A class used to represent the tight-binding Hamiltonian for DNA sequences.
-
-
Parameters:
-
-
dna_seqDNA_Seq
The DNA sequence object containing the sequence and model information.
-
-
ham_kwargsdict
Additional keyword arguments for the Hamiltonian construction.
-
-
-
-
Attributes:
-
-
dna_seqDNA_Seq
The DNA sequence object containing the sequence and model information.
-
-
tb_modelTB_Model
The tight-binding model associated with the DNA sequence.
-
-
tb_basislist
The tight-binding basis states.
-
-
tb_sites_flattenedlist
The flattened list of tight-binding sites.
-
-
tb_basis_sites_dictdict
Dictionary mapping the TB basis to the TB sites.
-
-
tb_sitesnp.ndarray
The array of TB sites.
-
-
descriptionstr
Description of the Hamiltonian (e.g., ‘1P’ or ‘2P’).
-
-
particleslist
List of particles considered (e.g., [‘electron’, ‘hole’]).
-
-
sourcestr
Source of the tight-binding parameters.
-
-
unitstr
Unit of the Hamiltonian parameters.
-
-
tb_params_electrondict
Tight-binding parameters for electrons.
-
-
tb_params_holedict
Tight-binding parameters for holes.
-
-
relaxationbool
Flag indicating if relaxation is considered.
-
-
interaction_paramfloat
Interaction parameter for the Hamiltonian.
-
-
eh_basislist
Electron-hole basis states.
-
-
nn_cutoffbool
Nearest-neighbor cutoff for interactions.
-
-
matrixnp.ndarray
The Hamiltonian matrix.
-
-
matrix_dimint
Dimension of the Hamiltonian matrix.
-
-
backbonebool
Flag indicating if the model has a backbone.
-
-
-
-
-
Methods
-
-
-
get_param_dicts()
-
Retrieves the tight-binding parameters for electrons and holes.
-
-
get_eigensystem()
-
Computes and returns the eigenvalues and eigenvectors of the Hamiltonian.
-
-
get_matrix()
-
Computes and returns the Hamiltonian matrix.
-
-
get_fourier(init_state, end_state, quantities)
-
Computes Fourier components of the Hamiltonian for given states.
-
-
get_amplitudes(init_state, end_state)
-
Computes and returns the amplitudes for given states.
-
-
get_frequencies(init_state, end_state)
-
Computes and returns the frequencies for given states.
-
-
get_average_pop(init_state, end_state)
-
Computes and returns the average population for given states.
-
-
get_backbone_pop(init_state)
-
Computes and returns the population of particles on the backbone sites.
-
-
-
-
-
-get_backbone_pop(init_state)
-
Calculate the population of particles on the backbone sites of a Fishbone
-model.
-
-
Parameters:
-
-
init_statestr
The initial state of the system.
-
-
-
-
Returns:
-
-
dict
A dictionary where keys are particle identifiers and values are the population
-of each particle on the backbone sites.
-
-
-
-
Raises:
-
-
AssertionError
If the model is not a Fishbone model.
-
-
-
-
-
-
-
-
-get_eigensystem()
-
Compute the eigenvalues and eigenvectors of the matrix. This method computes
-the eigenvalues and eigenvectors of the matrix associated with the instance. If
-the description is “2P” and relaxation is enabled, the ground state is deleted
-from the matrix before computing the eigensystem.
-
-
Returns:
-
-
tuple
-
A tuple containing:
-
eigenvaluesndarray
The eigenvalues of the matrix.
-
-
eigenvectorsndarray
The eigenvectors of the matrix.
-
-
-
-
-
-
-
-
-
-
-
-
-get_fourier(init_state, end_state, quantities)
-
Calculate the Fourier components of the transition between initial and end
-states.
-
-
Parameters:
-
-
init_statestr
The initial state from which the transition starts.
-
-
end_statestr
The end state to which the transition occurs.
-
-
quantitieslist of str
List of quantities to calculate. Possible values are “amplitude”, “frequency”, and “average_pop”.
-
-
-
-
Returns:
-
-
amplitudes_dictdict
Dictionary containing the amplitudes for each particle.
-
-
frequencies_dictdict
Dictionary containing the frequencies for each particle.
-
-
average_pop_dictdict
Dictionary containing the average population for each particle.
-
-
-
-
Raises:
-
-
AssertionError
If end_state is not in self.tb_basis.
-If init_state is not in self.eh_basis or self.tb_basis depending on the description.
-
-
-
-
-
-
-
-
-get_matrix()
-
Generate the tight-binding Hamiltonian matrix based on the system
-description.
-
-
Returns:
-
-
matrixnumpy.ndarray
The Hamiltonian matrix for the system.
-
-
-
-
Raises:
-
-
ValueError
If the description attribute is not “2P” or “1P”.
-
-
-
-
-
Notes
-
-
Note
-
-
For a “2P” description, the Hamiltonian matrix is generated using tb_ham_2P and may include interaction and relaxation terms if specified.
-
For a “1P” description, the Hamiltonian matrix is generated using tb_ham_1P for either electrons or holes based on the particles attribute.
-
-
-
-
-
-
-get_param_dicts()
-
Retrieves the tight-binding parameters for electrons and holes. This method
-loads the tight-binding parameters for both electrons and holes from the
-specified source and model name. If the unit of the loaded parameters does not
-match the expected unit, it converts the parameters to the expected unit.
A class used to solve master equations using the tight-binding Hamiltonian and
-Lindblad dissipator.
-
This class provides methods to initialize the solver, set up the Hamiltonian and Lindblad dissipator,
-and compute various properties such as populations, coherences, and ground state populations over time.
-
-
Parameters:
-
-
tb_hamTB_Ham
The tight-binding Hamiltonian.
-
-
lindblad_dissLindblad_Diss
The Lindblad dissipator.
-
-
me_kwargsdict, optional
Additional keyword arguments for the master equation solver.
-
-
-
-
Attributes:
-
-
me_kwargsdict
Keyword arguments for the master equation solver.
-
-
verbosebool
Flag for verbose output.
-
-
t_stepsint
Number of time steps.
-
-
t_endint
End time.
-
-
timesnp.ndarray
Array of time points.
-
-
t_unitstr
Time unit.
-
-
tb_hamTB_Ham
The tight-binding Hamiltonian.
-
-
tb_modelTB_Model
The tight-binding model.
-
-
lindblad_dissLindblad_Diss
The Lindblad dissipator.
-
-
init_statetuple or str
Initial state depending on the Hamiltonian description.
-
-
init_matrixqutip.Qobj
Initial density matrix.
-
-
resultlist
List to store the results.
-
-
groundstate_popdict
Dictionary to store ground state population.
-
-
popdict
Dictionary to store population of states.
-
-
cohdict
Dictionary to store coherence of states.
-
-
-
-
-
Methods
-
-
-
get_init_matrix()
-
Generate the initial state matrix for the quantum system based on the Hamiltonian description.
-
-
get_result()
-
Calculate and return the result of the master equation solver.
-
-
get_result_particle(particle)
-
Retrieve the reduced density matrix for a specified particle.
-
-
get_pop()
-
Calculate and return the population of particles in the system.
-
-
get_coh()
-
Calculate and return the coherence of the system.
-
-
get_groundstate_pop()
-
Calculate and return the ground state population.
-
-
reset()
-
Resets the solver’s state by clearing results and initializing dictionaries for populations and coherences.
-
-
-
-
-
-get_coh()
-
Calculate and return the coherence of the system.
-This method computes the coherence of the system based on the Hamiltonian
-description and the Lindblad dissipation operators. It supports two types
-of Hamiltonian descriptions: “2P” and “1P”.
-For “2P” description, it uses the coherence operators from the Lindblad
-dissipation.
-For “1P” description, it constructs the coherence operators based on the
-tensor basis permutations.
-The method then solves the master equation using the QuTiP mesolve function
-and calculates the coherence for each particle in the system.
-
-
Returns:
-
-
dict
A dictionary where the keys are particle identifiers and the values are
-the computed coherence values.
-
-
-
-
-
-
-
-
-get_groundstate_pop()
-
Calculate and return the ground state population. This function computes the
-ground state population of a system described by a two- particle (2P)
-Hamiltonian with relaxation. If the ground state population has already been
-computed, it returns the cached result.
-
-
Returns:
-
-
dict
A dictionary containing the ground state population with the key
-“groundstate”.
-
-
-
-
Raises:
-
-
AssertionError
If the Hamiltonian description is not “2P”.
-
-
AssertionError
If relaxation is not enabled in the Hamiltonian.
-
-
-
-
-
-
-
-
-get_init_matrix()
-
Generate the initial state matrix for the quantum system based on the
-Hamiltonian description. The method supports two types of descriptions for the
-tight-binding Hamiltonian (tb_ham): “2P” (two- particle) and “1P” (one-
-particle). Depending on the description and the initialization parameters, the
-initial state matrix is constructed either as a delocalized state over all
-exciton states or as a localized state on a single exciton state.
-
-
Returns:
-
-
qutip.Qobj
The initial state matrix of the quantum system as a Qobj instance from the QuTiP library.
-
-
-
-
Raises:
-
-
ValueError
If the Hamiltonian description is not recognized.
-
-
-
-
-
-
-
-
-get_pop()
-
Calculate and return the population of particles in the system. This method
-computes the population of particles based on the Hamiltonian description and
-the Lindblad dissipation operators. It uses the QuTiP library to solve the
-master equation and obtain the expectation values of the population operators.
-
-
Returns:
-
-
dict
A dictionary where the keys are particle-site combinations and the
-values are the corresponding population expectation values.
-
-
-
-
-
Notes
-
-
Note
-
-
If the population (self.pop) is already computed, it returns the cached result.
-
The method supports two types of Hamiltonian descriptions: “2P” and “1P”.
-
For “2P” description, it uses the population operators from self.lindblad_diss.pop_ops.
-
For “1P” description, it constructs the population operators based on the tight-binding basis (self.tb_ham.tb_basis).
-
The master equation is solved using qutip.mesolve with the Hamiltonian matrix, initial state, time points, collapse operators, and population operators.
-
-
-
-
-
-
-get_result()
-
Calculate and return the result of the master equation solver. This method
-checks if the result has already been calculated. If not, it constructs the
-Hamiltonian matrix and solves the master equation using QuTiP’s mesolve
-function. The result is then stored and returned.
-
-
Returns:
-
-
list
A list of quantum states representing the solution of the master
-equation at different time points.
-
-
-
-
-
-
-
-
-get_result_particle(particle)
-
Retrieve the reduced density matrix for a specified particle. This method
-checks if the result has already been calculated. If not, it calculates the
-result. Then, it checks if the reduced density matrix for the specified particle
-has been calculated. If not, it calculates the reduced density matrix for the
-specified particle and stores it.
-
-
Parameters:
-
-
particlestr
The particle for which the reduced density matrix is to be retrieved.
-
-
-
-
Returns:
-
-
list
A list of reduced density matrices for the specified particle.
-
-
-
-
-
-
-
-
-reset()
-
Resets the solver’s state by clearing results and initializing dictionaries
-for populations and coherences.
-
Notes
-
-
Note
-
-
Clears the result list (for the full the all reduced density matrices).
-
Initializes groundstate_pop, pop, and coh dictionaries.
Calculate the overlap between two orbitals using the Harrison expression and the Slater-Koster two-center interactions.
-
-
Parameters:
-
-
orbital1Orbital
The first orbital object containing its coordinates, atom type, orbital type, and atom identifier.
-
-
orbital2Orbital
The second orbital object containing its coordinates, atom type, orbital type, and atom identifier.
-
-
connectionstr
The type of connection between the orbitals, either “interbase” or “intrabase”.
-
-
-
-
Returns:
-
-
float
The calculated overlap between the two orbitals. Returns 0 if the distance between orbitals is zero,
-if the orbitals belong to the same atom in an intrabase connection, or if the distance exceeds the cutoff radius.
-
-
-
-
-
Notes
-
The directional cosines are used as projections on the coordinate axis rather than actual cosine values.
-The function includes a hydrogen correction factor obtained by optimization.
Calculate the tight-binding energies for monomers in a given directory.
-This function searches for XYZ files in the specified directory, loads the data,
-and calculates the HOMO and LUMO energies for each monomer. The results are
-returned as dictionaries.
-
-
Parameters:
-
-
directorystr
The directory containing the XYZ files.
-
-
-
-
Returns:
-
-
HOMO_dictdict
A dictionary where the keys are identifiers of the form ‘E_<base_identifier>’
-and the values are the HOMO energies in eV rounded to two decimal places.
-
-
LUMO_dictdict
A dictionary where the keys are identifiers of the form ‘E_<base_identifier>’
-and the values are the LUMO energies in eV rounded to two decimal places.
Calculate tight-binding (TB) parameters for a dimer in meV.
-
-
Parameters:
-
-
baseslist
List of base objects representing the bases in the dimer.
-
-
tb_model_namestr
Name of the tight-binding model. Can be “WM”, “LM”, or “ELM”.
-
-
double_strandedbool, optional
Flag indicating whether the dimer is double-stranded (default is True).
-
-
-
-
Returns:
-
-
tuple
A tuple containing two dictionaries:
-- HOMO_dict: Dictionary with HOMO (Highest Occupied Molecular Orbital) parameters.
-- LUMO_dict: Dictionary with LUMO (Lowest Unoccupied Molecular Orbital) parameters.
-
-
-
-
Raises:
-
-
AssertionError
If tb_model_name is not “WM” for single-stranded mode.
-If the length of bases is not 2 for single-stranded mode.
The name of the JSON file (without extension) to be converted.
-
-
directorystr
The directory where the JSON file is located and where the XYZ file will be saved.
-
-
-
-
Raises:
-
-
FileNotFoundError
If the JSON file does not exist in the specified directory.
-
-
KeyError
If the expected keys are not found in the JSON file.
-
-
ValueError
If the JSON file contains invalid data.
-
-
-
-
-
Notes
-
The JSON file is expected to follow a specific structure with atomic data under
-“PC_Compounds” -> “atoms” and coordinates under “coords” -> “conformers”.
-The atomic symbols are mapped from atomic numbers using a predefined dictionary.
-The JSON file is removed after conversion.
-
Examples
-
>>> convert_json_to_xyz("molecule","/path/to/directory")
-File successfully converted and saved at /path/to/directory/molecule.xyz
-
The name of the XYZ file (without the .xyz extension).
-
-
directorystr, optional
The directory where the XYZ file is located. Default is a subdirectory “geometries” within DATA_DIR.
-
-
-
-
Returns:
-
-
tuple
A tuple containing the identifier from the second line of the XYZ file and a
-DataFrame containing the atomic coordinates with columns [“Atom”, “X”, “Y”, “Z”].
-
-
-
-
-
Notes
-
-
-
The XYZ file is expected to have the following format:
-
The first line contains the number of atoms (ignored).
-
The second line contains a comment or identifier.
-
Subsequent lines contain atomic coordinates in the format: Atom X Y Z.
An instance of ME_Solver solver which contains the following attributes:
-
-
-
-
Returns:
-
-
numpy.ndarray
The dephasing equilibrium state as a density matrix.
-
-
-
-
-
-
-
-
-qDNA.evaluation.get_therm_eq_state(me_solver)
-
Calculate the thermal equilibrium state.
-
-
Parameters:
-
-
me_solverobject
An instance of a master equation solver which contains the tight-binding Hamiltonian (tb_ham)
-and the Lindblad dissipation parameters (lindblad_diss).
-
-
-
-
Returns:
-
-
numpy.ndarray
The thermal equilibrium state of the system. If the temperature is zero, returns the ground state.
-Otherwise, returns the thermal equilibrium state as a density matrix in the local basis.
-
-
-
-
-
Notes
-
-
The function first checks if the temperature is zero. If so, it returns the ground state.
-
For non-zero temperatures, it calculates the equilibrium values for each eigenvalue of the Hamiltonian,
-normalizes them, and transforms the resulting diagonal matrix to the local basis.
Calculates the time-averaged/ static population of the end state when initially
-in the initial state.
-
-
Parameters:
-
-
eigsnp.ndarray
Eigenvector matrix.
-
-
init_stateint
Initial state in the basis.
-
-
end_stateint
End state in the basis.
-
-
-
-
Returns:
-
-
float
The static population of the end state.
-
-
-
-
-
-
-
-
-qDNA.utils.calc_frequencies(eigv)
-
Calculates the frequencies corresponding to energy level differences.
-
-
Parameters:
-
-
eigvnp.ndarray
Eigenvalue vector.
-
-
-
-
Returns:
-
-
np.ndarray
A list of frequencies.
-
-
-
-
-
-
-
-
-qDNA.utils.calc_ipr_hamiltonian(eigs)
-
Calculates the inverse participation ratio (IPR) for each eigenstate of the
-Hamiltonian.
-
-
Parameters:
-
-
eigsnp.ndarray
Eigenvector matrix.
-
-
-
-
Returns:
-
-
list of float
The IPR values for each eigenstate.
-
-
-
-
-
Notes
-
-
Note
-
The IPR is a measure of the localization of an eigenstate. It is defined as the sum of the squared coefficients of the
-eigenvector. The IPR ranges from 1 to N, where N is the dimension of the Hilbert space. The IPR values can be used to
-distinguish between localized and delocalized eigenstates.
Calculate the trace distance between two density matrices. The trace distance is
-a measure of the distinguishability between two quantum states represented by their
-density matrices. It is defined as half the trace of the absolute difference between
-the two density matrices.
-
-
Parameters:
-
-
dm_1numpy.ndarray
The first density matrix.
-
-
dm_2numpy.ndarray
The second density matrix.
-
-
-
-
Returns:
-
-
float
The trace distance between the two density matrices.
-
-
-
-
Raises:
-
-
ValueError
If the density matrices do not have the same shape.
Eric R. Bittner. Frenkel exciton model of ultrafast excited state dynamics in AT DNA double helices. Journal of Photochemistry and Photobiology A: Chemistry, 190:328–334, 2007. doi:10.1016/j.jphotochem.2006.12.007.
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-[CMB08]
-
E. M. Conwell, P. M. McLaughlin, and S. M. Bloch. Charge-Transfer Excitons in DNA. The Journal of Physical Chemistry B, 112:2268–2272, 2008. doi:10.1021/jp077344x.
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-[CKK04]
-
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-[CHCK05]
-
C. Crespo-Hernandez, B. Cohen, and B. Kohler. Base stacking controls excited-state dynamics in A·T DNA. Nature, 436:1141–1144, 2005. doi:10.1038/nature03933.
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-[GB10]
-
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-[HRA24]
-
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-[KS19]
-
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-[LS19]
-
Konstantinos Lambropoulos and Constantinos Simserides. Tight-binding modeling of nucleic acid sequences: Interplay between various types of order or disorder and charge transport. Symmetry, 11:968, 2019. doi:10.3390/sym11080968.
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-[MSF21]
-
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-[MA05]
-
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-[Sim14]
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The text of this documentation is licensed under the Creative Commons Attribution 3.0 Unported License.
-Unless specifically indicated otherwise, all code samples, the source code of qDNA, and its reproductions in this documentation, are licensed under the terms of the 3-clause BSD license, reproduced below.
The canonical form of this license is available at https://creativecommons.org/licenses/by/3.0/, which should be considered the binding version of this license.
-It is reproduced here for convenience.
-
THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS
-PUBLIC LICENSE (“CCPL” OR “LICENSE”). THE WORK IS PROTECTED BY COPYRIGHT AND/OR
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-CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
-
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Welcome to the QuantumDNA Jupyter Notebook Tutorials! These tutorials and demonstrations are designed to help users explore and
-understand the functionalities of the qDNA package through practical examples.
-
For a detailed description of the classes and functions used in these tutorials, visit the API documentation.
The Jupyter notebooks in the tutorials folder provide step-by-step demonstrations of various features and functionalities of the qDNA package.
-Each tutorial focuses on a specific aspect, helping you get started with quantum physical description of DNA and applications of quantum biology.
Reproduces all the figures presented in the reference paper [HRA24].
-This serves as a comprehensive example of qDNA’s visualization and analysis features.
-
-
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.
-
-
Tight_Binding_Method
Explore predefined and custom tight-binding models. Includes calculating time-averaged exciton
-populations in the Fishbone Ladder Model (FLM) and simulating charge transfer in the
-Fenna-Matthews-Olson (FMO) complex.
-
-
Environment_Simulation
Model DNA excited-state relaxation and environmental interactions. This tutorial covers dephasing
-and thermalization models inspired by Quantum Biology.
-
-
Visualization
Use qDNA’s built-in plotting routines for effective result visualization. Learn to create custom
-visualizations tailored to your data.
-
-
Evaluation
Perform calculations for observables like exciton lifetimes, average charge separation, and dipole
-moments. Includes parallelization features for efficient computation.
QuantumDNA: A Toolbox for Evaluating Excited States and Charge Transfer in DNA
-
Welcome to QuantumDNA – a comprehensive tool for performing quantum mechanical calculations on DNA.
-QuantumDNA leverages the formalism of open quantum systems, utilizing tight-binding Hamiltonians to model DNA at a quantum level.
-This tool can handle a variety of tight-binding models and allows users to input custom parameters derived from ab initio calculations or experimental data.
-Furthermore, QuantumDNA enables users to define unique models, making it highly adaptable to a wide range of research needs.
-
Designed with accessibility in mind, QuantumDNA includes a user-friendly interface to make quantum calculations accessible to researchers of all technical backgrounds.
-
Some of the core functionalities of QuantumDNA include the calculation of exciton lifetimes, average charge separation, and dipole moments for excited states along DNA strands [HRA24].
Welcome to the installation guide for QuantumDNA. Follow the steps below to install the package, set up a virtual environment, and start using qDNA either through a Graphical User Interface or a Jupyter Notebook.
If all tests pass, the package has been successfully installed! You can now:
-
-
Launch the Graphical User Interface or
-
Start using qDNA inside a Jupyter Notebook.
-
-
Run the activation script as mentioned in the platform-specific instructions to start the Graphical User Interface or a Jupyter Notebook. It is recommended to always run the activation script.
-