While photons in free space barely interact, matter can mediate interactions between them resulting in optical nonlinearities. Such interactions at the single-quantum level result in an on-site photon repulsion [1, 2], crucial for photon-based quantum information processing and for realizing strongly interacting many-body states of light [3][4][5][6][7]. Here, we report repulsive dipole-dipole interactions between electric field tuneable, localized interlayer excitons in MoSe 2 /WSe 2 heterobilayer. The presence of a single, localized exciton with an out-of-plane, non-oscillating dipole moment increases the energy of the second excitation by ∼ 2 meV -an order of magnitude larger than the emission linewidth and corresponding to an inter-dipole distance of ∼ 5 nm. At higher excitation power, multi-exciton complexes appear at systematically higher energies. The magnetic field dependence of the emission polarization is consistent with spin-valley singlet nature of the dipolar molecular state. Our finding is an important step towards the creation of excitonic few-and many-body states such as dipolar crystals with spin-valley spinor in van der Waals (vdW) heterostructures.Optical response in atomically thin layered semiconductors is determined by excitons and other excitonic complexes such as trions and biexcitons which are strongly bound due to increased Coulomb interactions in truly 2D limit [5,9]. In addition, due to the type-II band alignment in heterobilayer of MoSe 2 /WSe 2 , an interlayer exciton comprising of an electron in the MoSe 2 layer and hole in the WSe 2 layer is found to be stable and long-lived [4,10,11,13]. As shown in Fig. 1a, due to the spatial separation of electron and hole, the interlayer exciton carries a static, out-of-plane electric dipole moment which allows for the tuning of its energy by an external electric field (E). The orientation of this dipole is fixed by the ordering of MoSe 2 and WSe 2 layers and hence leads to a repulsive interaction between interlayer excitons. arXiv:1910.08139v1 [cond-mat.mes-hall] 17 Oct 2019 10 µm WSe2 MoSe2 a b c U d-d on-site E x E x -+ Mo W Se ℎ + − Electric field Figure 1: Interlayer exciton dipoles in WSe 2 /MoSe 2 heterostructure. a, A schematic showing the interlayer exciton in WSe 2 -MoSe 2 heterobilayer under an external electric field E. Due to the type-II band alignment, electron and hole are separated in MoSe 2 and WSe 2 , respectively, forming a permanent out-ofplane dipole. The dipole energy red-shifts (blue-shifts) when E is parallel (anti-parallel) to the direction of dipole. b, Energy diagram of localized interlayer exciton and biexciton in a potential well. The energy of biexciton is raised up by on-site dipole-dipole interaction U on−site dd . c, An optical image of WSe 2 /MoSe 2 heterobilayer with graphite bottom gate. Monolayer WSe 2 (MoSe 2 ) is depicted in orange (yellow) dashed line. The final device has graphite bottom and top gates with h-BN as dielectric on both sides.This dipolar interaction is potentially interesting for inducing e...

Protamine proteins dramatically condense DNA in sperm to almost crystalline packing levels. Here, we measure the first step in the in vitro pathway, the folding of DNA into a single loop. Current models for DNA loop formation are one-step, all-or-nothing models with a looped state and an unlooped state. However, when we use a Tethered Particle Motion (TPM) assay to measure the dynamic, real-time looping of DNA by protamine, we observe the presence of multiple folded states that are long-lived (∼100 s) and reversible. In addition, we measure folding on DNA molecules that are too short to form loops. This suggests that protamine is using a multi-step process to loop the DNA rather than a one-step process. To visualize the DNA structures, we used an Atomic Force Microscopy (AFM) assay. We see that some folded DNA molecules are loops with a ∼10-nm radius and some of the folded molecules are partial loops—c-shapes or s-shapes—that have a radius of curvature of ∼10 nm. Further analysis of these structures suggest that protamine is bending the DNA to achieve this curvature rather than increasing the flexibility of the DNA. We therefore conclude that protamine loops DNA in multiple steps, bending it into a loop.

An analytical model for the free energy change during collapse of an RNA molecule from an extended to a compact conformation is proposed. It considers explicit binding of water and ion molecules to the RNA and the exchange of these molecules with the aqueous solution. Microscopic states of the system are captured on a two-dimensional square lattice and evaluated using contact energies. We compute the free energy as a function of a collapse variable and the number of ions bound to the RNA. The major driving force to the collapse of the RNA chain is the gain in water entropy once expelled from the surface of the RNA molecule illustrated by decomposing the free energy into species contributions and their energy and entropy components. The sensitivity of the conclusions of the model to variations in parameters is computed and appears to be weak.

Atomic force microscopes (AFMs) are ubiquitous in research laboratories and have recently been priced for use in teaching laboratories. Here we review several AFM platforms (Dimension 3000 by Digital Instruments, EasyScan2 by Nanosurf, ezAFM by Nanomagnetics, and TKAFM by Thorlabs) and describe various biophysical experiments that could be done in the teaching laboratory using these instruments. In particular, we focus on experiments that image biological materials and quantify biophysical parameters: 1) imaging cells to determine membrane tension, 2) imaging microtubules to determine their persistence length, 3) imaging the random walk of DNA molecules to determine their contour length, and 4) imaging stretched DNA molecules to measure the tensional force.2

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One of the most important biological processes is the dynamic folding and unfolding of deoxyribonucleic acid (DNA). The folding process is crucial for DNA to fit within the boundaries of the cell, while the unfolding process is essential for DNA replication and transcription. To accommodate both processes, the cell employs a highly active folding mechanism that has been the subject of intense study over the last few decades. Still, many open questions remain. What are the pathways for folding or unfolding? How does the folding equilibrium shift? And, what is the energy landscape for a particular process? Here, we review these emerging questions and the in vitro, optical methods that have provided answers, introducing the topic for those physicists seeking to step into biology. Specifically, we discuss two iconic experiments for DNA folding, the tethered particle motion (TPM) experiment and the optical tweezers experiment.

DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes proteins such as condensin. Here, however, we are interested in a different looping method whereby condensing agents (charge Rþ3) such as protamine proteins neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length (%1 mm) DNA fragments using atomic force microscopy. We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamine's in vivo role for looping DNA into toroids and the mechanism of DNA condensation by condensing agents more broadly.

studies of a broad range of complex, multistep enzymatic pathways in which rare intermediates have escaped classification due to limited throughput.