arXiv subjects

Andreas Hanke

Publications and source records attributed to Andreas Hanke.

At least 19 recordsLinked to original sources

arXiv2025

Higher-order exceptional points in a non-reciprocal waveguide beam splitter

Non-Hermitian systems have attracted significant interest because of their intriguing and useful properties, including exceptional points (EPs), where eigenvalues and the corresponding eigenstates of non-Hermitian operators become degenerate. In particular, quantum photonic systems with EPs exhibit an enhanced sensitivity to external perturbations, which increases with the order of the EP. As a result, higher-order EPs hold significant potential for advanced sensing applications, but they are challenging to achieve due to stringent symmetry requirements. In this work, we study the dynamics of a generalized lossy waveguide beam splitter with asymmetric coupling by introducing non-reciprocity as a tunable parameter to achieve higher-order EPs even without dissipation. Using the Schwinger representation, we analytically derive eigenvalues and numerically demonstrate the formation of EPs. Moreover, we analyze the evolution of NOON states under activated non-reciprocity, highlighting its impact on quantum systems. Our results open new pathways for realizing higher-order EPs in non-reciprocal open quantum systems.

quant-ph↗

arXiv2024

Rabi oscillations and entanglement between two atoms interacting by the Rydberg blockade studied by the Jaynes-Cummings Model

The interaction between atoms and a quantized radiation field is fundamentally important in quantum optics and quantum information science. Due to their unusual properties, Rydberg atoms are promising building blocks for two-qubit gates and atom-light quantum interfaces, exploiting the Rydberg blockade interaction, which prevents two atoms at close distance from being simultaneously excited to Rydberg states. Recently, this effect was used to engineer quantum processors based on arrays of interacting Rydberg atoms illuminated by Raman lasers. Motivated by these experiments, we extend the Jaynes-Cummings model to study the interaction between two Rydberg atoms interacting by the Rydberg blockade and a quantized radiation field. We consider both number (Fock) states of the field and single-mode quantum coherent states. In particular, we discuss different types of entanglements between various components of the total system consisting of the two Rydberg-interacting atoms and coherent states of the field, and show that the behavior is significantly different compared to a system with non-interacting atoms corresponding to the two-atom Tavis-Cummings model. Our results are relevant in view of atom-light quantum interfaces as components for future long-distance quantum communication.

quant-ph↗

arXiv2015

DNA cyclization and looping in the wormlike limit: normal modes and the validity of the harmonic approximation

For much of the last three decades Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, $J$, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last ten years, however, approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly dominated by anharmonic contributions. In the case of computed values of the J factor, deviations of the harmonic approximation from the exact value of $J$ as a function of DNA length have not been characterized. Using a recent, numerically exact method that accounts for both anharmonic and harmonic contributions to $J$ for wormlike chains of arbitrary size, we report here the apparent error that results from neglecting anharmonic behavior. For wormlike chains having contour lengths less than four times the persistence length the error in $J$ arising from the harmonic approximation is generally small, amounting to free energies less than the thermal energy, $k_B T$. For larger systems, however, the deviations between harmonic and exact $J$ values increase approximately linearly with size.

q-bio.BM↗

arXiv2015

Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P=20 and L/P=40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

q-bio.BM↗

arXiv2009

Casimir force waves induced by non-equilibrium fluctuations between vibrating plates

We study the fluctuation-induced, time-dependent force between two plates immersed in a fluid driven out of equilibrium mechanically by harmonic vibrations of one of the plates. Considering a simple Langevin dynamics for the fluid, we explicitly calculate the fluctuation-induced force acting on the plate at rest. The time-dependence of this force is characterized by a positive lag time with respect to the driving, indicating a finite speed of propagation of stress through the medium, reminiscent of waves. We obtain two distinctive contributions to the force, where one may be understood as directly emerging from the corresponding force in the static case, while the other is related to resonant dissipation in the cavity between the plates.

cond-mat.stat-mech↗

arXiv2008

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent $c$ for which we find the new value $c=4ν-1/2$ such that the transition is second order with $c=1.85<2$ in $d=3$. We show that a finite stretching force $F$ destabilizes DNA, corresponding to a lower melting temperature $T(F)$, in agreement with single-molecule DNA stretching experiments.

cond-mat.soft↗

arXiv2006

Single DNA conformations and biological function

From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.

physics.bio-ph↗

arXiv2005

Adsorption transition of a self-avoiding polymer chain onto a rigid rod

The subject of this work is the adsorption transition of a long flexible self-avoiding polymer chain onto a rigid thin rod. The rod is represented by a cylinder of radius R with a short-ranged attractive surface potential for the chain monomers. General scaling results are obtained by using renormalization group arguments in conjunction with available results for quantum field theories with curved boundaries [McAvity and Osborn 1993 Nucl. Phys. B 394, 728]. Relevant critical exponents are identified and estimated using geometric arguments.

cond-mat.stat-mech↗

arXiv2004

Probing molecular free energy landscapes by periodic loading

Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a challenge, in particular for the unstable barrier regions. We propose a new method for obtaining the full profile by introducing a periodic ramp and using Jarzynski's identity for obtaining equilibrium quantities from non-equilibrium data. Our simulated experiments show that this method delivers significant more accurate data than previous methods, under the constraint of equal experimental effort.

cond-mat.soft↗

arXiv2003

Tight and loose shapes in flat entangled dense polymers

We investigate the effects of topological constraints (entanglements) on two dimensional polymer loops in the dense phase, and at the collapse transition (Theta point). Previous studies have shown that in the dilute phase the entangled region becomes tight, and is thus localised on a small portion of the polymer. We find that the entropic force favouring tightness is considerably weaker in dense polymers. While the simple figure-eight structure, created by a single crossing in the polymer loop, localises weakly, the trefoil knot and all other prime knots are loosely spread out over the entire chain. In both the dense and Theta conditions, the uncontracted knot configuration is the most likely shape within a scaling analysis. By contrast, a strongly localised figure-eight is the most likely shape for dilute prime knots. Our findings are compared to recent simulations.

cond-mat.soft↗

arXiv2003

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.

cond-mat.soft↗

arXiv2003

Comment on "Why is the DNA denaturation transition first order?"

In this comment we argue that while the conclusions in the original paper (Y. Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct for asymptotically long DNA chains, they do not apply to the chains used in typical experiments. In the added last paragraph, we point out that for real DNA the average distance between denatured loops is not of the order of the persistence length of a single-stranded chain but much larger. This corroborates our reasoning that the double helix between loops is quite rigid, and thereby our conclusion.

cond-mat.stat-mech↗

arXiv2002

Entropy loss in long-distance DNA looping

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the entropy loss for a given configuration. Numerical values obtained for some examples suggest that the entropy loss encountered in loop closure in typical genetic switches may become a relevant factor which has to be overcome by the released bond energy between the looping contact sites.

cond-mat.stat-mech↗

arXiv2002

Normal and Lateral Casimir Forces between Deformed Plates

The Casimir force between macroscopic bodies depends strongly on their shape and orientation. To study this geometry dependence in the case of two deformed metal plates, we use a path integral quantization of the electromagnetic field which properly treats the many-body nature of the interaction, going beyond the commonly used pairwise summation (PWS) of van der Waals forces. For arbitrary deformations we provide an analytical result for the deformation induced change in Casimir energy, which is exact to second order in the deformation amplitude. For the specific case of sinusoidally corrugated plates, we calculate both the normal and the lateral Casimir forces. The deformation induced change in the Casimir interaction of a flat and a corrugated plate shows an interesting crossover as a function of the ratio of the mean platedistance H to the corrugation length λ: For λ\ll H we find a slower decay \sim H^{-4}, compared to the H^{-5} behavior predicted by PWS which we show to be valid only for λ\gg H. The amplitude of the lateral force between two corrugated plates which are out of registry is shown to have a maximum at an optimal wavelength of λ\approx 2.5 H. With increasing H/λ\gtrsim 0.3 the PWS approach becomes a progressively worse description of the lateral force due to many-body effects. These results may be of relevance for the design and operation of novel microelectromechanical systems (MEMS) and other nanoscale devices.

cond-mat.stat-mech↗

arXiv2002

Towards the molecular workshop: entropy-driven designer molecules, entropy activation, and nanomechanical devices

We introduce some basic concepts for designer molecules with functional units which are driven by entropic rather than energetic forces. This idea profits from the mechanically interlocked nature of topological molecules such as catenanes and rotaxanes, which allows for mobile elements whose accessible configuration space gives rise to entropic intramolecular forces. Such entropy-driven designer molecules open the possibility for externally controllable functional molecules and nanomechanical devices.

cond-mat.stat-mech↗

arXiv2002

Tightness of slip-linked polymer chains

We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip-links) enforce pair contacts between monomers. These slip-links divide a closed ring polymer into a number of sub-loops which can exchange length between each other. In the ideal chain limit, we find the joint probability density function for the sizes of segments within such a slip-linked polymer chain (paraknot). A particular segment is tight (small in size) or loose (of the order of the overall size of the paraknot) depending on both the number of slip-links it incorporates and its competition with other segments. When self-avoiding interactions are included, scaling arguments can be used to predict the statistics of segment sizes for certain paraknot configurations.

cond-mat.stat-mech↗

arXiv2001

Probing the Strong Boundary Shape Dependence of the Casimir Force

We study the geometry dependence of the Casimir energy for deformed metal plates by a path integral quantization of the electromagnetic field. For the first time, we give a complete analytical result for the deformation induced change in Casimir energy δ\cal E in an experimentally testable, nontrivial geometry, consisting of a flat and a corrugated plate. Our results show an interesting crossover for δ\cal E as a function of the ratio of the mean plate distance H, to the corrugation length λ: For λ\ll H we find a {\em slower} decay \sim H^{-4}, compared to the H^{-5} behavior predicted by the commonly used pairwise summation of van der Waals forces, which is valid only for λ\gg H.

cond-mat.stat-mech↗

arXiv2001

Correlation functions near Modulated and Rough Surfaces

In a system with long-ranged correlations, the behavior of correlation functions is sensitive to the presence of a boundary. We show that surface deformations strongly modify this behavior as compared to a flat surface. The modified near surface correlations can be measured by scattering probes. To determine these correlations, we develop a perturbative calculation in the deformations in height from a flat surface. Detailed results are given for a regularly patterned surface, as well as for a self-affinely rough surface with roughness exponent $ζ$. By combining this perturbative calculation in height deformations with the field-theoretic renormalization group approach, we also estimate the values of critical exponents governing the behavior of the decay of correlation functions near a self-affinely rough surface. We find that for the interacting theory, a large enough $ζ$ can lead to novel surface critical behavior. We also provide scaling relations between roughness induced critical exponents for thermodynamic surface quantities.

cond-mat.stat-mech↗