Biomedical subjects

Abraham Nitzan

Publications and source records attributed to Abraham Nitzan.

15 recordsLinked to original sources

PubMed2006

Optical properties of current carrying molecular wires.

We consider several fundamental optical phenomena involving single molecules in biased metal-molecule-metal junctions. The molecule is represented by its highest occupied and lowest unoccupied molecular orbitals, and the analysis involves the simultaneous consideration of three coupled fluxes: the electronic current through the molecule, energy flow between the molecule and electron-hole excitations in the leads, and the incident and/or emitted photon flux. Using a unified theoretical approach based on the nonequilibrium Green's function method we derive expressions for the absorption line shape (not an observable but a useful reference for considering yields of other optical processes) and for the current induced molecular emission in such junctions. We also consider conditions under which resonance radiation can induce electronic current in an unbiased junction. We find that current driven molecular emission and resonant light induced electronic currents in single molecule junctions can be of observable magnitude under appropriate realizable conditions. In particular, light induced current should be observed in junctions involving molecular bridges that are characterized by strong charge-transfer optical transitions. For observing current induced molecular emission we find that in addition to the familiar need to control the damping of molecular excitations into the metal substrate the phenomenon is also sensitive to the way in which the potential bias is distributed on the junction.

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PubMed2006

Molecular transport junctions: current from electronic excitations in the leads.

Using a model comprising a two-level bridge connecting free electron reservoirs we show that coupling of a molecular bridge to electron-hole excitations in the leads can markedly effect the source-drain current through a molecular junction. In some cases, e.g., molecules that exhibit strong charge transfer transitions, the contribution from electron-hole excitations can exceed the Landauer elastic current and dominate the observed conduction.

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PubMed2006

Electron transfer mechanism and the locality of the system-bath interaction: a comparison of local, semilocal, and pure dephasing models.

We simulate the effects of two types of dephasing processes, a nonlocal dephasing of system eigenstates and a dephasing of semilocal eigenstates, on the rate and mechanism of electron transfer (eT) through a series of donor-bridge-acceptor systems, D-B(N)-A, where N is the number of identical bridge units. Our analytical and numerical results show that pure dephasing, defined as the perturbation of system eigenstates through the system-bath interaction, does not disrupt coherent eT because it induces no localization; electron transfer may proceed through superexchange in a system undergoing only pure dephasing. A more physically reasonable description may be obtained via a system-bath interaction that reflects the perturbation of more local electronic structure by local nuclear distortions and dipole interactions. The degree of locality of this interaction is guided by the structure of the system Hamiltonian and by the nature of the measurement performed on the system (i.e., the nature of the environment). We compare our result from this "semilocal" model with an even more local phenomenological dephasing model. We calculate electron transfer rate by obtaining nonequilibrium steady-state solutions for the elements of a reduced density matrix; a semigroup formalism is used to write down the dissipative part of the equation of motion.

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PubMed2006

Molecular heat pump.

We propose a molecular device that pumps heat against a thermal gradient. The system consists of a molecular element connecting two thermal reservoirs that are characterized by different spectral properties. The pumping action is achieved by applying an external force that periodically modulates molecular levels. This modulation affects periodic oscillations of the internal temperature of the molecule and the strength of its coupling to each reservoir resulting in a net heat flow in the desired direction. The heat flow is examined in the slow and fast modulation limits and for different modulation wave forms, thus making it possible to optimize the device performance.

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PubMed2005

Current-induced light emission and light-induced current in molecular-tunneling junctions.

The interaction of metal-molecule-metal junctions with light is considered within a simple generic model. We show, for the first time, that light-induced current in unbiased junctions can take place when the bridging molecule is characterized by a strong charge-transfer transition. The same model shows current-induced light emission under potential bias that exceeds the molecular excitation energy. Results based on realistic estimates of molecule-lead coupling and molecule-radiation field interaction suggest that both effects should be observable.

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PubMed2005

Path-integral computations of tunneling processes.

The application of the path-integral methodology of Chandler and Wolynes [D. Chandler and P. G. Wolynes, J. Chem. Phys. 74, 4078 (1981)] to the calculation of one-electron-tunneling probabilities is revisited. We show that the evaluation of the kink free energy that is related to the tunneling splitting is associated with "polymer bead" distributions over a continuous distribution of scaled barriers, which makes both the calculation and its physical interpretation relatively difficult. In particular, we find that relative to other available techniques the method converges slowly and suffers from inaccuracies associated with the finite-temperature aspect of the calculation, and that past tentative identification of the bead distribution over the barrier with a physical picture of a "tunneling path" should be reassessed.

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PubMed2005

Heat rectification in molecular junctions.

Heat conduction through molecular chains connecting two reservoirs at different temperatures can be asymmetric for forward and reversed temperature biases. Based on analytically solvable models and on numerical simulations we show that molecules rectify heat when two conditions are satisfied simultaneously: the interactions governing the heat conduction are nonlinear, and the junction has some structural asymmetry. We consider several simplified models where a two-level system (TLS) simulates a highly anharmonic vibrational mode, and asymmetry is introduced either through different coupling of the molecule to the contacts, or by considering internal molecular asymmetry. In the first case, we present analytical results for the asymmetric heat current flowing through a single anharmonic mode using different forms for the TLS-reservoirs coupling. We also demonstrate numerically, studying a realistic molecular model, that a uniform anharmonic molecular chain connecting asymmetrically two thermal reservoirs rectifies heat. This effect is stronger for longer chains, where nonlinear interactions dominate the transfer process. When asymmetry is related to the internal level structure of the molecule, numerical simulations reveal a nontrivial rectification behavior. We could still explain this behavior in terms of an effective system-bath coupling. Our study suggests that heat rectification is a fundamental characteristic of asymmetric nonlinear thermal conductors. This phenomenon is important for heat control in nanodevices and for understanding of energy flow in biomolecules.

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PubMed2005

Molecular transport junctions: asymmetry in inelastic tunneling processes.

Inelastic electron tunneling spectroscopy (IETS) measurements are usually carried out in the low-voltage ("Ohmic", i.e., linear) regime where the elastic conduction/voltage characteristic is symmetric to voltage inversion. Inelastic features, normally observed in the second derivative d(2)I/dV(2) are also symmetric (in fact antisymmetric) in many cases, but asymmetry is sometimes observed. We show that such asymmetry can occur because of different energy dependences of the two contact self-energies. This may be attributed to differences in contact density of states (different contact material) or different energy dependence of the coupling (STM-like geometry or asymmetric positioning of molecular vibrational modes in the junction). The asymmetry scales with the difference between the energy dependence of these self-energies and disappears when this dependence is the same for the two contacts. Our nonequilibrium Green function approach goes beyond proposed WKB scattering theory in properly accounting for Pauli exclusion, as well as providing a path to generalizations, including consideration of phonon dynamics and higher-order perturbation theory.

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PubMed2005

Spin-boson thermal rectifier.

Rectification of heat transfer in nanodevices can be realized by combining the system inherent anharmonicity with structural asymmetry. We analyze this phenomenon within the simplest anharmonic system-a spin-boson nanojunction model. We consider two variants of the model that yield, for the first time, analytical solutions: a linear separable model in which the heat reservoirs contribute additively, and a nonseparable model suitable for a stronger system-bath interaction. Both models show asymmetric (rectifying) heat conduction when the couplings to the heat reservoirs are different.

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PubMed2005

Hysteresis, switching, and negative differential resistance in molecular junctions: a polaron model.

Within a simple mean-field model (self-consistent Hartree approximation) we discuss the possibility of polaron formation on a molecular wire as a mechanism for negative differential resistance (NDR), switching, and/or hysteresis in the I-V characteristic of molecular junctions. This mechanism differs from earlier proposed mechanisms of charging and conformational change. The polaron model captures the essential physics and provides qualitative correspondence with experimental data. The importance of active redox centers in the molecule is indicated.

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PubMed2004

Inelastic electron tunneling spectroscopy in molecular junctions: peaks and dips.

We study inelastic electron tunneling through a molecular junction using the nonequilibrium Green's function formalism. The effect of the mutual influence between the phonon and the electron subsystems on the electron tunneling process is considered within a general self-consistent scheme. Results of this calculation are compared to those obtained from the simpler Born approximation and the simplest perturbation theory approaches, and some shortcomings of the latter are pointed out. The self-consistent calculation allows also for evaluating other related quantities such as the power loss during electron conduction. Regarding the inelastic spectrum, two types of inelastic contributions are discussed. Features associated with real and virtual energy transfer to phonons are usually observed in the second derivative of the current I with respect to the voltage Phi when plotted against Phi. Signatures of resonant tunneling driven by an intermediate molecular ion appear as peaks in the first derivative dI/dPhi and may show phonon sidebands. The dependence of the observed vibrationally induced lineshapes on the junction characteristics, and the linewidth associated with these features are also discussed.

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PubMed2003

Electron transport in molecular wire junctions.

Molecular conductance junctions are structures in which single molecules or small groups of molecules conduct electrical current between two electrodes. In such junctions, the connection between the molecule and the electrodes greatly affects the current-voltage characteristics. Despite several experimental and theoretical advances, including the understanding of simple systems, there is still limited correspondence between experimental and theoretical studies of these systems.

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PubMed2003

The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents.

A composite continuum theory for calculating ion current through a protein channel of known structure is proposed, which incorporates information about the channel dynamics. The approach is utilized to predict current through the Gramicidin A ion channel, a narrow pore in which the applicability of conventional continuum theories is questionable. The proposed approach utilizes a modified version of Poisson-Nernst-Planck (PNP) theory, termed Potential-of-Mean-Force-Poisson-Nernst-Planck theory (PMFPNP), to compute ion currents. As in standard PNP, ion permeation is modeled as a continuum drift-diffusion process in a self-consistent electrostatic potential. In PMFPNP, however, information about the dynamic relaxation of the protein and the surrounding medium is incorporated into the model of ion permeation by including the free energy of inserting a single ion into the channel, i.e., the potential of mean force along the permeation pathway. In this way the dynamic flexibility of the channel environment is approximately accounted for. The PMF profile of the ion along the Gramicidin A channel is obtained by combining an equilibrium molecular dynamics (MD) simulation that samples dynamic protein configurations when an ion resides at a particular location in the channel with a continuum electrostatics calculation of the free energy. The diffusion coefficient of a potassium ion within the channel is also calculated using the MD trajectory. Therefore, except for a reasonable choice of dielectric constants, no direct fitting parameters enter into this model. The results of our study reveal that the channel response to the permeating ion produces significant electrostatic stabilization of the ion inside the channel. The dielectric self-energy of the ion remains essentially unchanged in the course of the MD simulation, indicating that no substantial changes in the protein geometry occur as the ion passes through it. Also, the model accounts for the experimentally observed saturation of ion current with increase of the electrolyte concentration, in contrast to the predictions of standard PNP theory.

Cell Membrane Permeability↗

PubMed2003

NEGF-HF method in molecular junction property calculations.

Electron-electron interaction is an essential issue in predicting the properties of a molecular conduction junction. An accurate treatment requires taking proper account of the potential distribution across the junction as well as for the change in electronic structure under the external voltage drop. Another important point is the necessity to treat molecules as open quantum systems. In this paper we address these issues within the framework of the non-equilibrium Green's function formalism at the Hartree-Fock level (NEGF-HF), which permits a self-consistent treatment of the problem. We apply the method to study the experimentally observed asymmetry in the I-V curves with respect to polarity of voltage bias in Hg-Au junctions containing bilayers of alkanethiols of various chain lengths. The origin of the effect is suggested to be the asymmetric behavior of the character of the highest occupied molecular orbital (HOMO) of the junction at opposite biases, which leads to different effective barriers for electron transfer across the junction at opposite signs of the voltage drop. The calculated potential profile shows the capacitor-like nature for the junction with the weak link.

Algorithms↗

PubMed2002

Molecular wires acting as coherent quantum ratchets.

The effect of laser fields on electron transport through a molecular wire weakly coupled to two leads is investigated. The molecular wire acts as a coherent quantum ratchet if the molecule is composed of periodically arranged, asymmetric chemical groups. This setup presents a quantum rectifier with a finite dc response in the absence of a static bias. The nonlinear current is evaluated in closed form within the Floquet basis of the isolated, driven wire. The current response reveals multiple current reversals together with a nonlinear dependence on the amplitude and the frequency of the laser field. The current saturates for long wires at a nonzero value, while it may change sign upon decreasing its length.

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