Seminars / Webinars
Thursday 8 September 2022, 11:00 (EET)
Biophysical chaos: Bubbles in DNA molecules
Malcolm Hillebrand
Department of Mathematics and Applied Mathematics
University of Cape Town
Abstract:
In this talk, I will discuss the investigation of the phenomenon of DNA “bubbles”, thermal openings in the double strand. This will be presented through numerical simulations of the dynamics of DNA in the coarse-grained nonlinear Peyrard-Bishop-Dauxois (PBD) model. With this, we have studied various aspects of these bubbles and the nonlinearity of the strand, using a rationally-determined definition for determining the open/closed state of a base pair. These aspects include the inherent lifetimes and occurrence probabilities of bubbles in random sequences as well as viral and bacterial promoters, and further timescale studies of out-of-equilibrium fluctuations in the double strand. These results will be discussed in the context of the chaotic dynamics inherent to the nonlinear model, including Lyapunov exponents and the deviation vector distribution.
Past webinar recordings are available here
Past Webinars
| Date | Speaker | Title |
| 14 Oct 2022 | George Contopoulos |
(Spirals and bars in galaxies: One-day workshop) The spiral arms of galaxies (29:51) |
| 14 Oct 2022 | Kanak Saha |
(Spirals and bars in galaxies: One-day workshop) Revisiting spiral structures in galaxies (1:21:30) |
| 14 Oct 2022 | Lia Athanassoula |
(Spirals and bars in galaxies: One-day workshop) Understanding the Formation and Evolution of Bars using Simulations (2:24:23) |
| 14 Oct 2022 | Christos Efthymiopoulos |
(Spirals and bars in galaxies: One-day workshop) Manifolds and spirals under multiple pattern speeds (3:41:07) |
| 14 Oct 2022 | P. Grosbol European Southern Observatory (ESO), Munich, Germany |
(Spirals and bars in galaxies: One-day workshop) Interaction between spirals and bars in disk galaxies (4:33) |
| 14 Oct 2022 | M. Harsoula Research Center for Astronomy and Applied Mathematics, Academy of Athens |
(Spirals and bars in galaxies: One-day workshop) The building blocks of the spiral arms in galaxies (1:00:15) |
| 14 Oct 2022 | T. Naab Max-Planck Institut fuer Astrophysik, (MPA), Munich, Germany |
(Spirals and bars in galaxies: One-day workshop) The formation of galactic star cluster populations (1:45:06) |
| 14 Oct 2022 | P.A. Patsis Research Center for Astronomy and Applied Mathematics, Academy of Athens |
(Spirals and bars in galaxies: One-day workshop) Open questions about the association of observed structures and orbits in galactic disks (2:21:15) |
| 8 Sep 2022 | Malcolm Hillebrand Department of Mathematics and Applied Mathematics University of Cape Town |
Biophysical chaos: Bubbles in DNA molecules |
| 20 Jul 2022 | Suraj Dhiwar Prime Minister's Research Scholar, Department of Physics, IIT Guwahati, India |
Star Formation Quenching in L* Ellipticals | 18 Jul 2022 | Samik Mitra Prime Minister's Research Scholar, Department of Physics, IIT Guwahati, India |
Properties of general relativistic magneto-hydrodynamics accretion flows around black holes in steady-state limit (Watch here) |
| 12 Jul 2022 | Christos Efthymiopoulos University of Padova, Department of Mathematics |
The information approach to the interpretation of quantum mechanics (Watch here) |
| 5 Jul 2022 | Kanak Saha Inter-University Centre for Astronomy and Astrophysics, Pune, India |
Growth and survival of bars in disk galaxies (Watch here) |
| 28 Jun 2022 | Georgios Loukes-Gerakopoulos Astronomical Institute of the CAS, Czech Republic |
Celestial Mechanics of Extreme Mass Ratio Inspirals (Watch here) |
| 14 Jun 2022 | Matthaios Katsanikas Research Center for Astronomy and Applied Mathematics, Academy of Athens |
Stickiness in 3D rotating galactic potentials (Watch here) |
| 9 Jun 2022 | Makrina Agaoglou Instituto de Ciencias Matematicas, Madrid, Spain |
Transport processes on a Potential Energy Surface with four wells, four index-1 saddles and an index-2 saddle (Watch here) |
| 24 May 2022 | Susanna Parenti Institut d'Astrophysique Spatiale, France |
Validation of a wave heated 3D MHD coronal-wind model using Polarized Brightness and EUV observations (Watch here) |
| 17 May 2022 | Konstantina Zouloumi Research Center for Astronomy & Applied Mathematics & Department of Astrophysics, Astronomy and Mechanics, University of Athens |
NAAF determination of the multiple pattern speeds and the manifolds in a simulation of a barred spiral galaxy (Watch here) |
| 3 May 2022 | Antonios Tsokaros University of Illinois at Urbana-Champaign, USA |
Numerical general relativity and astrophysics in the era of multimessenger astronomy (Watch here) |
| 18 Apr 2022 | Stavros Pastras Research Center for Astronomy and Applied Mathematics, Academy of Athens & Department of Physics, Section of Astrophysics, Astronomy and Mechanics, University of Athens |
Gasflows in barred spiral galaxies by means of two different hydrocodes (Watch here) |
| 12 Apr 2022 | Spyridon Aleiferis UK Atomic Energy Authority, Culham Science Centre, Abingdon, UK |
Taming of the stars: how to control fusion plasmas (Watch here) |
| 31 Mar 2022 | Evangelos Melas University of Athens, Department of Economics |
Asymptotic symmetries and representation theory in General Relativity in three and four space-time dimensions (Watch here) |
| 29 Mar 2022 | Georgios Doulis Institute of Theoretical Physics, University of Jena, Germany |
Entropy as shock indicator in neutron star merger simulations (Watch here) |
| 15 Mar 2022 | Dimitris Stamatellos Jeremiah Horrocks Institute for Mathematics, Physics & Astronomy, University of Central Lancashire, Preston, UK |
The formation and evolution of disc-instability planets (Watch here) |
| 10 Mar 2022 | Damianos Iosifidis Aristotle University of Thessaloniki |
Perfect Hyperfluids (Watch here) |
| 8 Mar 2022 | Antonios Nathanail University of Athens, Department of Physics |
Still observing light from the binary neutron star merger first detected in 2017 (Watch here) |
| 3 Mar 2022 | Karnesis Nikolaos Aristotle University of Thessaloniki, School of Physics |
Detecting Gravitational Waves from space (Watch here) |
| 22 Feb 2022 | Athanasios C. Tzemos Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Chaos and Bohmian Quantum Potential (Watch here) |
| 15 Feb 2022 | Ioannis Contopoulos Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Quantum Interference: reality or an illusion of the detector? (Watch here) |
| 8 Feb 2022 | Charis Anastopoulos Department of Physics, University of Patras |
Gravitational effects in macroscopic quantum systems (Watch here) |
| 1 Feb 2022 | Konstantinos N. Gourgouliatos Department of Physics, University of Patras |
Magnetic Field Evolution in Neutron Star Crusts: Hall effect and beyond ( Watch here) |
| 18 Jan 2022 | Athanasios C. Tzemos Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Born's rule in the case of 3 entangled Bohmian qubits (Watch here) |
| 11 Jan 2022 | Constantinos Kalapotharakos University of Maryland and Astrophysics Science Division, NASA/Goddard Space Flight Center, USA |
Interpreting the Thermal and Non-Thermal High-Energy Emission in Multipolar Field Pulsar Magnetospheres (Watch here) |
| 14 Dec 2021 | Thorsten Naab Max-Planck-Institute for Astrophysics, Garching, Germany |
The GRIFFIN project - towards realistic simulations of galactic star cluster populations (Watch here) |
| 7 Dec 2021 | Ivan Minchev Leibniz-Institut für Astrophysik Potsdam (AIP) |
Modeling the Galactic disk in the age of Gaia (Watch here) |
| 30 Nov 2021 | Edoardo Legnaro Research Center for Astronomy and Applied Mathematics of the Academy of Athens and University of Thessaloniki |
Analytic Theory for Secular Lunisolar Resonances (Watch here) |
| 9 Nov 2021 | Dimitri A. Gadotti ESO – European Southern Observatory |
Nuclear discs in external galaxies and the Milky Way: building "bulges" without mergers (Watch here) |
| 26 Oct 2021 | Demosthenes Kazanas NASA Goddard Space Flight Center, Corresponding Member of the Academy of Athens |
Gravity beyond Einstein? Yes, but in which direction? (Watch here) |
| 13 Jul 2021 | Dimitris Christodoulou University of Massachusetts |
Major-Body Clustering in the Solar System (Watch here) |
| 24 Jun 2021 | Panos A. Patsis Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Building blocks of 3D, X-shaped bulges and thick spirals (Watch here) |
| 8 Jun 2021 | George Contopoulos Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Μια συνοπτική έκθεση της Φιλοσοφίας της Φυσικής και των Μαθηματικών (Διαθέσιμη μαγνητοσκοπημένη) |
| 1 Jun 2021 | Christos Efthymiopoulos Department of Mathematics Tullio Levi-Civita, University of Padua (Work in collaboration with Rita Mastroianni) |
Secular dynamics for exoplanetary systems with two planets in mutually inclined orbits (Watch here) |
| 13 May 2021 | Athanasios C. Tzemos Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Born's Rule in the case of two entangled Bohmian qubits
(Watch here) |
| 22 Apr 2021 | Costis Gontikakis Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Study of the emission measure during a solar flare observed with IRIS spectrograph (Watch here) |
Seminars in 2020
| Date | Speaker | Title |
| 3 Mar 2020 | Anastasios Anastasiadis National Observatory of Athens / IAASARS |
Unveiling Current Challenges in Space Weather Forecasting: The SAWS-ASPECS tool |
| 25 Feb 2020 | Vasileios Basios Université Libre de Bruxelles, Interdisciplinary Centre for Nonlinear Phenomena & Complex Systems (Cenoli-ULB) & Département de Physique des Systèmes Complexes et Mécanique Statistique |
Labyrinth Chaos: Conservative, non-Hamiltonian Chaos without Attractors |
| 18 Feb 2020 | Elias Koulouridis National Observatory of Athens / IAASARS |
Tracing the Universe: X-ray surveys and cosmology |
| 11 Feb 2020 | Costis Gontikakis Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Moss, the trace of hot loops in EUV, an ongoing research |
| 28 Jan 2020 | Athanassios C. Tzemos Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Chaos and ergodicity in the trajectories of two entangled Bohmian qubits |
| 21 Jan 2020 | George Dimopoulos National Observatory of Athens |
Coronal properties of Sy I Active Galaxies |
| 14 Jan 2020 | Panos A. Patsis Research Center for Astronomy and Applied Mathematics of the Academy of Athens |
Some open issues in Galactic Dynamics and the contribution of Image Processing in resolving them |
A list of all previous seminars from 2008 to 2020 is available here.
