Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides

Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-molecule biology. The Pacific Biosceinces RS2 sequencer utilizes sequencing by synthesis within nanophotonic zero mode waveguides. A number of years ago this instrument was unlocked by Pacific Biosciences for custom use by researchers allowing them to monitor biological interactions at the single-molecule level with high throughput. In this capability letter we demonstrate the use of the RS2 sequencer for real time observation of DNA-to-RNA transcription and RNA-protein interactions. We use a relatively complex model – transcription of structured ribosomal RNA from E. coli and interactions of ribosomal RNA with ribosomal proteins. We also show evidence of observation of transcriptional pausing without the application of an external force (as is required for single-molecule pausing studies using optical traps). Overall, in the unlocked, custom mode, the RS2 sequencer can be used to address a wide variety of biological assembly and interaction questions at the single-molecule level with high throughput. This instrument is available for use at the Center for Integrated Nanotechnologies Gateway located at Los Alamos National Laboratory.

One-loop structure of parton distribution for the gluon condensate and “zero modes”

We present results for one-loop corrections to the recently introduced “gluon condensate” PDF F(x). In particular, we give expression for the gg-part of its evolution kernel. To enforce strict compliance with the gauge invariance requirements, we have used on-shell states for external gluons, and have obtained identical results both in Feynman and light-cone gauges. No “zero mode” δ(x) terms were found for the twist-4 gluon PDF F(x). However a q2δ(x) term was found for the ξ = 0 GPD F(x, q2) at nonzero momentum transfer q. Overall, our results do not agree with the original attempt of one-loop calculations of F(x) for gluon states, which sets alarm warning for calculations that use matrix elements with virtual external gluons and for lattice renormalization procedures based on their results.

The time traveler’s guide to the quantization of zero modes

We study the relationship between the quantization of a massless scalar field on the two-dimensional Einstein cylinder and in a spacetime with a time machine. We find that the latter picks out a unique prescription for the state of the zero mode in the Einstein cylinder. We show how this choice arises from the computation of the vacuum Wightman function and the vacuum renormalized stress-energy tensor in the time-machine geometry. Finally, we relate the previously proposed regularization of the zero mode state as a squeezed state with the time-machine warp parameter, thus demonstrating that the quantization in the latter regularizes the quantization in an Einstein cylinder.

Axion fragmentation on the lattice

We analyze the phenomenon of axion fragmentation when an axion field rolls over many oscillations of a periodic potential. This is particularly relevant for the case of relaxion, in which fragmentation provides the necessary energy dissipation to stop the field evolution. We compare the results of a linear analysis with the ones obtained from a classical lattice simulation, finding an agreement in the stopping time of the zero mode between the two within an $$ \mathcal{O}(1) $$ O 1 difference. We finally speculate on the generation of bubbles with different VEVs of the axion field, and discuss their cosmological consequences.

Quasinormal modes of a semi-holographic black brane and thermalization

We study the quasinormal modes and non-linear dynamics of a simplified model of semi-holography, which consistently integrates mutually interacting perturbative and strongly coupled holographic degrees of freedom such that the full system has a total conserved energy. We show that the thermalization of the full system can be parametrically slow when the mutual coupling is weak. For typical homogeneous initial states, we find that initially energy is transferred from the black brane to the perturbative sector, later giving way to complete transfer of energy to the black brane at a slow and constant rate, while the entropy grows monotonically for all time. Larger mutual coupling between the two sectors leads to larger extraction of energy from the black brane by the boundary perturbative system, but also quicker irreversible transfer of energy back to the black brane. The quasinormal modes replicate features of a dissipative system with a softly broken symmetry including the so-called k-gap. Furthermore, when the mutual coupling is below a critical value, there exists a hybrid zero mode with finite momentum which becomes unstable at higher values of momentum, indicating a Gregory-Laflamme type instability. This could imply turbulent equipartitioning of energy between the boundary and the holographic degrees of freedom in the presence of inhomogeneities.