J.M. Thijssen
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1
In this thesis, we implemented a Büttiker probe (BP) in a 6-helicene model based on the previous work of Geyer [9]. The probe mimics the decoherence in a two-terminal CISS experiment. Moreover, this enables us to magnetise both leads independently. By altering the magnetisation of the leads and the orientation of the Büttiker probe, we were able to analyse many possible experimental setups. This enabled us to express the current difference in terms of bias voltage, magnetisation and BP orientation, where the latter was the research objective.
Isotropic Büttiker probes lead to a CISS effect, which is absent in a coherent electron transport model. Further research is needed to determine the exact nature of the numerical errors in our isotropic BP experiments. The results of anisotropic BPs can be explained assuming that the current difference is linear in the anisotropy of the BP. Further research is needed to strengthen this conjecture. These results are supported for lead magnetisation along an axis, perpendicular to the helical axis of the molecule, as well as magnetisation along this helical axis. ...
In this thesis, we implemented a Büttiker probe (BP) in a 6-helicene model based on the previous work of Geyer [9]. The probe mimics the decoherence in a two-terminal CISS experiment. Moreover, this enables us to magnetise both leads independently. By altering the magnetisation of the leads and the orientation of the Büttiker probe, we were able to analyse many possible experimental setups. This enabled us to express the current difference in terms of bias voltage, magnetisation and BP orientation, where the latter was the research objective.
Isotropic Büttiker probes lead to a CISS effect, which is absent in a coherent electron transport model. Further research is needed to determine the exact nature of the numerical errors in our isotropic BP experiments. The results of anisotropic BPs can be explained assuming that the current difference is linear in the anisotropy of the BP. Further research is needed to strengthen this conjecture. These results are supported for lead magnetisation along an axis, perpendicular to the helical axis of the molecule, as well as magnetisation along this helical axis.
Chapter 1 serves as an introduction to the field of molecular electronics, discussing the origin of the field and landmarks, and provides theoretical considerations concerning charge transport in metal-molecule-metal junctions. Finally, a general introduction on quantuminterference is given.
Chapter 2 broadly discusses the MCBJ experimental method, where the mechanical and electrical equipment for two set-ups is discussed alongside the modus operandi for doing fast-breaking experiments. Subsequently, data analysis using machine learning methods will be discussed. Ultimately, reference measurements on bare gold electrodes and an oligo(phenylene-ethynylene) (OPE) molecule were performed as a benchmark for roomtemperature high-bias and current-voltage characterization on other molecules. For high-bias experiments we note that measurements can be performed reliably and shows in the case of the OPE molecule that its conductance increases as a function of applied bias voltage in agreement with the single-level model.
Chapter 3 revolves around the study of the electrical properties of molecules containing a cyclophane core. For molecules containing a paracyclophane core we observe that ortho-connections suppress the conductance more so than a para-connection as compared to a meta-connection. Additionally, we find para-connections to cyclophane units to be the common denominator in showing mechanosensitive behaviour, i.e., in which themolecule changes its conductance strongly due to mechanical deformation.
In Chapter 4 we have developed a method to reconstruct the observed destructive quantum interference dip in a molecule with a naphthalenophane core, opting for establishing a closer link between theory and experiment. Two complementary techniques at room temperature were used for this study: (i) the MCBJ technique, which allows for large statistical sampling fortifying the robustness of the dip reconstructionmethod; (ii) the alternating-current scanning tunneling microscopy break-junction technique (ACSTM- BJ) allowing for the continuous simultaneous measurements of the conductance and the corresponding thermopower, providing additional information on the destructive quantum interference dip. We find a sinusoidal response of the thermopower across the conductance dip without a sign change. Theoretical calculations on conductance and thermopower including electrode distance and energy alignment variations emphasize the crucial role of thermal fluctuations at roomtemperature.
For Chapter 5 we change pace and shift towards molecular switches. Three differently anchored norbordaniene molecules were investigated under high-bias circumstances. For all compounds, we find two conductance states. We find no full switching between two conductance states, as the two states are present across a wide-range of applied bias voltages and no clear population differences between the states are found. Alternatively to the explanation of the switching within the molecule itself, one can argue that either we observe two different configurations of the molecular junction or that interactions of the short linkers of the molecules, by interactions with the gold surface, quench the switching between the states unlike previous published results using a molecule with the same backbone but with longer linkers.
Chapter 6 investigates the effect of chemical design on the conductance of macrocyclic structures, studying them with different substituents. We observe a clear difference in conductance between para- and meta-connections in the core using thiophene and benzene substituents, consecutively. Here, the created para- connected path shows a higher conductance than its meta counterpart. Different connections, para and meta, in molecules with the same backbone show less of an effect on the conductance of the molecular junction. Additionally, preliminary results of one of the compounds using room temperature current-voltage characteristics shows a negative differential conductance and hysteretic behaviour.
Lastly, in Chapter 7 we conclude the obtained results from this dissertation and place them in a broader perspective.
...
Chapter 1 serves as an introduction to the field of molecular electronics, discussing the origin of the field and landmarks, and provides theoretical considerations concerning charge transport in metal-molecule-metal junctions. Finally, a general introduction on quantuminterference is given.
Chapter 2 broadly discusses the MCBJ experimental method, where the mechanical and electrical equipment for two set-ups is discussed alongside the modus operandi for doing fast-breaking experiments. Subsequently, data analysis using machine learning methods will be discussed. Ultimately, reference measurements on bare gold electrodes and an oligo(phenylene-ethynylene) (OPE) molecule were performed as a benchmark for roomtemperature high-bias and current-voltage characterization on other molecules. For high-bias experiments we note that measurements can be performed reliably and shows in the case of the OPE molecule that its conductance increases as a function of applied bias voltage in agreement with the single-level model.
Chapter 3 revolves around the study of the electrical properties of molecules containing a cyclophane core. For molecules containing a paracyclophane core we observe that ortho-connections suppress the conductance more so than a para-connection as compared to a meta-connection. Additionally, we find para-connections to cyclophane units to be the common denominator in showing mechanosensitive behaviour, i.e., in which themolecule changes its conductance strongly due to mechanical deformation.
In Chapter 4 we have developed a method to reconstruct the observed destructive quantum interference dip in a molecule with a naphthalenophane core, opting for establishing a closer link between theory and experiment. Two complementary techniques at room temperature were used for this study: (i) the MCBJ technique, which allows for large statistical sampling fortifying the robustness of the dip reconstructionmethod; (ii) the alternating-current scanning tunneling microscopy break-junction technique (ACSTM- BJ) allowing for the continuous simultaneous measurements of the conductance and the corresponding thermopower, providing additional information on the destructive quantum interference dip. We find a sinusoidal response of the thermopower across the conductance dip without a sign change. Theoretical calculations on conductance and thermopower including electrode distance and energy alignment variations emphasize the crucial role of thermal fluctuations at roomtemperature.
For Chapter 5 we change pace and shift towards molecular switches. Three differently anchored norbordaniene molecules were investigated under high-bias circumstances. For all compounds, we find two conductance states. We find no full switching between two conductance states, as the two states are present across a wide-range of applied bias voltages and no clear population differences between the states are found. Alternatively to the explanation of the switching within the molecule itself, one can argue that either we observe two different configurations of the molecular junction or that interactions of the short linkers of the molecules, by interactions with the gold surface, quench the switching between the states unlike previous published results using a molecule with the same backbone but with longer linkers.
Chapter 6 investigates the effect of chemical design on the conductance of macrocyclic structures, studying them with different substituents. We observe a clear difference in conductance between para- and meta-connections in the core using thiophene and benzene substituents, consecutively. Here, the created para- connected path shows a higher conductance than its meta counterpart. Different connections, para and meta, in molecules with the same backbone show less of an effect on the conductance of the molecular junction. Additionally, preliminary results of one of the compounds using room temperature current-voltage characteristics shows a negative differential conductance and hysteretic behaviour.
Lastly, in Chapter 7 we conclude the obtained results from this dissertation and place them in a broader perspective.
In this thesis we explore the possibility of using matrix product states (MPS) to study spin-selectivity in boundary-driven electron transport through tight-binding models of chiral molecules, a novel approach in the field of CISS. To this end, we use a model proposed by Fransson in 2019, which considers interacting electrons in a Hubbard model with a spin-orbit interaction adapted from the Kane-Mele model. In this thesis work, the fermionic Hubbard model is mapped to a double spin chain using the Jordan-Wigner transformation. The state of the system is described by a matrix product density operator (MPDO) which is vectorised to a matrix product state (MPS). The system dynamics are described by a vectorised Lindblad equation. The advantage of this approach lies in the fact that it does not require the use of any systematic approximations to the Hamiltonian, in contrast to previous studies. The developed method is validated against the results of previous works studying the boundary-driven Heisenberg-XXZ model and the boundary-driven Hubbard model.
The method is shown to be capable of reproducing chirality-induced spin-selective effects for short chains. The results of this study show a finite magnetocurrent that is odd in bias voltage with an associated magnetoresistance of less than 1%. This is in line with previous studies of this model, but two orders of magnitude lower than experimentally measured values. However, these results are obtained using highly inflated values for the spin-orbit interaction strength. In multiple cases, the results do not satisfy the Onsager-Casimir and Büttiker reciprocity principles, which state that the magnetocurrent should vanish in the low-driving and in the non-interacting regimes. Moreover, the continuity of the current in the steady state was not fully satisfied.
We provide evidence that indicates these problems result from the time-integration error introduced by the Suzuki-Trotter decomposition. We expect that these can be mitigated using higher order time-integration schemes. From the results of this study we can conclude that matrix product states are a viable tool to study CISS in bound-electron transport. However, the method presented in this thesis suffer from numerical errors. We present several suggestions for improvement which address these shortcomings.
...
In this thesis we explore the possibility of using matrix product states (MPS) to study spin-selectivity in boundary-driven electron transport through tight-binding models of chiral molecules, a novel approach in the field of CISS. To this end, we use a model proposed by Fransson in 2019, which considers interacting electrons in a Hubbard model with a spin-orbit interaction adapted from the Kane-Mele model. In this thesis work, the fermionic Hubbard model is mapped to a double spin chain using the Jordan-Wigner transformation. The state of the system is described by a matrix product density operator (MPDO) which is vectorised to a matrix product state (MPS). The system dynamics are described by a vectorised Lindblad equation. The advantage of this approach lies in the fact that it does not require the use of any systematic approximations to the Hamiltonian, in contrast to previous studies. The developed method is validated against the results of previous works studying the boundary-driven Heisenberg-XXZ model and the boundary-driven Hubbard model.
The method is shown to be capable of reproducing chirality-induced spin-selective effects for short chains. The results of this study show a finite magnetocurrent that is odd in bias voltage with an associated magnetoresistance of less than 1%. This is in line with previous studies of this model, but two orders of magnitude lower than experimentally measured values. However, these results are obtained using highly inflated values for the spin-orbit interaction strength. In multiple cases, the results do not satisfy the Onsager-Casimir and Büttiker reciprocity principles, which state that the magnetocurrent should vanish in the low-driving and in the non-interacting regimes. Moreover, the continuity of the current in the steady state was not fully satisfied.
We provide evidence that indicates these problems result from the time-integration error introduced by the Suzuki-Trotter decomposition. We expect that these can be mitigated using higher order time-integration schemes. From the results of this study we can conclude that matrix product states are a viable tool to study CISS in bound-electron transport. However, the method presented in this thesis suffer from numerical errors. We present several suggestions for improvement which address these shortcomings.
In this thesis the hydrodynamic limit of the Freezing Model is studied. The model consists of an integer line on which particles can get frozen to different degrees, analogous to jumping to another integer line, with certain rates and can get unfrozen with certain rates per frozen layer. The main result of the thesis is a proof that the hydrodynamic limit for the Freezing model converges to a system of PDE’s describing the particle density for each layer, either the ground layer or a frozen one. Firstly, it is proven that the position of a random walker in the Freezing Model, appropriately scaled, converges to a so-called Switching Brownian Motion. This together with duality is used in the rest of the proof. Secondly, it is proven that the expectation of the empirical field densities of the layers converges towards the solutions of the aforementioned PDE’s. Lastly, it is proven that the variance of the empirical field density converges to 0. Under an additional diffusive scaling of the system of PDE’s for the particle densities, a condition for diffusive behaviour is set up involving the ratio of the freezing and unfreezing rates. It is shown that the PDE’s collapse into the heat equation if this condition is satisfied. Finally, the case where the condition is not satisfied is investigated. The model is then no longer memoryless like a Markov process and shows sub-diffusive behaviour. The rescaled position of a single particle then no longer converges to Brownian motion, but to Brownian motion on the time scale on which the particle occupies the ground layer. This time scale is t β−1 with 1 < β < 2. This grows slower than t for large enough t. Additionally, simulations in Python were built to show that the model exhibits diffusive or nondiffusive behaviour depending on the jump rates of the process. Before everything, some mathematical preliminaries about probability theory, Markov theory, random walks and duality are given. ...
In this thesis the hydrodynamic limit of the Freezing Model is studied. The model consists of an integer line on which particles can get frozen to different degrees, analogous to jumping to another integer line, with certain rates and can get unfrozen with certain rates per frozen layer. The main result of the thesis is a proof that the hydrodynamic limit for the Freezing model converges to a system of PDE’s describing the particle density for each layer, either the ground layer or a frozen one. Firstly, it is proven that the position of a random walker in the Freezing Model, appropriately scaled, converges to a so-called Switching Brownian Motion. This together with duality is used in the rest of the proof. Secondly, it is proven that the expectation of the empirical field densities of the layers converges towards the solutions of the aforementioned PDE’s. Lastly, it is proven that the variance of the empirical field density converges to 0. Under an additional diffusive scaling of the system of PDE’s for the particle densities, a condition for diffusive behaviour is set up involving the ratio of the freezing and unfreezing rates. It is shown that the PDE’s collapse into the heat equation if this condition is satisfied. Finally, the case where the condition is not satisfied is investigated. The model is then no longer memoryless like a Markov process and shows sub-diffusive behaviour. The rescaled position of a single particle then no longer converges to Brownian motion, but to Brownian motion on the time scale on which the particle occupies the ground layer. This time scale is t β−1 with 1 < β < 2. This grows slower than t for large enough t. Additionally, simulations in Python were built to show that the model exhibits diffusive or nondiffusive behaviour depending on the jump rates of the process. Before everything, some mathematical preliminaries about probability theory, Markov theory, random walks and duality are given.
In this report a three dimensional model is constructed to describe the motion of the centre of mass, with the purpose to determine the spring constant and the rest length in a simple prosthetic leg. The research question is: can a three dimensional spring-mass model accurately track the centre of mass and can this be used to determine the optimal properties of the spring of a simple prosthetic leg?
The spring mass model consists of two springs connected to the ground and the centre of mass. The springs do not exert a force on the centre of mass if they are extended. The model incorporates steps by moving the ground connection points instantaneously over fixed points on a rail. The model can be used in two distinct ways. The first generates a periodic trajectory by finding the optimal initial positions y0 and z0 (PPFA) and the second finds the optimal spring parameters k and u to fit a data set (DFA). The optimal conditions are found by discretizing the parameter space and using an iterative process. The space around the best parameters becomes the parameter space for the next iteration.
The PPFA shows that the initial lateral displacement is nearly constant with respect to the spring constant when the rest length is chosen such that the centre of mass is at constant height if the model is stationary. The PPFA also shows that there are two distinct y-trajectories possible for walking. Running, however, has only one trajectory. Several versions of the model are fit to the data: only discretised step widths, discretised step widths and a x0-offset, and distinct legs. There is not much difference between these models. The x0-offset is only Δs = -0.02m confirming that the position of the feet does align with the extreme values of the y- and z-position. The model fits the general characteristics well but fine details in the motion are lost. Future research should investigate how cumbersome these deviations of the data are perceived by people using a simple prosthetic. ...
In this report a three dimensional model is constructed to describe the motion of the centre of mass, with the purpose to determine the spring constant and the rest length in a simple prosthetic leg. The research question is: can a three dimensional spring-mass model accurately track the centre of mass and can this be used to determine the optimal properties of the spring of a simple prosthetic leg?
The spring mass model consists of two springs connected to the ground and the centre of mass. The springs do not exert a force on the centre of mass if they are extended. The model incorporates steps by moving the ground connection points instantaneously over fixed points on a rail. The model can be used in two distinct ways. The first generates a periodic trajectory by finding the optimal initial positions y0 and z0 (PPFA) and the second finds the optimal spring parameters k and u to fit a data set (DFA). The optimal conditions are found by discretizing the parameter space and using an iterative process. The space around the best parameters becomes the parameter space for the next iteration.
The PPFA shows that the initial lateral displacement is nearly constant with respect to the spring constant when the rest length is chosen such that the centre of mass is at constant height if the model is stationary. The PPFA also shows that there are two distinct y-trajectories possible for walking. Running, however, has only one trajectory. Several versions of the model are fit to the data: only discretised step widths, discretised step widths and a x0-offset, and distinct legs. There is not much difference between these models. The x0-offset is only Δs = -0.02m confirming that the position of the feet does align with the extreme values of the y- and z-position. The model fits the general characteristics well but fine details in the motion are lost. Future research should investigate how cumbersome these deviations of the data are perceived by people using a simple prosthetic.
with traditional numerical methods, a new field has emerged which incorporates
the residual of a PDE into the loss function of an Artificial Neural Network. This
method is called Physics-Informed Neural Network (PINN). In this thesis, we study dense neural networks (DNNs), including codes developed in the context of this bachelor project. We derive the backpropagation equations necessary for training and use different configurations in a DNN to test its interpolating accuracy. We distinguish between a-PINNs which use automatic differentiation to evaluate a PDE, and n-PINNs which approximate differential operators in a PDE with numerical differentiation. We compare both PINNs on the harmonic oscillator, the 1D heat equation and the 1-soliton and 2-soliton solutions of the Korteweg-De Vries (KdV) equation. Both PINNs could accurately converge to the solution, except to the 2-soliton solution, where the a-PINN outperformed the n-PINN. Furthermore, we tested a highly nonlinear problem of the KdV equation, which can be described by a train of solitons. We observed that PINNs are inaccurate if insufficient training samples are used for training. Adding training samples on the interior from a numerical solution leads to a good qualitative agreement, though more effort is required to find a better network configuration to obtain more accurate predictions.
Additionally, PINNs were used for inverse problems to derive an unknown coefficient in a PDE and proved to be highly accurate for noiseless data. When we
generated training samples with 10% noise from a uniform distribution, the PINN
results’ relative error stayed within a margin of under 2%. However, inverse PINNs are much more inefficient compared to nonlinear least squares methods like the Levenberg–Marquardt algorithm.
As of now, PINNs are still very early in development and stand no match against
traditional numerical methods to a known PDE. They may, however, provide a
useful alternative in the future as they are constantly being improved. ...
with traditional numerical methods, a new field has emerged which incorporates
the residual of a PDE into the loss function of an Artificial Neural Network. This
method is called Physics-Informed Neural Network (PINN). In this thesis, we study dense neural networks (DNNs), including codes developed in the context of this bachelor project. We derive the backpropagation equations necessary for training and use different configurations in a DNN to test its interpolating accuracy. We distinguish between a-PINNs which use automatic differentiation to evaluate a PDE, and n-PINNs which approximate differential operators in a PDE with numerical differentiation. We compare both PINNs on the harmonic oscillator, the 1D heat equation and the 1-soliton and 2-soliton solutions of the Korteweg-De Vries (KdV) equation. Both PINNs could accurately converge to the solution, except to the 2-soliton solution, where the a-PINN outperformed the n-PINN. Furthermore, we tested a highly nonlinear problem of the KdV equation, which can be described by a train of solitons. We observed that PINNs are inaccurate if insufficient training samples are used for training. Adding training samples on the interior from a numerical solution leads to a good qualitative agreement, though more effort is required to find a better network configuration to obtain more accurate predictions.
Additionally, PINNs were used for inverse problems to derive an unknown coefficient in a PDE and proved to be highly accurate for noiseless data. When we
generated training samples with 10% noise from a uniform distribution, the PINN
results’ relative error stayed within a margin of under 2%. However, inverse PINNs are much more inefficient compared to nonlinear least squares methods like the Levenberg–Marquardt algorithm.
As of now, PINNs are still very early in development and stand no match against
traditional numerical methods to a known PDE. They may, however, provide a
useful alternative in the future as they are constantly being improved.
The effect of the Breit interaction on chiral induced spin selectivity
A derivation of the Breit equation and the implementation in a simulation of electron transport
The Breit interaction has been suggested as a possible explanation, but has not yet been researched in the context of CISS.
In this thesis, first a derivation of the Breit equation is given, which in the second part is being used to construct a simulation of electron transport through a simple chiral molecule.
The spin-polarization for the transmission including the Breit interaction was compared to the case excluding the Breit interaction, and the two were found to be substantially different. From that it followed that the influence of the Breit interaction on the transport of an electron through a chiral molecule is significant and it should therefore not be disregarded in calculations on CISS. ...
The Breit interaction has been suggested as a possible explanation, but has not yet been researched in the context of CISS.
In this thesis, first a derivation of the Breit equation is given, which in the second part is being used to construct a simulation of electron transport through a simple chiral molecule.
The spin-polarization for the transmission including the Breit interaction was compared to the case excluding the Breit interaction, and the two were found to be substantially different. From that it followed that the influence of the Breit interaction on the transport of an electron through a chiral molecule is significant and it should therefore not be disregarded in calculations on CISS.
Single-qubit dynamics
Determining the density matrix of a qubit in closed and open quantum systems when considering free evolution and weak measurements
Furthermore, as an application of active particle motion, a connection is made with the Dirac equation. On the basis of this connection, a Monte Carlo method is developed to find the ground state of a Dirac equation with static potential. The core idea of this method is based on the Diffusion Monte Carlo method for the Schrödinger equation. ...
Furthermore, as an application of active particle motion, a connection is made with the Dirac equation. On the basis of this connection, a Monte Carlo method is developed to find the ground state of a Dirac equation with static potential. The core idea of this method is based on the Diffusion Monte Carlo method for the Schrödinger equation.