arXiv subjects

Michael Zwolak

Publications and source records attributed to Michael Zwolak.

71 records · Page 4Linked to original sources

arXiv2010

Quantum Darwinism in non-ideal environments

Quantum Darwinism provides an information-theoretic framework for the emergence of the objective, classical world from the quantum substrate. The key to this emergence is the proliferation of redundant information throughout the environment where observers can then intercept it. We study this process for a purely decohering interaction when the environment, E, is in a non-ideal (e.g., mixed) initial state. In the case of good decoherence, that is, after the pointer states have been unambiguously selected, the mutual information between the system, S, and an environment fragment, F, is given solely by F's entropy increase. This demonstrates that the environment's capacity for recording the state of S is directly related to its ability to increase its entropy. Environments that remain nearly invariant under the interaction with S, either because they have a large initial entropy or a misaligned initial state, therefore have a diminished ability to acquire information. To elucidate the concept of good decoherence, we show that - when decoherence is not complete - the deviation of the mutual information from F's entropy change is quantified by the quantum discord, i.e., the excess mutual information between S and F is information regarding the initial coherence between pointer states of S. In addition to illustrating these results with a single qubit system interacting with a multi-qubit environment, we find scaling relations for the redundancy of information acquired by the environment that display a universal behavior independent of the initial state of S. Our results demonstrate that Quantum Darwinism is robust with respect to non-ideal initial states of the environment: the environment almost always acquires redundant information about the system but its rate of acquisition can be reduced.

quant-ph↗

arXiv2009

Quantum Darwinism in a hazy environment

Quantum Darwinism recognizes that we - the observers - acquire our information about the "systems of interest" indirectly from their imprints on the environment. Here, we show that information about a system can be acquired from a mixed-state, or hazy, environment, but the storage capacity of an environment fragment is suppressed by its initial entropy. In the case of good decoherence, the mutual information between the system and the fragment is given solely by the fragment's entropy increase. For fairly mixed environments, this means a reduction by a factor 1-h, where h is the haziness of the environment, i.e., the initial entropy of an environment qubit. Thus, even such hazy environments eventually reveal the state of the system, although now the intercepted environment fragment must be larger by ~1/(1-h) to gain the same information about the system.

quant-ph↗

arXiv2009

Effect of Noise on DNA Sequencing via Transverse Electronic Transport

Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow for rapid DNA sequencing. However, fluctuations of the environment, such as ionic and DNA motion, introduce important scattering processes that may affect the viability of this approach to sequencing. To understand this issue, we have analyzed a simple model that captures the role of this complex environment in electronic dephasing and its ability to remove charge carriers from current-carrying states. We find that these effects do not strongly influence the current distributions due to the off-resonant nature of tunneling through the nucleotides - a result we expect to be a common feature of transport in molecular junctions. In particular, only large scattering strengths, as compared to the energetic gap between the molecular states and the Fermi level, significantly alter the form of the current distributions. Since this gap itself is quite large, the current distributions remain protected from this type of noise, further supporting the possibility of using transverse electronic transport measurements for DNA sequencing.

cond-mat.soft↗

arXiv2009

Finite representations of continuum environments

Understanding dissipative and decohering processes is fundamental to the study of quantum systems. An accurate and generic method for investigating these processes is to simulate both the system and environment, which, however, is computationally very demanding. We develop a novel approach to constructing finite representations of the environment based on the influence of different frequency scales on the system's dynamics. As an illustration, we analyze a solvable model of an optical mode decaying into a reservoir. The influence of the environment modes is constant for small frequencies, but drops off rapidly for large frequencies, allowing for a very sparse representation at high frequencies that gives a significant computational speedup in simulating the environment. This approach provides a general framework for simulating open quantum systems.

quant-ph↗

arXiv2009

Quantized ionic conductance in nanopores

Ionic transport in nanopores is a fundamentally and technologically important problem in view of its occurrence in biological processes and its impact on novel DNA sequencing applications. Using microscopic calculations, here we show that ion transport may exhibit strong nonlinearities as a function of the pore radius reminiscent of the conductance quantization steps as a function of the transverse cross section of quantum point contacts. In the present case, however, conductance steps originate from the break up of the hydration layers that form around ions in aqueous solution. Once in the pore, the water molecules form wavelike structures due to multiple scattering at the surface of the pore walls and interference with the radial waves around the ion. We discuss these effects as well as the conditions under which the step-like features in the ionic conductance should be experimentally observable.

cond-mat.soft↗

arXiv2007

Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport

We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA bases. We find that the intrinsic measurement bandwidth of the electrodes helps the detection of single bases by averaging over the current distributions of each base. We also find that although the overall magnitude of the current may change dramatically with different detection conditions, the intrinsic distinguishability of the bases is not significantly affected by pore size and transverse field strength. The latter is the result of very effective stabilization of the DNA by the transverse field induced by the probes, so long as that field is much larger than the field that drives DNA through the pore. In addition, the ions and water together effectively screen the charge on the nucleotides, so that the electron states participating in the transport properties of the latter ones resemble those of the uncharged species. Finally, water in the environment has negligible direct influence on the transverse electrical current.

cond-mat.soft↗

arXiv2007

Physical approaches to DNA sequencing and detection

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single nucleotide level. This is in sharp contrast to current techniques and instruments which probe, through chemical elongation, electrophoresis, and optical detection, length differences and terminating bases of strands of DNA. In this Colloquium we review several physical approaches to DNA detection that have the potential to deliver fast and low-cost sequencing. Center-fold to these approaches is the concept of nanochannels or nanopores which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. We emphasize the physics behind these methods and ideas, critically describe their advantages and drawbacks, and discuss future research opportunities in this field.

physics.bio-ph↗

arXiv2007

Reply to Comment on "Dynamical corrections to the DFT-LDA electron conductance in nanoscale systems"

We reply to the comment by Jung, Bokes, and Godby (arXiv:0706.0140) on our paper Phys. Rev. Lett. 94, 186810 (2005). We show that the results in their comment should not be taken as an indication that the viscosity corrections to the conductance of real nanoscale structures are small. A more accurate treatment of the density and current density distribution and of the electronic correlations may yield much larger corrections in realistic systems.

cond-mat.mes-hall↗

arXiv2007

Numerical ansatz for solving integro-differential equations with increasingly smooth memory kernels: spin-boson model and beyond

We present an efficient and stable numerical ansatz for solving a class of integro-differential equations. We define the class as integro-differential equations with increasingly smooth memory kernels. The resulting algorithm reduces the computational cost from the usual T^2 to T*C(T), where T is the total simulation time and C(T) is some function. For instance, C(T) is equal to lnT for polynomially decaying memory kernels. Due to the common occurrence of increasingly smooth memory kernels in physical, chemical, and biological systems, the algorithm can be applied in quite a wide variety of situations. We demonstrate the performance of the algorithm by examining two cases. First, we compare the algorithm to a typical numerical procedure for a simple integro-differential equation. Second, we solve the NIBA equations for the spin-boson model in real time.

cond-mat.other↗

arXiv2007

Comment on "Characterization of the tunneling conductance across DNA bases"

In a recent article, Zikic {\it et al.} [Phys. Rev. E {\bf 74}, 011919 (2006)] present first-principles calculations of the DNA nucleotides electrical conductance. They report qualitative and quantitative differences with previous work, in particular with that of Zwolak and Di Ventra [Nano Lett. {\bf 5}, 421 (2005)] and Lagerqvist {\it et al.} [Nano Lett. {\bf 6}, 779 (2006)]. In this comment we address the alleged discrepancies and show that Zikic {\it et al.} have seriously misread and misunderstood the existing literature. In addition, we point out the deficiencies of their approach in calculating the conductance of nucleotides and the consequent erroneous conclusions they report.

cond-mat.soft↗

arXiv2006

Fast DNA Sequencing via Transverse Electronic Transport

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, e.g., orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict and cure diseases from the perspective of the genetic makeup of each individual.

cond-mat.soft↗

arXiv2005

Inelastic current-voltage characteristics of atomic and molecular junctions

We report first-principles calculations of the inelastic current-voltage (I-V) characteristics of a gold point contact and a molecular junction in the nonresonant regime. Discontinuities in the I-V curves appear in correspondence to the normal modes of the structures. Due to the quasi-one-dimensional nature of these systems, specific modes with large longitudinal component dominate the inelastic I-V curves. In the case of the gold point contact, our results are in good agreement with recent experimental data. For the molecular junction, we find that the inelastic I-V curves are quite sensitive to the structure of the contact between the molecule and the electrodes thus providing a powerful tool to extract the bonding geometry in molecular wires.

cond-mat.mes-hall↗

arXiv2005

Theory of local heating in nanoscale conductors

We report first-principles calculations of local heating in nanoscale junctions formed by a single molecule and a gold point contact. Due to a larger heat dissipation, the single molecule heats up less than the gold point contact. We also find, at zero temperature, a threshold bias $V_{onset}$ of about 6 mV and 11 mV for the molecule and the point contact, respectively, is required to excite the smallest vibrational mode and generate heat. The latter estimate is in very good agreement with recent experimental results on the same system. At a given external bias $V$ below $V_{onset}$, heating becomes noticeable when the background temperature is on the order of $\sim e(V_{onset}-V)/k_{B}$. Above $V_{onset}$, local heating increases dramatically with increasing bias but is also considerably suppressed by thermal dissipation into the electrodes. The results provide a microscopic picture of current-induced heat generation in atomic-scale structures.

cond-mat.mes-hall↗

arXiv2005

Dynamical corrections to the DFT-LDA electron conductance in nanoscale systems

Using time-dependent current-density functional theory, we derive analytically the dynamical exchange-correlation correction to the DC conductance of nanoscale junctions. The correction pertains to the conductance calculated in the zero-frequency limit of time-dependent density-functional theory within the adiabatic local-density approximation. In particular, we show that in linear response the correction depends non-linearly on the gradient of the electron density; thus, it is more pronounced for molecular junctions than for quantum point contacts. We provide specific numerical examples to illustrate these findings.

cond-mat.mes-hall↗

arXiv2004

Inelastic effects on the transport properties of alkanethiols

Using first-principles approaches we investigate local heating and the inelastic contribution to the current for various alkanethiols sandwiched between metal electrodes. In the absence of good heat dissipation into the bulk electrodes, we find that the local temperature of the alkanethiols is relatively insensitive to their length. This is due to the rates of heating and cooling processes scaling similarly with length. On the other hand, when considering heat dissipation into the bulk electrodes, the local temperature of alkanethiols decreases as their length increases. We also find that the inelastic scattering profile displays an odd-even effect with length which compares well with experimental results. This effect is due to the alternating direction of the CH3 group motion with respect to current flow with increasing C atoms in the chain, and is very sensitive to the structure of the carbon-sulfur-gold bond. Inelastic scattering profiles can therefore help illuminate the bonding configuration of molecules to metallic surfaces.

cond-mat.mes-hall↗

arXiv2004

Electronic signature of DNA nucleotides via transverse transport

We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries a unique signature due to the different electronic and chemical structure of the four bases. This signature is independent of the nearest-neighbor nucleotides. Furthermore, except for the nucleotides with Guanine and Cytosine bases, we find that the difference in conductance of the nucleotides is large for most orientations of the bases with respect to the electrodes. By exploiting these differences it may be possible to sequence single-stranded DNA by scanning its length with conducting probes.

cond-mat.other↗

arXiv2004

Mixed-state dynamics in one-dimensional quantum lattice systems: a time-dependent superoperator renormalization algorithm

We present an algorithm to study mixed-state dynamics in one-dimensional quantum lattice systems. The algorithm can be used, e.g., to construct thermal states or to simulate real time evolutions given by a generic master equation. Its two main ingredients are (i) a superoperator renormalization scheme to efficiently describe the state of the system and (ii) the time evolving block decimation (TEBD) technique to efficiently update the state during a time evolution. The computational cost of a simulation increases significantly with the amount of correlations between subsystems but it otherwise depends only linearly in the system size. We present simulations involving quantum spins and fermions in one spatial dimension.

cond-mat.str-el↗