another lazy commit

dehe1011 · Dec 3, 2024 · 3cc8d05 · 3cc8d05
1 parent fbb0200
commit 3cc8d05
Show file tree

Hide file tree

Showing 51 changed files with 71,353 additions and 739 deletions.
diff --git a/.gitignore b/.gitignore
@@ -9,9 +9,9 @@ main.py
 qDNA/data/raw/geometries/
 
 # documentation
-docs/_build
-docs/_static
-docs/_templates
+docs/_build/
+docs/_static/
+docs/_templates/
 
 # created by coverage
 htmlcov/

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,19 +4,23 @@ include installation.md
 include LICENSE.txt
 include CITATION.bib
 
+# Include the MANIFEST file itself
+include MANIFEST.in
+
 # Include requirement files
 include requirements/*.txt
 
-# Include the MANIFEST file itself
-include MANIFEST.in
+# Include files in the package's root directory
+include qDNA/visualization/*.mplstyle
+include qDNA/defaults.yaml
 
 # Include all .py files
 recursive-include qDNA *.py
-include qDNA/defaults.yaml
 
 # Include specific data files
 include qDNA/data/data_paper/*.json
 include qDNA/data/figures_paper/*.pdf
-include qDNA/data/figures_paper/*.png
-include qDNA/data/raw/tb_params/*.json
+include qDNA/data/figures_tutorials/*.png
 include qDNA/data/raw/*.json
+include qDNA/data/raw/tb_params/*.json
+include qDNA/data/raw/lcao_params/*.json
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 <p align="center">
-    <img src="docs/figures/qDNA_logo.png">
+    <img src="docs/figures/qDNA_logo2.png">
 </p>
 <p align="center">
     <a href="https://opensource.org/licenses/BSD-3-Clause">

diff --git a/docs/biblio.bib b/docs/biblio.bib
@@ -21,39 +21,7 @@ @article{Siebert2023
     pages = {145},
 }
 
-% machine learning to predict DNA conductance and charge transport
-@article{Korol2019,
-    author = {Korol, Roman and Segal, Dvira},
-    title = {{Machine Learning Prediction of DNA Charge Transport}},
-    journal = {The Journal of Physical Chemistry B},
-    volume = {123},
-    pages = {2801--2811},
-    year = {2019},
-    doi = {10.1021/acs.jpcb.8b12557},
-}
-
-% machine learning applied to light harvesting complexes in photosynthesis (e.g. FMO complex), the method seems to be of use for DNA photophysics (in my opinion)
-@article{Ullah2022,
-  title    = {{Predicting the future of excitation energy transfer in
-              light-harvesting complex with artificial intelligence-based
-              quantum dynamics}},
-  author   = {Ullah, Arif and Dral, Pavlo O},
-  journal  = {Nature Communications},
-  volume   =  {13},
-  pages    =  {1930},
-  year     =  {2022},
-}
-
-% connects DNA cvharge transfer to SSH chains and uses an atomistic approach
-@article{Cramer2004,
-    author = {Cramer, Tobias and Krapf, Sebastian and Koslowski, Thorsten},
-    title = {{DNA Charge Transfer: An Atomistic Model}},
-    journal = {The Journal of Physical Chemistry B},
-    volume = {108},
-    pages = {11812--11819},
-    year = {2004},
-    doi = {10.1021/jp049712s},
-}
+% TB params
 
 % TB parameters, used by Simserides et al.
 @article{Hawke2010,
@@ -88,6 +56,19 @@ @article{Simserides2014
    year = {2014},
 }
 
+% improved TB parameters (including all atomic orbitals in the LCAO method), benchmarked with ab initio DFT and post-HF methods, including natural deformations simulated with molecular dynamics methods
+@article{Mantela2021,
+    author = {Marilena Mantela and Constantinos Simserides and Rosa Di Felice},
+    doi = {10.3390/ma14174930},
+    journal = {Materials},
+    title = {{LCAO electronic structure of nucleic acid bases and other heterocycles and transfer integrals in B-DNA, including structural variability}},
+    volume = {14},
+    year = {2021},
+    pages = {4930},
+}
+
+% TB model
+
 % Review about TB models and the methods used and result obtained by the Simserides group in Athens
 @article{Lambropoulos2019,
     author = {Konstantinos Lambropoulos and Constantinos Simserides},
@@ -99,28 +80,54 @@ @article{Lambropoulos2019
     pages = {968},
 }
 
-% improved TB parameters (including all atomic orbitals in the LCAO method), benchmarked with ab initio DFT and post-HF methods, including natural deformations simulated with molecular dynamics methods
-@article{Mantela2021,
-    author = {Marilena Mantela and Constantinos Simserides and Rosa Di Felice},
-    doi = {10.3390/ma14174930},
-    journal = {Materials},
-    title = {{LCAO electronic structure of nucleic acid bases and other heterocycles and transfer integrals in B-DNA, including structural variability}},
-    volume = {14},
-    year = {2021},
-    pages = {4930},
+@article{Mantela2023,
+	title = {Charge transport properties of ideal and natural {DNA} segments, as mutation detectors},
+	volume = {25},
+	doi = {10.1039/D3CP00268C},
+	number = {11},
+	journal = {Physical Chemistry Chemical Physics},
+	author = {Mantela, Marilena and Lambropoulos, Konstantinos and Simserides, Constantinos},
+	year = {2023},
+	pages = {7750--7762},
 }
 
-% exciton states in DNA, uses TB parameters from Mehrez2005
-@article{Bittner2007,
-   author = {Eric R. Bittner},
-   doi = {10.1016/j.jphotochem.2006.12.007},
-   journal = {Journal of Photochemistry and Photobiology A: Chemistry},
-   pages = {328--334},
-   title = {{Frenkel exciton model of ultrafast excited state dynamics in AT DNA double helices}},
-   volume = {190},
-   year = {2007},
+% experiments
+
+@article{Giese1999,
+	title = {On the {Mechanism} of {Long}-{Range} {Electron} {Transfer} through {DNA}},
+	volume = {38},
+	doi = {10.1002/(SICI)1521-3773(19990401)38:7<996::AID-ANIE996>3.0.CO;2-4},
+	number = {7},
+	journal = {Angewandte Chemie International Edition},
+	author = {Giese, Bernd and Wessely, Stephan and Spormann, Martin and Lindemann, Ute and Meggers, Eric and Michel-Beyerle, Maria E.},
+	year = {1999},
+	pages = {996--998},
 }
 
+@article{Giese2001,
+	title = {Direct observation of hole transfer through {DNA} by hopping between adenine bases and by tunnelling},
+	volume = {412},
+	doi = {10.1038/35085542},
+	number = {6844},
+	journal = {Nature},
+	author = {Giese, Bernd and Amaudrut, Jérôme and Köhler, Anne-Kathrin and Spormann, Martin and Wessely, Stephan},
+	year = {2001},
+	pages = {318--320},
+}
+
+% one of the most important pump-probe experiments on DNA
+@article{Crespo-Hernandez2005,
+   author={C. Crespo-Hernandez and B. Cohen and B. Kohler},
+   doi = {10.1038/nature03933},
+   journal = {Nature},
+   pages = {1141-1144},
+   title = {{Base stacking controls excited-state dynamics in A·T DNA}},
+   volume = {436},
+   year = {2005},
+}
+
+% reviews
+
 % one of the most cited reviews about charge transfer in DNA
 @article{Genereux2010,
    author = {Joseph C. Genereux and Jacqueline K. Barton},
@@ -155,17 +162,6 @@ @article{Giese2002
     doi = {10.1146/annurev.biochem.71.083101.134037}
 }
 
-% one of the most important pump-probe experiments on DNA
-@article{Crespo-Hernandez2005,
-   author={C. Crespo-Hernandez and B. Cohen and B. Kohler},
-   doi = {10.1038/nature03933},
-   journal = {Nature},
-   pages = {1141-1144},
-   title = {{Base stacking controls excited-state dynamics in A·T DNA}},
-   volume = {436},
-   year = {2005},
-}
-
 % in this book the charge transfer in DNA is discussed. Even though it was puplished in 2007 most results still hold since the field was not that active after 2010
 @book{Chakraboty2007,
     author = {T. Chakraboty},
@@ -175,6 +171,30 @@ @book{Chakraboty2007
     address = {Berlin, Heidelberg},
 }
 
+% excitons
+
+@article{Bittner2006,
+	title = {Lattice theory of ultrafast excitonic and charge-transfer dynamics in {DNA}},
+	volume = {125},
+	doi = {10.1063/1.2335452},
+	number = {9},
+	journal = {The Journal of Chemical Physics},
+	author = {Bittner, Eric R.},
+	year = {2006},
+	pages = {094909},
+}
+
+% exciton states in DNA, uses TB parameters from Mehrez2005
+@article{Bittner2007,
+   author = {Eric R. Bittner},
+   doi = {10.1016/j.jphotochem.2006.12.007},
+   journal = {Journal of Photochemistry and Photobiology A: Chemistry},
+   pages = {328--334},
+   title = {{Frenkel exciton model of ultrafast excited state dynamics in AT DNA double helices}},
+   volume = {190},
+   year = {2007},
+}
+
 % one of the few papers that use Coulomb interaction, but for two excess electrons, not for electron and hole
 @article{Tornow2010,
     author = {Sabine Tornow and Ralf Bulla and Frithjof B. Anders and Gertrud Zwicknagl},
@@ -197,6 +217,8 @@ @article{Conwell2008
     doi = {10.1021/jp077344x},
 }
 
+% Quantum Biology (FMO complex)
+
 @misc{quantum_HEOM,
   author       = {J.W. Abbott},
   title        = {Quantum\_HEOM},

diff --git a/docs/figures/qDNA_logo2.png b/docs/figures/qDNA_logo2.png
diff --git a/docs/figures/user_interface_figures/menu_1_light.png b/docs/figures/user_interface_figures/menu_1_light.png
diff --git a/docs/figures/user_interface_figures/menu_2_light.png b/docs/figures/user_interface_figures/menu_2_light.png
diff --git a/docs/figures/user_interface_figures/plot_1_light.png b/docs/figures/user_interface_figures/plot_1_light.png
diff --git a/docs/guide/guide.rst b/docs/guide/guide.rst
@@ -29,6 +29,7 @@ Below is a list of available tutorials. Click on each to access the detailed not
    Environment Simulation <tutorials/3_Environment_Simulation>
    Visualization <tutorials/4_Visualization>
    Evaluation <tutorials/5_Evaluation>
+   Reproduce Papers <tutorials/6_Reproduce_Papers>
 
 Descriptions
 ------------
@@ -37,7 +38,7 @@ Descriptions
   Reproduces all the figures presented in the reference paper :cite:`Herb2024`.
   This serves as a comprehensive example of `qDNA`'s visualization and analysis features.
 
-**Tight_Binding_Parameters**
+**Tight Binding Parameters**
   Learn the Linear Combination of Atomic Orbitals (LCAO) approach using Slater–Koster two-center
   integrals and Harrison-type expressions. Ideal for tight-binding model parameterization.
 
@@ -58,6 +59,11 @@ Descriptions
   Perform calculations for observables like exciton lifetimes, average charge separation, and dipole
   moments. Includes parallelization features for efficient computation.
 
+**Reproduce Papers**
+  Reproduce the plots from the papers :cite:`Giese1999`, :cite:`Giese2001`, :cite:`Bittner2006`,
+  :cite:`Bittner2007`, :cite:`Simserides2014` and :cite:`Mantela2023` using the `qDNA` package. This tutorial
+  demonstrates the package's capabilities in generating results that have already been published elsewhere.
+
 
 Getting Started
 ===============

diff --git a/docs/guide/tutorials/1_Tight_Binding_Parameters.ipynb b/docs/guide/tutorials/1_Tight_Binding_Parameters.ipynb
diff --git a/docs/guide/tutorials/2_Tight_Binding_Method.ipynb b/docs/guide/tutorials/2_Tight_Binding_Method.ipynb
diff --git a/docs/guide/tutorials/3_Environment_Simulation.ipynb b/docs/guide/tutorials/3_Environment_Simulation.ipynb
diff --git a/docs/guide/tutorials/4_Visualization.ipynb b/docs/guide/tutorials/4_Visualization.ipynb
diff --git a/docs/guide/tutorials/5_Evaluation.ipynb b/docs/guide/tutorials/5_Evaluation.ipynb