Investigating Biological Matter with Theoretical Nuclear Physics Methods

The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such systems, collective excitations, cooperative transitions and phase transitions emerge as the result of the interplay of strong correlations with quantum or thermal fluctuations. In view of such an observation, some theoretical methods initially developed in the context of theoretical nuclear physics have been adapted to investigate the dynamics of biomolecules. In this talk, we review some of our recent studies performed along this direction. In particular, we discuss how the path integral formulation of the molecular dynamics allows to overcome some of the long-standing problems and limitations which emerge when simulating the protein folding dynamics at the atomistic level of detail.Comment: Prepared for the proceedings of the "XII Meeting on the Problems of Theoretical Nuclear Physics" (Cortona11

Novel Roles for Selected Genes in Meiotic DNA Processing

High-throughput studies of the 6,200 genes of Saccharomyces cerevisiae have provided valuable data resources. However, these resources require a return to experimental analysis to test predictions. An in-silico screen, mining existing interaction, expression, localization, and phenotype datasets was developed with the aim of selecting minimally characterized genes involved in meiotic DNA processing. Based on our selection procedure, 81 deletion mutants were constructed and tested for phenotypic abnormalities. Eleven (13.6%) genes were identified to have novel roles in meiotic DNA processes including DNA replication, recombination, and chromosome segregation. In particular, this analysis showed that Def1, a protein that facilitates ubiquitination of RNA polymerase II as a response to DNA damage, is required for efficient synapsis between homologues and normal levels of crossover recombination during meiosis. These characteristics are shared by a group of proteins required for Zip1 loading (ZMM proteins). Additionally, Soh1/Med31, a subunit of the RNA pol II mediator complex, Bre5, a ubiquitin protease cofactor and an uncharacterized protein, Rmr1/Ygl250w, are required for normal levels of gene conversion events during meiosis. We show how existing datasets may be used to define gene sets enriched for specific roles and how these can be evaluated by experimental analysis

Lie symmetries for two-dimensional charged particle motion

We find the Lie point symmetries for non-relativistic two-dimensional charged particle motion. These symmetries comprise a quasi-invariance transformation, a time-dependent rotation, a time-dependent spatial translation and a dilation. The associated electromagnetic fields satisfy a system of first-order linear partial differential equations. This system is solved exactly, yielding four classes of electromagnetic fields compatible with Lie point symmetries

Unitary relations in time-dependent harmonic oscillators

For a harmonic oscillator with time-dependent (positive) mass and frequency, an unitary operator is shown to transform the quantum states of the system to those of a harmonic oscillator system of unit mass and time-dependent frequency, as well as operators. For a driven harmonic oscillator, it is also shown that, there are unitary transformations which give the driven system from the system of same mass and frequency without driving force. The transformation for a driven oscillator depends on the solution of classical equation of motion of the driven system. These transformations, thus, give a simple way of finding exact wave functions of a driven harmonic oscillator system, provided the quantum states of the corresponding system of unit mass are given.Comment: Submitted to J. Phys.

Frobenius theorem and invariants for Hamiltonian systems

We apply Frobenius integrability theorem in the search of invariants for one-dimensional Hamiltonian systems with a time-dependent potential. We obtain several classes of potential functions for which Frobenius theorem assures the existence of a two-dimensional foliation to which the motion is constrained. In particular, we derive a new infinite class of potentials for which the motion is assurately restricted to a two-dimensional foliation. In some cases, Frobenius theorem allows the explicit construction of an associated invariant. It is proven the inverse result that, if an invariant is known, then it always can be furnished by Frobenius theorem

Three-dimensional resonating metamaterials for low-frequency vibration attenuation

Recent advances in additive manufacturing have enabled fabrication of phononic crystals and metamaterials which exhibit spectral gaps, or stopbands, in which the propagation of elastic waves is prohibited by Bragg scattering or local resonance effects. Due to the high level of design freedom available to additive manufacturing, the propagation properties of the elastic waves in metamaterials are tunable through design of the periodic cell. In this paper, we outline a new design approach for metamaterials incorporating internal resonators, and provide numerical and experimental evidence that the stopband exists over the irreducible Brillouin zone of the unit cell of the metamaterial (i.e. is a three-dimensional stopband). The targeted stopband covers a much lower frequency range than what can be realised through Bragg scattering alone. Metamaterials have the ability to provide (a) lower frequency stopbands than Bragg-type phononic crystals within the same design volume, and/or (b) comparable stopband frequencies with reduced unit cell dimensions. We also demonstrate that the stopband frequency range of the metamaterial can be tuned through modification of the metamaterial design. Applications for such metamaterials include aerospace and transport components, as well as precision engineering components such as vibration-suppressing platforms, supports for rotary components, machine tool mounts and metrology frames

The Performance and Calibration of the CRAFT Fly's Eye Fast Radio Burst Survey

Since January 2017, the Commensal Real-time ASKAP Fast Transients survey (CRAFT) has been utilising commissioning antennas of the Australian SKA Pathfinder (ASKAP) to survey for fast radio bursts (FRBs) in fly's eye mode. This is the first extensive astronomical survey using phased array feeds (PAFs), and a total of 20 FRBs have been reported. Here we present a calculation of the sensitivity and total exposure of this survey, using the pulsars B1641-45 (J1644-4559) and B0833-45 (J0835-4510, i.e.\ Vela) as calibrators. The design of the survey allows us to benchmark effects due to PAF beamshape, antenna-dependent system noise, radio-frequency interference, and fluctuations during commissioning on timescales from one hour to a year. Observation time, solid-angle, and search efficiency are calculated as a function of FRB fluence threshold. Using this metric, effective survey exposures and sensitivities are calculated as a function of the source counts distribution. The implied FRB rate is significantly lower than the $37$\,sky$^{-1}$\,day$^{-1}$ calculated using nominal exposures and sensitivities for this same sample by \citet{craft_nature}. At the Euclidean power-law index of $-1.5$, the rate is $10.7_{-1.8}^{+2.7}\,{\rm (sys)} \, \pm \, 3\,{\rm (stat)}$\,sky$^{-1}$\,day$^{-1}$ above a threshold of $57\pm6\,{\rm (sys)}$\,Jy\,ms, while for the best-fit index for this sample of $-2.1$, it is $16.6_{-1.5}^{+1.9} \,{\rm (sys)}\, \pm 4.7\,{\rm (stat)}$\,sky$^{-1}$\,day$^{-1}$ above a threshold of $41.6\pm1.5\,{\rm (sys)}$\,Jy\,ms. This strongly suggests that these calculations be performed for other FRB-hunting experiments, allowing meaningful comparisons to be made between them.Comment: 21 pages, 15 figures, 2 tables, accepted for publication in PAS