Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence.

After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.

A quantum physics layer of epigenetics: a hypothesis deduced from charge transfer and chirality-induced spin selectivity of DNA.

BACKGROUND: Epigenetic mechanisms are informational cellular processes instructing normal and diseased phenotypes. They are associated with DNA but without altering the DNA sequence. Whereas chemical processes like DNA methylation or histone modifications are well-accepted epigenetic mechanisms, we herein propose the existence of an additional quantum physics layer of epigenetics. RESULTS: We base our hypothesis on theoretical and experimental studies showing quantum phenomena to be active in double-stranded DNA, even under ambient conditions. These phenomena include coherent charge transfer along overlapping pi-orbitals of DNA bases and chirality-induced spin selectivity. Charge transfer via quantum tunneling mediated by overlapping orbitals results in charge delocalization along several neighboring bases, which can even be extended by classical (non-quantum) electron hopping. Such charge transfer is interrupted by flipping base(s) out of the double-strand e.g., by DNA modifying enzymes. Charge delocalization can directly alter DNA recognition by proteins or indirectly by DNA structural changes e.g., kinking. Regarding sequence dependency, charge localization, shown to favor guanines, could influence or even direct epigenetic changes, e.g., modification of cytosines in CpG dinucleotides. Chirality-induced spin selectivity filters electrons for their spin along DNA and, thus, is not only an indicator for quantum coherence but can potentially affect DNA binding properties. CONCLUSIONS: Quantum effects in DNA are prone to triggering and manipulation by external means. By the hypothesis put forward here, we would like to foster research on "Quantum Epigenetics" at the interface of medicine, biology, biochemistry, and physics to investigate the potential epigenetic impact of quantum physical principles on (human) life.

Single-Qubit Error Mitigation by Simulating Non-Markovian Dynamics.

Quantum simulation is a powerful tool to study the properties of quantum systems. The dynamics of open quantum systems are often described by completely positive (CP) maps, for which several quantum simulation schemes exist. Such maps, however, represent only a subset of a larger class of maps: the general dynamical maps which are linear, Hermitian preserving, and trace preserving but not necessarily positivity preserving. Here we present a simulation scheme for these general dynamical maps, which occur when the underlying system-reservoir model undergoes entangling (and thus non-Markovian) dynamics. Such maps also arise as the inverse of CP maps, which are commonly used in error mitigation. We illustrate our simulation scheme on an IBM quantum processor, demonstrating its ability to recover the initial state of a Lindblad evolution. This paves the way for a novel form of quantum error mitigation. Our scheme only requires one ancilla qubit as an overhead and a small number of one and two qubit gates. Consequently, we expect it to be of practical use in near-term quantum devices.

A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems.

Boolean networks are commonly used in systems biology to dynamically model gene regulatory interactions. Here, we present a protocol for implementing Boolean network dynamics as quantum circuits. We describe steps for accessing cloud-based quantum processing units offered by IBM and IonQ and downloading and parsing logic for gene regulatory networks. We then detail procedures for performing simulations of quantum circuits on local devices and visualizing measurement results. For complete details on the use and execution of this protocol, please refer to Weidner et al.1.

Sliding states of a soft-colloid cluster crystal: Cluster versus single-particle hopping.

We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential and a sideways constant pulling force which would promote a sliding state. For a few sample particle densities and amplitudes of the periodic corrugation potential we investigate the depinning from the statically pinned to the dynamically sliding regime. This sliding state exhibits the competition between a dynamics where entire clusters are pulled from a minimum to the next and a dynamics where single colloids or smaller groups leave a cluster and move across the corrugation energy barrier to join the next cluster downstream in the force direction. Both kinds of sliding states can occur either coherently across the entire sample or asynchronously: the two regimes result in different average mobilities. Finite temperature tends to destroy separate sliding regimes, generating a smoother dependence of the mobility on the driving force.