Eric Sembrat's Test Bonanza

Abstract: DNA duplex separation and formation underlie our most fundamental genetic processes. One of the most powerful tools for exploring these binding and unbinding reactions is single-molecule force spectroscopy. This method applies tension to a single DNA strand and observes the change in its extension or kinetics with a microscope. However, these experiments typically study longer DNA molecules (>10 bp) subject to higher forces (> 10 bp); hence, the behavior of short DNA subject to weak forces is not well understood. In particular, it is not clear whether statistical chain models ordinarily used to explain force spectroscopy data are applicable at these small scales. To remedy this, we focused solely on short DNA duplexes (< 10 bp) subject to very weak forces (< 7 piconewtons). For this purpose, we used two tools: an experimental technique called single-molecule fluorescence resonance energy transfer (smFRET), and the coarse-grained DNA simulation code oxDNA. The experiments implemented a simple, high-throughput DNA assay, dubbed “DNA bows”, which exploit the bending rigidity of DNA to exert very weak forces on short DNA strands. With this method, we demonstrate that weak force accelerates the hybridization and dehybridization of short oligonucleotides from 2-6 piconewtons, contradicting the predictions of simple chain models. We next used oxDNA to investigate how the extension of short DNA changes with force throughout its binding and unbinding transitions. Regardless of force, we find that the transition state of an oligoduplex is at least as extended as its bound state, in agreement with our experiments. We also find that extension is a poor reaction coordinate at 3 piconewtons and below. These results establish the nature of DNA duplex transitions at the force and length scales relevant to DNA biology as well as emerging DNA nanotechnologies.

Abstract

Geometrically frustrated systems have an inherent incompatibility between the lattice geometry and the magnetic interactions, resulting in macroscopically degenerate ground-state manifolds. The single-ion anisotropy and magnetic interactions in spin-ice systems give rise to unusual non-collinear spin textures, such as Pauling states and emergent quasiparticle excitations equivalent to magnetic monopoles. The effective spin correlation strength (Jeff) determines the relative energies of the different spin-ice states and the magneto-chemical potential (MCP) associated with monopole formation. There is an enticing potential of using these monopoles for the development of new quantum information applications. To realize this, thin films are required. The thin films in my group are grown using pulsed laser deposition and characterized using capacitive torque magnetometry and neutron measurements [1,2]. Our thin-film work has already shown that epitaxial strain and the amount of disorder in the spin ice films play important roles in determining their magnetic properties. In this talk, I will show how we have benchmarked capacitive torque magnetometry as a unique tool to characterize the transitions between noncollinear spin textures in spin-ice single crystals. Studying these magnetic-field-induced phase transitions allows extraction of Jeff and the MCP of monopole formation [3]. I will also talk about thin films grown on yttria-stabilized zirconia substrates, which we have investigated using the same approach. These films show modified spin ice physics depending on the growth conditions.

Beekman acknowledges the support of the National Research Foundation, under Grant No. NSF DMR-1847887 (CAREER). Use of National High Magnetic Field Laboratory user facilities was supported by NSF Cooperative Agreements No. DMR-1157490, No. DMR-1644779, and the state of Florida.

[1] K. Barry, B. Zhang, N. Anand, Y. Xin, A. Vailionis, J. Neu, C. Heikes, C. Cochran, H. Zhou, Y. Qiu, W. Ratcliff, T. Siegrist, & and C. Beekman, Phys. Rev. Materials, 3, 084412 (2019)

[2] C. Thompson, D. Reig-i-Plessis, L. Kish, A. A. Aczel, B. Zhang, E. Karapetrova, G. J. MacDougall, and C. Beekman, Phys. Rev. Materials 2, 104411 (2018)

[3] N. Anand, K. Barry, J. N. Neu, D. E. Graf, Q. Huang, H. Zhou, T. Siegrist, H. J. Changlani & C. Beekman, Nature Communications 13, 3818 (2022)

Title: Probing the Trillion Degree Little Bang in Heavy Ion Collisions
Abstract: In relativistic collisions of large nuclei, a hot and dense medium referred to as the Quark Gluon Plasma (QGP) can be formed, which explodes and evaporates very soon after collisions. The long-distance behavior of such a medium resembles a liquid, and its inner working is still an open question. In this talk I will explain how we can probe the QGP using streams of energetic particles produced in hard collisions known as jets. These jets penetrate the QGP, and through strong interactions, the substructure of jets can tell us information about short-distance medium properties. The upcoming data from Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory and also the Run 3 of the Large Hadron Collider (LHC) at the European Organization for Nuclear Research (CERN) will hopefully shed light on the microscopic picture of the QGP.

Abstract

The possibility of binary black hole (BH) mergers in active galactic nucleus (AGN) accretion disks has recently received much attention. The community has studied the evolution of pre-existing BH binaries in AGN disks. However, how to form these BH binaries initially remains an open question. In this talk, I will show that close encounters between single BHs may produce these BH binaries in AGN disks. I will start with an N-body study. We explore the characteristics of the close encounters in an AGN disk and calculate the rate of binary formation due to gravitational-wave capture. Then I will present our 2D hydrodynamics simulations where BH close encounters happen in a live gaseous disk. We describe a departure-drag mechanism that can produce long-lived binaries, assess the probability of gas-assist formation of binaries, and characterize the properties of the resulting BH binary orbits.

Bio

Jiaru Li is an astronomy Ph.D. student at Cornell University, advised by Prof. Dong Lai. He also spent two years of grad school at Los Alamos National Laboratory as a CSES student fellow, where he worked with the group led by Dr. Hui Li. Jiaru Li received his bachelor's degree at the University of Toronto, where he worked with Prof. Artur Izmaylov on quantum chemistry. His current research interests include exoplanet dynamics, protoplanetary disks, and the dynamical evolution of objects embedded in disks.

Title

Intermediate-mass black holes: past, present, future

Abstract

Despite their key importance from stellar to cosmological scales, intermediate-mass black holes (IMBHs) are one of the unsolved puzzles of modern astronomy with no conclusive evidence for their existence. While the classical approach to detect them based on the use of optical and infrared data is limited to nearby systems, gravitational wave (GW) missions have the potential to shed light on IMBHs up to the distant Universe. IMBH sources are most likely to be produced in dense stellar environments, where IMBHs can form GW-emitting binaries through dynamical interactions with other compact objects. The intermediate mass-ratio inspiral of a stellar compact remnant into an IMBH is a potential target for multi-band detection, since LISA measurements will alert astronomers of an incoming merger detectable within the next few years by LIGO/Virgo/Kagra, Einstein Telescope, and Cosmic Explorer. I will discuss the formation and evolution of IMBHs, which characterize the typical GW signal expected for current and upcoming missions, offering for the first time the opportunity to demonstrate the existence of IMBHs beyond any reasonable doubt. The next decade may bring hundreds of events, promising a spectacular range of new science from stellar evolution to cosmology. The future of the darkest black holes appears bright.

Title: Black hole mergers in AGN disks and Few-body code SpaceHub

Abstract: Active galactic nucleus (AGN) disks may be important sites for stellar mass binary black hole (BBH) mergers, but the detailed processes that lead to a BBH merger in an AGN disk are not yet well-constrained. Binary formation in AGN disks could be extremely efficient due to the so-called migration trap in AGN disks. Dynamical encounters in the migration trap could play a critical role in merging binaries in the AGN channel. I will show via numerical experiments with the high-accuracy, high-precision code SpaceHub that broken symmetry in dynamical encounters in AGN disks can lead to an asymmetry between prograde and retrograde BBH mergers. An asymmetric distribution of mass-weighted projected spin of the BBH mergers that is unlikely to be predicted in other merger channels will show in the AGN merger channel. I will also present the open source few-body gravity integration toolkit SpaceHub. SpaceHub offers a variety of algorithmic methods, which we show out-perform other methods in the literature and allow for fast, precise and accurate computations to deal with few-body problems ranging from interacting black holes to planetary dynamics. With algorithmic regularization, chain algorithm, active round-off error compensation and a symplectic kernel implementation, SpaceHub is the fastest and most accurate tool to treat black hole dynamics with extreme mass ratios, extreme eccentricities and very close encounters.