qDNA 0.1.1__tar.gz

qDNA-0.1.1/CITATION.bib

@@ -0,0 +1,8 @@
+@misc{QuantumDNA,
+  author = {Dennis Herb},
+  title = {QuantumDNA},
+  year = {2024},
+  url = {https://github.com/dehe1011/QuantumDNA},
+  doi = {10.5281/zenodo.12734027},
+  note = {\texttt{github.com/dehe1011/QuantumDNA}}
+}

qDNA-0.1.1/LICENSE.txt

@@ -0,0 +1,27 @@
+Copyright (c) 2024 Dennis Herb
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

qDNA-0.1.1/MANIFEST.in

@@ -0,0 +1,7 @@
+include README.md
+include LICENSE.txt
+include VERSION
+include environment.yml
+include CITATION.bib
+include configs/*.yaml
+include data/raw/tb_params/*.json

qDNA-0.1.1/PKG-INFO

@@ -0,0 +1,226 @@
+Metadata-Version: 2.1
+Name: qDNA
+Version: 0.1.1
+Summary: A package to calculate lifetimes, average charge separation and dipole moments of excited states along DNA within the formalism of open quantum systems.
+Home-page: https://github.com/dehe1011/QuantumDNA
+Author: Dennis Herb
+Author-email: dennis.herb@uni-ulm.de
+License: UNKNOWN
+Platform: UNKNOWN
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+
+<p align="center">
+    <img src="docs/figures/qDNA_logo.png"
+        height="130">
+</p>
+<p align="center">
+    <a href="https://opensource.org/licenses/BSD-3-Clause">
+        <img src="https://img.shields.io/badge/license-New%20BSD-blue.svg"
+            alt="License"></a>
+    <a href="https://doi.org/10.5281/zenodo.12734026">
+        <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.12734026.svg"
+            alt="DOI"></a>
+    <a href="https://quantumdna.readthedocs.io/en/latest/?badge=latest">
+        <img src="https://readthedocs.org/projects/quantumdna/badge/?version=latest"
+            alt="Documentation Status"></a>
+    <a href="https://github.com/dehe1011/QuantumDNA/releases">
+        <img src="https://img.shields.io/badge/version-0.1.1-blue"
+            alt="Release"></a>
+    <a href='https://coveralls.io/github/dehe1011/QuantumDNA?branch=main'>
+        <img src='https://coveralls.io/repos/github/dehe1011/QuantumDNA/badge.svg?branch=main' 
+            alt='Coverage Status' /></a>
+</p>
+
+---
+
+# QuantumDNA
+
+**Author: [Dennis Herb](https://github.com/dehe1011)**
+
+This Python package can be cited as:
+
+> *QuantumDNA (github.com/dehe1011/QuantumDNA)*, D. Herb, 2024, DOI: [10.5281/zenodo.12734027](https://doi.org/10.5281/zenodo.12734027)
+
+## What's new
+
+**July 2024**
+
+* Added a graphical user interface (GUI) to the package such that it is easier accessible for users that are less familiar with computer science. The user interface is based on the [customtkinter](https://customtkinter.tomschimansky.com/) package by Tom Schimansky. 
+* Added a Jupyter Notebook ```QuantumDNA/docs/tutorials/3_Paper.ipynb``` that reproduces all figures contained in our paper (and the supplementary) [D. Herb, M. Rossini and J. Ankerhold, *Physical Review E 109*, 064413 (2024).](https://doi.org/10.1103/PhysRevE.109.064413)
+* Added a [documentation](https://quantumdna.readthedocs.io/en/latest/) available on Read the Docs 
+
+
+## Introduction
+
+Welcome to QuantumDNA, a powerful and flexible tool designed to calculate lifetimes, average charge separation, and dipole moments of excited states along DNA. Leveraging the formalism of open quantum systems and based on tight-binding Hamiltonians, QuantumDNA is equipped to handle various tight-binding models. Users can incorporate custom tight-binding parameters from ab-initio calculations or experimental data, as well as define their own models, making the tool highly adaptable. QuantumDNA is regularly updated to ensure it remains at the cutting edge and includes a user-friendly interface to be accessible even to researchers less familiar with computer science. Results from several research papers can be reproduced with QuantumDNA.
+
+### Key Features
+
+* Versatile Calculations: Calculate lifetimes, charge separation, and dipole moments.
+* Customizable Models: Add and use custom tight-binding parameters and models.
+* User-Friendly Interface: Designed for ease of use by all researchers.
+* Regular Updates: Stay current with the latest advancements and improvements.
+* Parallelization: Supports parallel computing for the calculation of excited state properties for large ensembles of DNA sequences, optimizing performance within the computationally intensive context of open quantum systems.
+
+### Example Program
+
+To test QuantumDNA, you can run the following simple example where the exciton lifetime and the average charge separation of a double-stranded GCG DNA sequence are calculated. You can try different sequences, tight-binding models, and keyword arguments to investigate how these factors affect the exciton lifetime and average charge separation. For example you might find that in general more uniform sequences show higher values. Do you know the reason for this observation? 
+
+```python
+
+from qDNA import calc_lifetime, calc_dipole
+
+# input
+upper_strand = 'GCG'
+tb_model_name = 'ELM'
+kwargs = dict(unit='rad/ps', relax_rate=3, source='Hawke2010')
+
+# calculation 
+lifetime = calc_lifetime(upper_strand, tb_model_name, **kwargs)
+dipole = calc_dipole(upper_strand, tb_model_name, **kwargs)
+
+# output 
+print(f"Exciton lifetime {lifetime} fs")
+print(f"Average charge separation {dipole} A")
+
+```
+
+
+## Getting started 
+
+**NOTE**: These set-up instructions have only been tested on Windows and may not work on macOS. 
+
+**Pre-requisites**
+
+* Conda ([Download Anaconda](https://www.anaconda.com/download) or [Download Miniconda](https://docs.anaconda.com/miniconda/))
+* Git ([Download](https://gitforwindows.org/))
+* Python ([Download](https://www.python.org/downloads/))
+
+### Installation 
+
+Open the Anconda Powershell Prompt. Copy and execute the following ```commands```.
+
+1. Clone the Github repository:\
+```git clone https://github.com/dehe1011/QuantumDNA.git```\
+```cd QuantumDNA ```
+
+2. Create and active a virtual environment:\
+``` powershell -ExecutionPolicy Bypass -File tools/scripts/activate.ps1 ```
+
+If all tests worked you have successfully installed the package and the user interface opens automatically. You can access all the implemented functionalities. Enjoy :)
+
+### Usage
+
+After you have already installed the package, you can either access the code via the user interface or in a Jupyter Notebook. Open the Anconda Powershell Prompt again and use the following ``` commands ```:
+
+1. Open the user interface: 
+
+    (i) Navigate to the package directory: 
+    ``` Set-Location -Path "C:\Users\<YourUsername>\QuantumDNA ``` \
+    (ii) Run the activation script:
+    ``` powershell -ExecutionPolicy Bypass -File tools/scripts/activate.ps1 ```
+
+2. Open a new Jupyter notebook: 
+
+    (i) ``` jupyter notebook ``` \
+    (ii) Select the kernel to "Python (qDNA)"
+
+To remove the virtual environment use ``` conda remove --name qDNA --all ```. Don't forget to delete the folder "QuantumDNA" that contains the cloned GitHub repository. 
+
+
+## Documentation
+
+The documentation for the [latest release](https://quantumdna.readthedocs.io/en/latest/) is available for reading on Read The Docs. The [package website](https://dehe1011.github.io/QuantumDNA/) contains general information about the project and planned future developments. 
+
+### Tutorials
+
+The code contains some tutorials and demostrations to better understand and explore the functionalities. 
+
+In the ```QuantumDNA/docs/tutorials``` folder you can find the notebook **3_Paper.ipynb** that contains and reproduces all the figures contained in [D. Herb, M. Rossini and J. Ankerhold, Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence.](https://arxiv.org/abs/2402.16892)
+
+In the ```QuantumDNA/docs/tutorials``` folder, there exist the following tutorials:
+
+* **0_TB_Model.ipynb**: tutorials on predefined and custom tight-binding models.
+* **1_Plotting_Routines.ipynb**: tutorial on the predefined plotting routines.
+* **2_Open_System.ipynb**: tutorial on different ways to treat DNA relaxation the DNA environment.
+* **Exploration_Notebook.ipynb**: if you are interested how single functions behave, this is the place where you can test the functionality isolated from the rest of the code. 
+
+
+### Graphical user interface
+
+The usage of the graphical user interface is demonstrated in the following images. Many functionalities of the code can be accessed in a very user friendly manner from the menu window:
+
+![](docs/figures/user_interface_figures/menu_1.png)
+> _Screenshot of the menu of the user interface._
+
+![](docs/figures/user_interface_figures/plot_1.png)
+> _Plot obtained after pressing the submit button on the menu (see image above)._
+
+![](docs/figures/user_interface_figures/menu3.png)
+> _Screenshot of the menu of the user interface with calculations of the exciton lifetime and average charge separation displayed in the frame on the bottom right._
+
+### Shortcuts
+
+To increase the readability of the code I collected some of the shortcuts that are used requently: 
+
+* ham: hamiltonian
+* dm: density matrix
+* tb: tight-binding
+* eigv: eigenvalue/ eigenenergy
+* eigs: eigenstates/ eigenvectors
+* dim: dimension
+* fig: figure
+* op: operator
+* loc: local
+* glob: global
+* deph: dephasing
+* therm: thermalizing
+* seq: sequence
+* calc: calculate
+
+
+## References
+
+Papers from our group:
+
+* [R. Siebert, O. Ammerpohl, M. Rossini et al. A quantum physics layer of epigenetics: a hypothesis deduced from charge transfer and chirality-induced spin selectivity of DNA. *Clin Epigenet 15*, 145 (2023).](https://doi.org/10.1186/s13148-023-01560-3)
+* [D. Herb, M. Rossini and J. Ankerhold, Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence. *Physical Review E 109*, 064413 (2024).](https://doi.org/10.1103/PhysRevE.109.064413)
+
+Tight-binding parameters:
+
+* [L.G.D. Hawke, G. Kalosakas and C. Simserides, Electronic parameters for charge transfer along DNA. *The European Physical Journal E 32*, 291 (2010)](https://doi.org/10.1140/EPJE/I2010-10650-Y)
+* [C. Simserides, A systematic study of electron or hole transfer along DNA dimers, trimers and polymers. *Chemical Physics 440*, 31 (2014)](https://doi.org/10.1016/j.chemphys.2014.05.024)
+* [M. Mantela, C. Simserides and R. Di Felice, LCAO electronic structure of nucleic acid bases and other heterocycles and transfer integrals in B-DNA, including structural variability. *Materials 14*, 4930 (2021)](https://doi.org/10.3390/ma14174930)
+
+Tight-binding models:
+
+* [K. Lambropoulos and C. Simserides, Tight-binding modeling of nucleic acid sequences: Interplay between various types of order or disorder and charge transport. *Symmetry 11*, 968 (2019)](https://doi.org/10.3390/sym11080968)
+
+Excitons and electron-hole Coulomb interaction:
+
+* [C. Crespo-Hernandez, B. Cohen and B. Kohler, Base stacking controls excited-state dynamics in A·T DNA. *Nature 436*, 1141 (2005)](https://doi.org/10.1038/nature03933)
+* [E.R. Bittner, Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA. *Journal of Chemical Physics 125*, 094909 (2006)](https://doi.org/10.1063/1.2335452)
+* [E.M. Conwell, P.M. McLaughlin and S.M. Bloch, Charge-Transfer Excitons in DNA. *The Journal of Physical Chemistry B 112*, 2268 (2008)](https://doi.org/10.1021/jp077344x)
+* [S. Tornow, R. Bulla, F.B. Anders and G. Zwicknagl, Multiple-charge transfer and trapping in DNA dimers. *Physical Review B 82*, 195106 (2010)](https://doi.org/10.1103/PhysRevB.82.195106)
+
+Biological relevance of DNA charge transfer:
+
+* [J.C. Genereux and J.K. Barton, Mechanisms for  DNA charge transport. *Chemical Reviews 110*, 1642 (2010)](https://doi.org/10.1021/cr900228f)
+* [A.R. Arnold, M.A. Grodick and J.K. Barton, DNA Charge Transport: from Chemical Principles to the Cell. *Cell Chemical Biology 23*, 183 (2016)](https://doi.org/10.1016/j.chembiol.2015.11.010)
+
+Simulation of open quantum systems:
+
+* [J.R. Johansson, P.D. Nation and Franco Nori, QuTiP: An open-source Python framework for the dynamics of open quantum systems. *Computer Physics Communications 183*, 1760 (2012)](https://doi.org/10.1016/j.cpc.2012.02.021)
+* [quantum_HEOM (github.com/jwa7/quantum_HEOM), J.W. Abbott, 2022](https://doi.org/10.5281/zenodo.7230160)
+
+
+## Support
+
+For support, please contact the author at dennis.herb@uni-ulm.de or visit our community forum.
+
+

qDNA-0.1.1/README.md

@@ -0,0 +1,208 @@
+<p align="center">
+    <img src="docs/figures/qDNA_logo.png"
+        height="130">
+</p>
+<p align="center">
+    <a href="https://opensource.org/licenses/BSD-3-Clause">
+        <img src="https://img.shields.io/badge/license-New%20BSD-blue.svg"
+            alt="License"></a>
+    <a href="https://doi.org/10.5281/zenodo.12734026">
+        <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.12734026.svg"
+            alt="DOI"></a>
+    <a href="https://quantumdna.readthedocs.io/en/latest/?badge=latest">
+        <img src="https://readthedocs.org/projects/quantumdna/badge/?version=latest"
+            alt="Documentation Status"></a>
+    <a href="https://github.com/dehe1011/QuantumDNA/releases">
+        <img src="https://img.shields.io/badge/version-0.1.1-blue"
+            alt="Release"></a>
+    <a href='https://coveralls.io/github/dehe1011/QuantumDNA?branch=main'>
+        <img src='https://coveralls.io/repos/github/dehe1011/QuantumDNA/badge.svg?branch=main' 
+            alt='Coverage Status' /></a>
+</p>
+
+---
+
+# QuantumDNA
+
+**Author: [Dennis Herb](https://github.com/dehe1011)**
+
+This Python package can be cited as:
+
+> *QuantumDNA (github.com/dehe1011/QuantumDNA)*, D. Herb, 2024, DOI: [10.5281/zenodo.12734027](https://doi.org/10.5281/zenodo.12734027)
+
+## What's new
+
+**July 2024**
+
+* Added a graphical user interface (GUI) to the package such that it is easier accessible for users that are less familiar with computer science. The user interface is based on the [customtkinter](https://customtkinter.tomschimansky.com/) package by Tom Schimansky. 
+* Added a Jupyter Notebook ```QuantumDNA/docs/tutorials/3_Paper.ipynb``` that reproduces all figures contained in our paper (and the supplementary) [D. Herb, M. Rossini and J. Ankerhold, *Physical Review E 109*, 064413 (2024).](https://doi.org/10.1103/PhysRevE.109.064413)
+* Added a [documentation](https://quantumdna.readthedocs.io/en/latest/) available on Read the Docs 
+
+
+## Introduction
+
+Welcome to QuantumDNA, a powerful and flexible tool designed to calculate lifetimes, average charge separation, and dipole moments of excited states along DNA. Leveraging the formalism of open quantum systems and based on tight-binding Hamiltonians, QuantumDNA is equipped to handle various tight-binding models. Users can incorporate custom tight-binding parameters from ab-initio calculations or experimental data, as well as define their own models, making the tool highly adaptable. QuantumDNA is regularly updated to ensure it remains at the cutting edge and includes a user-friendly interface to be accessible even to researchers less familiar with computer science. Results from several research papers can be reproduced with QuantumDNA.
+
+### Key Features
+
+* Versatile Calculations: Calculate lifetimes, charge separation, and dipole moments.
+* Customizable Models: Add and use custom tight-binding parameters and models.
+* User-Friendly Interface: Designed for ease of use by all researchers.
+* Regular Updates: Stay current with the latest advancements and improvements.
+* Parallelization: Supports parallel computing for the calculation of excited state properties for large ensembles of DNA sequences, optimizing performance within the computationally intensive context of open quantum systems.
+
+### Example Program
+
+To test QuantumDNA, you can run the following simple example where the exciton lifetime and the average charge separation of a double-stranded GCG DNA sequence are calculated. You can try different sequences, tight-binding models, and keyword arguments to investigate how these factors affect the exciton lifetime and average charge separation. For example you might find that in general more uniform sequences show higher values. Do you know the reason for this observation? 
+
+```python
+
+from qDNA import calc_lifetime, calc_dipole
+
+# input
+upper_strand = 'GCG'
+tb_model_name = 'ELM'
+kwargs = dict(unit='rad/ps', relax_rate=3, source='Hawke2010')
+
+# calculation 
+lifetime = calc_lifetime(upper_strand, tb_model_name, **kwargs)
+dipole = calc_dipole(upper_strand, tb_model_name, **kwargs)
+
+# output 
+print(f"Exciton lifetime {lifetime} fs")
+print(f"Average charge separation {dipole} A")
+
+```
+
+
+## Getting started 
+
+**NOTE**: These set-up instructions have only been tested on Windows and may not work on macOS. 
+
+**Pre-requisites**
+
+* Conda ([Download Anaconda](https://www.anaconda.com/download) or [Download Miniconda](https://docs.anaconda.com/miniconda/))
+* Git ([Download](https://gitforwindows.org/))
+* Python ([Download](https://www.python.org/downloads/))
+
+### Installation 
+
+Open the Anconda Powershell Prompt. Copy and execute the following ```commands```.
+
+1. Clone the Github repository:\
+```git clone https://github.com/dehe1011/QuantumDNA.git```\
+```cd QuantumDNA ```
+
+2. Create and active a virtual environment:\
+``` powershell -ExecutionPolicy Bypass -File tools/scripts/activate.ps1 ```
+
+If all tests worked you have successfully installed the package and the user interface opens automatically. You can access all the implemented functionalities. Enjoy :)
+
+### Usage
+
+After you have already installed the package, you can either access the code via the user interface or in a Jupyter Notebook. Open the Anconda Powershell Prompt again and use the following ``` commands ```:
+
+1. Open the user interface: 
+
+    (i) Navigate to the package directory: 
+    ``` Set-Location -Path "C:\Users\<YourUsername>\QuantumDNA ``` \
+    (ii) Run the activation script:
+    ``` powershell -ExecutionPolicy Bypass -File tools/scripts/activate.ps1 ```
+
+2. Open a new Jupyter notebook: 
+
+    (i) ``` jupyter notebook ``` \
+    (ii) Select the kernel to "Python (qDNA)"
+
+To remove the virtual environment use ``` conda remove --name qDNA --all ```. Don't forget to delete the folder "QuantumDNA" that contains the cloned GitHub repository. 
+
+
+## Documentation
+
+The documentation for the [latest release](https://quantumdna.readthedocs.io/en/latest/) is available for reading on Read The Docs. The [package website](https://dehe1011.github.io/QuantumDNA/) contains general information about the project and planned future developments. 
+
+### Tutorials
+
+The code contains some tutorials and demostrations to better understand and explore the functionalities. 
+
+In the ```QuantumDNA/docs/tutorials``` folder you can find the notebook **3_Paper.ipynb** that contains and reproduces all the figures contained in [D. Herb, M. Rossini and J. Ankerhold, Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence.](https://arxiv.org/abs/2402.16892)
+
+In the ```QuantumDNA/docs/tutorials``` folder, there exist the following tutorials:
+
+* **0_TB_Model.ipynb**: tutorials on predefined and custom tight-binding models.
+* **1_Plotting_Routines.ipynb**: tutorial on the predefined plotting routines.
+* **2_Open_System.ipynb**: tutorial on different ways to treat DNA relaxation the DNA environment.
+* **Exploration_Notebook.ipynb**: if you are interested how single functions behave, this is the place where you can test the functionality isolated from the rest of the code. 
+
+
+### Graphical user interface
+
+The usage of the graphical user interface is demonstrated in the following images. Many functionalities of the code can be accessed in a very user friendly manner from the menu window:
+
+![](docs/figures/user_interface_figures/menu_1.png)
+> _Screenshot of the menu of the user interface._
+
+![](docs/figures/user_interface_figures/plot_1.png)
+> _Plot obtained after pressing the submit button on the menu (see image above)._
+
+![](docs/figures/user_interface_figures/menu3.png)
+> _Screenshot of the menu of the user interface with calculations of the exciton lifetime and average charge separation displayed in the frame on the bottom right._
+
+### Shortcuts
+
+To increase the readability of the code I collected some of the shortcuts that are used requently: 
+
+* ham: hamiltonian
+* dm: density matrix
+* tb: tight-binding
+* eigv: eigenvalue/ eigenenergy
+* eigs: eigenstates/ eigenvectors
+* dim: dimension
+* fig: figure
+* op: operator
+* loc: local
+* glob: global
+* deph: dephasing
+* therm: thermalizing
+* seq: sequence
+* calc: calculate
+
+
+## References
+
+Papers from our group:
+
+* [R. Siebert, O. Ammerpohl, M. Rossini et al. A quantum physics layer of epigenetics: a hypothesis deduced from charge transfer and chirality-induced spin selectivity of DNA. *Clin Epigenet 15*, 145 (2023).](https://doi.org/10.1186/s13148-023-01560-3)
+* [D. Herb, M. Rossini and J. Ankerhold, Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence. *Physical Review E 109*, 064413 (2024).](https://doi.org/10.1103/PhysRevE.109.064413)
+
+Tight-binding parameters:
+
+* [L.G.D. Hawke, G. Kalosakas and C. Simserides, Electronic parameters for charge transfer along DNA. *The European Physical Journal E 32*, 291 (2010)](https://doi.org/10.1140/EPJE/I2010-10650-Y)
+* [C. Simserides, A systematic study of electron or hole transfer along DNA dimers, trimers and polymers. *Chemical Physics 440*, 31 (2014)](https://doi.org/10.1016/j.chemphys.2014.05.024)
+* [M. Mantela, C. Simserides and R. Di Felice, LCAO electronic structure of nucleic acid bases and other heterocycles and transfer integrals in B-DNA, including structural variability. *Materials 14*, 4930 (2021)](https://doi.org/10.3390/ma14174930)
+
+Tight-binding models:
+
+* [K. Lambropoulos and C. Simserides, Tight-binding modeling of nucleic acid sequences: Interplay between various types of order or disorder and charge transport. *Symmetry 11*, 968 (2019)](https://doi.org/10.3390/sym11080968)
+
+Excitons and electron-hole Coulomb interaction:
+
+* [C. Crespo-Hernandez, B. Cohen and B. Kohler, Base stacking controls excited-state dynamics in A·T DNA. *Nature 436*, 1141 (2005)](https://doi.org/10.1038/nature03933)
+* [E.R. Bittner, Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA. *Journal of Chemical Physics 125*, 094909 (2006)](https://doi.org/10.1063/1.2335452)
+* [E.M. Conwell, P.M. McLaughlin and S.M. Bloch, Charge-Transfer Excitons in DNA. *The Journal of Physical Chemistry B 112*, 2268 (2008)](https://doi.org/10.1021/jp077344x)
+* [S. Tornow, R. Bulla, F.B. Anders and G. Zwicknagl, Multiple-charge transfer and trapping in DNA dimers. *Physical Review B 82*, 195106 (2010)](https://doi.org/10.1103/PhysRevB.82.195106)
+
+Biological relevance of DNA charge transfer:
+
+* [J.C. Genereux and J.K. Barton, Mechanisms for  DNA charge transport. *Chemical Reviews 110*, 1642 (2010)](https://doi.org/10.1021/cr900228f)
+* [A.R. Arnold, M.A. Grodick and J.K. Barton, DNA Charge Transport: from Chemical Principles to the Cell. *Cell Chemical Biology 23*, 183 (2016)](https://doi.org/10.1016/j.chembiol.2015.11.010)
+
+Simulation of open quantum systems:
+
+* [J.R. Johansson, P.D. Nation and Franco Nori, QuTiP: An open-source Python framework for the dynamics of open quantum systems. *Computer Physics Communications 183*, 1760 (2012)](https://doi.org/10.1016/j.cpc.2012.02.021)
+* [quantum_HEOM (github.com/jwa7/quantum_HEOM), J.W. Abbott, 2022](https://doi.org/10.5281/zenodo.7230160)
+
+
+## Support
+
+For support, please contact the author at dennis.herb@uni-ulm.de or visit our community forum.

qDNA-0.1.1/VERSION

@@ -0,0 +1 @@
+0.1.1

qDNA-0.1.1/configs/config.yaml

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+# This file contains all the default values used for the simulations
+project_name: "QuantumDNA"
+
+verbose: False
+DNA_BASES: ["A", "T", "G", "C", "c"]
+
+SOURCES: ['Hawke2010', 'Simserides2014', 'Mantela2021', 'Simserides2024']
+DESCRIPTIONS: ["1P", "2P"]
+PARTICLES: ["electron", "hole", "exciton"]
+UNITS: ['meV', 'eV', '100meV', 'rad/ps', 'rad/fs', '1/cm', 'K', 'J', '1/fs', '1/ps']
+T_UNITS: ['fs', 'ps']
+SPECTRAL_DENSITIES: ['debye', 'ohmic']
+TB_MODELS: ['WM', 'LM', 'ELM', 'FWM', 'FLM', 'FELM', 'FC']
+
+ham_kwargs_default:
+    source: 'Hawke2010'
+    description: '2P'
+    particles: ['electron','hole','exciton']
+    unit: 'rad/ps' 
+    interaction_param: 0. # in rad/ps
+    relaxation: True
+    nn_cutoff: True
+
+diss_kwargs_default:
+    loc_deph_rate: 0. # rad/fs
+    glob_deph_rate: 0. # rad/fs
+    uniform_relaxation: True
+    relax_rate: 0. # rad/fs
+    relax_rates: {'A': 0, 'T': 0, 'G': 0, 'C': 0, 'B': 0}
+    loc_therm: False
+    glob_therm: False
+    deph_rate: 7. # in rad/ps
+    cutoff_freq: 20. # in rad/ps
+    reorg_energy: 1. # in rad/ps
+    temperature: 300. # in K
+    spectral_density: 'debye'
+    exponent: 1.
+
+me_kwargs_default: 
+    t_steps: 500.
+    t_end: 3. # ps
+    t_unit: 'ps'
+    init_e_state: '(0, 0)'
+    init_h_state: '(0, 0)'
+    solver_method: 'adams'

qDNA-0.1.1/data/raw/tb_params/Hawke2010_electron_ELM.json

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+[{"E_A": -44, "E_T": -49, "E_G": -45, "E_C": -43, "t_AA": 0.16, "t_AT": 0.07, "t_AG": 0.01, "t_AC": -0.03, "t_TA": -0.07, "t_TT": -0.3, "t_TG": -0.17, "t_TC": 0.22, "t_GA": 0.3, "t_GT": -0.32, "t_GG": 0.2, "t_GC": 0.43, "t_CA": -0.12, "t_CT": 0.63, "t_CG": 0.15, "t_CC": -0.47, "h_AT": -0.09, "h_GC": 0.16, "h_TA": -0.09, "h_CG": 0.16, "r+_AA": 0.06, "r+_AT": 0.02, "r+_AG": 0.03, "r+_AC": -0.02, "r+_TA": 0.02, "r+_TT": 0.02, "r+_TG": 0.03, "r+_TC": -0.02, "r+_GA": 0.03, "r+_GT": 0.03, "r+_GG": -0.02, "r+_GC": -0.03, "r+_CA": -0.02, "r+_CT": -0.02, "r+_CG": -0.03, "r+_CC": 0.02, "r-_AA": 0.29, "r-_AT": 0.03, "r-_AG": -0.06, "r-_AC": -0.03, "r-_TA": 0.03, "r-_TT": 0.002, "r-_TG": 0.02, "r-_TC": -0.002, "r-_GA": -0.06, "r-_GT": 0.02, "r-_GG": -0.05, "r-_GC": -0.04, "r-_CA": -0.03, "r-_CT": -0.002, "r-_CG": -0.04, "r-_CC": 0.003}, {"source": "Hawke2010", "particle": "electron", "tb_model_name": "ELM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Hawke2010_electron_LM.json

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+[{"E_A": -44, "E_T": -49, "E_G": -45, "E_C": -43, "t_AA": 0.16, "t_AT": 0.07, "t_AG": 0.01, "t_AC": -0.03, "t_TA": -0.07, "t_TT": -0.3, "t_TG": -0.17, "t_TC": 0.22, "t_GA": 0.3, "t_GT": -0.32, "t_GG": 0.2, "t_GC": 0.43, "t_CA": -0.12, "t_CT": 0.63, "t_CG": 0.15, "t_CC": -0.47, "h_AT": -0.09, "h_GC": 0.16, "h_TA": -0.09, "h_CG": 0.16}, {"source": "Hawke2010", "particle": "electron", "tb_model_name": "LM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Hawke2010_electron_WM.json

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+[{"E_A": -49, "E_T": -49, "E_G": -45, "E_C": -45, "t_AA": -0.29, "t_AT": 0.005, "t_AG": 0.03, "t_AC": 0.32, "t_TA": 0.02, "t_TT": -0.29, "t_TG": 0.17, "t_TC": -0.01, "t_GA": -0.01, "t_GT": 0.32, "t_GG": 0.2, "t_GC": -0.1, "t_CA": 0.17, "t_CT": 0.03, "t_CG": -0.08, "t_CC": 0.2}, {"source": "Hawke2010", "particle": "electron", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Hawke2010_hole_ELM.json

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+[{"E_A": -83, "E_T": -90, "E_G": -80, "E_C": -88, "t_AA": -0.08, "t_AT": 0.68, "t_AG": -0.05, "t_AC": 0.68, "t_TA": 0.26, "t_TT": -1.17, "t_TG": 0.28, "t_TC": -0.86, "t_GA": -0.79, "t_GT": 0.73, "t_GG": -0.62, "t_GC": 0.8, "t_CA": 0.05, "t_CT": -1.07, "t_CG": -0.01, "t_CC": -0.66, "h_AT": -0.12, "h_GC": -0.12, "h_TA": -0.12, "h_CG": -0.12, "r+_AA": 0.02, "r+_AT": 0.09, "r+_AG": 0.04, "r+_AC": 0.05, "r+_TA": 0.09, "r+_TT": 0.04, "r+_TG": 0.05, "r+_TC": 0.02, "r+_GA": 0.04, "r+_GT": 0.05, "r+_GG": 0.03, "r+_GC": 0.04, "r+_CA": 0.05, "r+_CT": 0.02, "r+_CG": 0.04, "r+_CC": 0.01, "r-_AA": 0.48, "r-_AT": -0.03, "r-_AG": -0.03, "r-_AC": -0.05, "r-_TA": -0.03, "r-_TT": 0.005, "r-_TG": 0.05, "r-_TC": 0.005, "r-_GA": -0.03, "r-_GT": 0.05, "r-_GG": -0.44, "r-_GC": 0.04, "r-_CA": 0.05, "r-_CT": 0.005, "r-_CG": 0.04, "r-_CC": 0.01}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "ELM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Hawke2010_hole_FWM.json

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+[{"E_A": -83, "E_T": -83, "E_G": -80, "E_C": -80, "t_AA": -0.08, "t_AT": 0.2, "t_AG": -0.05, "t_AC": 0.02, "t_TA": 0.47, "t_TT": -0.08, "t_TG": -0.04, "t_TC": -0.79, "t_GA": -0.79, "t_GT": 0.02, "t_GG": -0.62, "t_GC": 0.01, "t_CA": -0.04, "t_CT": -0.05, "t_CG": -0.44, "t_CC": -0.62, "t_BB": 0.1, "h_AB": 0.1, "h_TB": 0.1, "h_GB": 0.1, "h_CB": 0.1, "h_BA": 0.1, "h_BT": 0.1, "h_BG": 0.1, "h_BC": 0.1}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Hawke2010_hole_LM.json

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+[{"E_A": -83, "E_T": -90, "E_G": -80, "E_C": -88, "t_AA": -0.08, "t_AT": 0.68, "t_AG": -0.05, "t_AC": 0.68, "t_TA": 0.26, "t_TT": -1.17, "t_TG": 0.28, "t_TC": -0.86, "t_GA": -0.79, "t_GT": 0.73, "t_GG": -0.62, "t_GC": 0.8, "t_CA": 0.05, "t_CT": -1.07, "t_CG": -0.01, "t_CC": -0.66, "h_AT": -0.12, "h_GC": -0.12, "h_TA": -0.12, "h_CG": -0.12}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "LM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Hawke2010_hole_WM.json

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+[{"E_A": -83, "E_T": -83, "E_G": -80, "E_C": -80, "t_AA": -0.08, "t_AT": 0.2, "t_AG": -0.05, "t_AC": 0.02, "t_TA": 0.47, "t_TT": -0.08, "t_TG": -0.04, "t_TC": -0.79, "t_GA": -0.79, "t_GT": 0.02, "t_GG": -0.62, "t_GC": 0.01, "t_CA": -0.04, "t_CT": -0.05, "t_CG": -0.44, "t_CC": -0.62}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Mantela2021_electron_WM.json

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+[{"E_A": -43.1, "E_T": -43.1, "E_G": -41.4, "E_C": -41.4, "t_AA": 0.22, "t_AT": 0.01, "t_AG": 0.11, "t_AC": 0.01, "t_TA": 0.02, "t_TT": 0.22, "t_TG": 0.09, "t_TC": 0.06, "t_GA": 0.06, "t_GT": 0.01, "t_GG": 0.02, "t_GC": 0.19, "t_CA": 0.09, "t_CT": 0.11, "t_CG": 0.09, "t_CC": 0.02}, {"source": "Mantela2021", "particle": "electron", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Mantela2021_hole_WM.json

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+[{"E_A": -84.9, "E_T": -84.9, "E_G": -83, "E_C": -83, "t_AA": 0.38, "t_AT": 0.5, "t_AG": 0.37, "t_AC": 0.16, "t_TA": 0.37, "t_TT": 0.38, "t_TG": 0.28, "t_TC": 1.42, "t_GA": 1.42, "t_GT": 0.16, "t_GG": 1.16, "t_GC": 0.1, "t_CA": 0.28, "t_CT": 0.37, "t_CG": 0.75, "t_CC": 116}, {"source": "Mantela2021", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Simserides2014_electron_WM.json

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+[{"E_A": -49, "E_T": -49, "E_G": -45, "E_C": -45, "t_AA": -0.29, "t_AT": 0.005, "t_AG": 0.03, "t_AC": 0.32, "t_TA": 0.02, "t_TT": -0.29, "t_TG": 0.17, "t_TC": -0.01, "t_GA": -0.01, "t_GT": 0.32, "t_GG": 0.2, "t_GC": -0.1, "t_CA": 0.17, "t_CT": 0.03, "t_CG": -0.08, "t_CC": 0.2}, {"source": "Simserides2014", "particle": "electron", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Simserides2014_hole_WM.json

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+[{"E_A": -83, "E_T": -83, "E_G": -80, "E_C": -80, "t_AA": -0.2, "t_AT": 0.35, "t_AG": -0.3, "t_AC": 0.1, "t_TA": 0.5, "t_TT": -0.2, "t_TG": -0.1, "t_TC": -1.1, "t_GA": -1.1, "t_GT": 0.1, "t_GG": -1.0, "t_GC": 0.1, "t_CA": -0.1, "t_CT": -0.3, "t_CG": -0.5, "t_CC": -1.0}, {"source": "Simserides2014", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

qDNA-0.1.1/data/raw/tb_params/Simserides2024_electron_ELM.json

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+[{"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_c": -0.290, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_cc": 0.056, "t_Cc": 0.067, "t_cC": 0.091, "t_cG": 0.031, "t_Gc": 0.002, "h_GC": 0.073, "h_Gc": 0.069, "h_AT": 0.002, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_cc": 0.097, "r-_Cc": 0.094, "r-_cC": 0.094, "r-_cG": 0.084, "r-_Gc": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_cc": 0.192, "r+_Cc": 0.186, "r+_cC": 0.186, "r+_cG": 0.030, "r+_Gc": 0.030}, {"source": "Simserides2024", "particle": "electron", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "}]

qDNA-0.1.1/data/raw/tb_params/Simserides2024_electron_FELM.json

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+[{"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_c": -0.290, "E_B": -5.000, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_cc": 0.056, "t_Cc": 0.067, "t_cC": 0.091, "t_cG": 0.031, "t_Gc": 0.002, "t_BB": 0.700, "h_GC": 0.073, "h_Gc": 0.069, "h_AT": 0.002, "h_cB": 0.066, "h_GB": 0.092, "h_CB": 0.047, "h_AB": 0.260, "h_TB": 0.079, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_cc": 0.097, "r-_Cc": 0.094, "r-_cC": 0.094, "r-_cG": 0.084, "r-_Gc": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_cc": 0.192, "r+_Cc": 0.186, "r+_cC": 0.186, "r+_cG": 0.030, "r+_Gc": 0.030}, {"source": "Simserides2024", "particle": "electron", "tb_model_name": "FELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' and sugar-phosphate backbone denoted as 'B' "}]

qDNA-0.1.1/data/raw/tb_params/Simserides2024_hole_ELM.json

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+[{"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_c": -7.630, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_cc": 0.105, "t_Cc": 0.098, "t_cC": 0.067, "t_cG": 0.029, "t_Gc": 0.208, "h_GC": 0.026, "h_Gc": 0.028, "h_AT": 0.034, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_cc": 0.004, "r-_Cc": 0.004, "r-_cC": 0.004, "r-_cG": 0.027, "r-_Gc": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_cc": 0.000, "r+_Cc": 0.000, "r+_cC": 0.000, "r+_cG": 0.002, "r+_Gc": 0.002}, {"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "}]

qDNA-0.1.1/data/raw/tb_params/Simserides2024_hole_FELM.json

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+[{"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_c": -7.630, "E_B": -9.400, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_cc": 0.105, "t_Cc": 0.098, "t_cC": 0.067, "t_cG": 0.029, "t_Gc": 0.208, "t_BB": 0.026, "h_GC": 0.026, "h_Gc": 0.028, "h_AT": 0.034, "h_cB": 0.178, "h_GB": 0.016, "h_CB": 0.173, "h_AB": 0.024, "h_TB": 0.179, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_cc": 0.004, "r-_Cc": 0.004, "r-_cC": 0.004, "r-_cG": 0.027, "r-_Gc": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_cc": 0.000, "r+_Cc": 0.000, "r+_cC": 0.000, "r+_cG": 0.002, "r+_Gc": 0.002}, {"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' and the sugar-phosphate backbone denoted as 'B' "}]