithm
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| |<math> r, tol, k </math> <math> MAXITER </math> <math> \alpha, \beta, \gamma, \delta, \mu </math>
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| |Matlab
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| |Numerical Analysis, Linear Algebra, Mathematical Optimization
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| |-
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| |Data Interpretation
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| |Determine Intermediate States & Kinetics
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| |.png
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| | -
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| | -
| |
| | -
| |
| | -
| |
| | -
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| |}
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| <br/>
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| ===Applied Methods===
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|
| |
| {| class="wikitable"
| |
| !ID
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| !Name
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| !Process Step
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| !Parameter
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| !realised/implemented by
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| |-
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| |doi:[[doi:10.1007/s10910-020-01201-7|10.1007/s10910-020-01201-7]]
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| |NMF Algorithm
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| |Data Analysis
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| |<math> r, tol, k </math> <math> MAXITER </math> <math> \alpha, \beta, \gamma, \delta, \mu </math>
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| |[https://www.mdpi.com/2079-3197/6/1/20/s1 Matlab Script]
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| |-
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| |wikidata:[[wikidata:Q420904|Q420904]]
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| |SVD
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| |Data Analysis - Pre-Processing
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| |<math> k </math>
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| |Matlab R2019a
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| |-
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| |wikidata:[[wikidata:Q43219517|Q43219517]]
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| |Pseudoinverse
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| |Data Analysis - Initializing
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| |<math> tol </math>
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| |Matlab R2019a
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| |-
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| |doi:[[doi:10.1016/j.laa.2004.10.026|10.1016/j.laa.2004.10.026]]
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| |PCCA+
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| |Data Analysis - Initializing
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| |<math> r </math>
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| |[https://www.mdpi.com/2079-3197/6/1/20/s1 Matlab Script]
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| |-
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| |wikidata:[[wikidata:Q1253278|Q1253278]]
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| |Nelder-Mead Algorithm
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| |Data Analysis - Minimizing
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| |<math> \alpha, \beta, \gamma, \delta, \mu, MAXITER </math>
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| |Matlab R2019a
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| |-
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| |wikidata:[[wikidata:Q43219517|Q43219517]]
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| |Pseudoinverse
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| |Data Analysis - Recovering
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| |<math> tol </math>
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| |Matlab R2019a
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| |}
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| <br/>
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| ===Software used===
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|
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| {| class="wikitable"
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| !ID
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| !Name
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| !Description
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| !Version
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| !Programming Language
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| !Dependencies
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| !versioned
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| !published
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| !documented
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| |-
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| | -
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| |iC Raman
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| |Data Acquisition & Reaction Analysis
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| |4.1
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| | ?
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| |Windows
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| |Yes
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| |Yes
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| |[https://www.mt.com/de/de/home/products/L1_AutochemProducts/AutoChem_software/iC_Raman.html#documents Yes]
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| |-
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| |sw:[https://swmath.org/software/558 558]
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| |Matlab
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| |Programming and numeric Computing
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| |R2019a
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| |C,C++,Fortran,Java
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| |Windows, Mac, Linux
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| |Yes
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| |Yes
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| |[https://de.mathworks.com/help/matlab/ Yes]
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| |}
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| <br/>
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| ===Experimental Devices/Instruments and Computer-Hardware===
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|
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| {| class="wikitable"
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| !ID
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| !Name
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| !Description
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| !Version
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| !Part Nr
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| !Serial Nr
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| !Location
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| !Software
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| |-
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| | -
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| |Raman RXN1
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| |Spectrometer
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| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |-
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| | -
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| |GenunineIntel
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| |Intel(R) Core(TM) i7-9700T CPU @ 2.00 GHz
| |
| |
| |
| |
| |
| |
| |
| |
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| |
| |
| |}
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| <br/>
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| ===Input Data===
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|
| |
| {| class="wikitable"
| |
| !ID
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| !Name
| |
| !Size
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| !Data Structure
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| !Format Representation
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| !Format Exchange
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| !binary/text
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| !proprietary
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| !to publish
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| !to archive
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| |-
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| | -
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| |Spectroscopic & Meta Data
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| |small
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| | -
| |
| | -
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| |.icraman
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| |binary
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| |Yes
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| |Yes
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| |Yes
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| |-
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| | -
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| |Spectroscopic Data ( <math> \mathbf{M} </math>)
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| |small
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| |Matlab Array
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| |dense matrix (csv)
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| |.txt
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| |text
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| |No
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| |Yes
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| |Yes
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| |-
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| | -
| |
| |<math> r </math>
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| |small
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| |integer
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| |
| |
| |
| |
| |text
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| |No
| |
| |Yes
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| |Yes
| |
| |-
| |
| | -
| |
| |<math> \alpha, \beta, \gamma, \delta, \mu </math>
| |
| |small
| |
| |float
| |
| |
| |
| |
| |
| |text
| |
| |No
| |
| |Yes
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| |Yes
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| |}
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| <br/>
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| ===Output Data===
| |
| {| class="wikitable"
| |
| !ID
| |
| !Name
| |
| !Size
| |
| !Data Structure
| |
| !Format Representation
| |
| !Format Exchange
| |
| !binary/text
| |
| !proprietary
| |
| !to publish
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| !to archive
| |
| |-
| |
| | -
| |
| |Component Spectra (<math> \mathbf{W} </math>)
| |
| |small
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| |Matlab Array
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| |plot
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| |.png
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| |binary
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| |No
| |
| |Yes
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| |Yes
| |
| |-
| |
| | -
| |
| |Concentration Profile (<math>\mathbf{H} </math>)
| |
| |small
| |
| |Matlab Array
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| |plot
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| |.png
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| |binary
| |
| |No
| |
| |Yes
| |
| |Yes
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| |}
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| <br/>
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| ==Reproducibility==
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| ===Reproducibility of the Experiments on the original Devices/Instruments/Hardware===
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| Yes
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|
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| ===Reproducibility of the Experiments on other Devices/Instruments/Hardware===
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| Yes
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|
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| ===Transferability of the Experiments to===
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| a) other solutes, solvents, parameter
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|
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| b) other chemical reactions
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| =Legend=
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| The following abbreviations are used in the document to indicate/resolve IDs:
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|
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| doi: https://dx.doi.org/
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|
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| sw: https://swmath.org/software/
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|
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| wikidata: https://www.wikidata.org/wiki/
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|
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| [[Category: Workflow]]
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