Seminar of participants of poster presentations by young scientists on 60th PAC CMP meeting

Laboratory of Information Technologies

Date and Time: Wednesday, 22 January 2025, at 11:00 AM

Venue: room 310, Meshcheryakov Laboratory of Information Technologies, online on Webinar

Link to join online

1. Seminar topic: “The influence of phospholipid composition on membrane interaction with amyloid beta peptides within molecular dynamics simulations”

   Speakers: Dina Badreeva, Norbert Kucerka

   Abstract:
   

   At the present time, there is a hypothesis about the key role of amyloid beta peptide in the onset of Alzheimer’s disease. Its interaction with cell membranes is considered to cause a disruption of their permeability and integrity, which may trigger further neurodegenerative processes [1]. The experimental study showed that the peptide takes part in the morphological changes of the phospholipid membrane during its transition through the main lipid phase transition temperature [2]. However, this research did not allow the authors to look into the processes and resulting structures at the atomic level. The latter results are better achieved in theoretical studies that they have carried out recently.

   It has been suggested that different phase states within one membrane may play a key role in the process of phospholipid membrane destruction in the presence of amyloid beta peptides. In order to shed some light on this, the interaction of Aβ(25-35) with DPPC and DOPC phospholipids, which have different tail lengths and might form rafts, at different temperatures was simulated using the coarse-grained and all-atom molecular dynamics method in the GROMACS 2019.3 software package. Using the coarse-grained approach, the researchers have obtained the type of structures that are formed from a box of randomly distributed components at different temperatures below and above the main transition. Whereas all-atom consideration has allowed determining the influence of rafts on the internal location of peptides in the membrane.

   1. Martel A., et al. Membrane permeation versus amyloidogenicity: a multitechnique study of islet amyloid polypeptide interaction with model membranes. Journal of the American Chemical Society, 2017, 139, 137-148.
   2. Ivankov O., et al. Amyloid-beta peptide (25–35) triggers a reorganization of lipid membranes driven by temperature changes. Scientific Reports, 2021, 11(1), 21990.



2. Seminar topic: “Methods of high-performance numerical study of physical characteristics of superconducting Josephson structures in dependence of parameters of the models”

   Speakers: Maxim Bashashin, Ilhom Rahmonov, Elena Zemlyanaya

   Abstract:
   

   Methods and software packages for parallel implementation of studying two models of superconducting structures are presented. The first model describes a system of coupled long Josephson junctions taking into account the inductive and capacitive coupling between neighboring junctions and electromagnetic radiation at their boundaries. The second model describes the structure of a point φ0 junction with spin-orbit coupling in a ferromagnetic layer and a pulsed current source acting on it.

   The new parallel computing methods made it possible to successfully study the physical characteristics in these models in a wide range of parameters. The parallel software packages have been deposited to the JINR program library and are freely available. The calculations were performed on the HybriLIT computing resources of the JINR Multifunctional Information and Computing Complex.

3. Seminar topic: “Simulation of a controllable magnetisation reversal in a chain of Phi-0 junctions by an ac voltage pulse”

   Speakers: Adiba Rahmonova, Oksana Streltsova, Ilhom Rahmonov, Maxim Zuev

   Abstract:
   

   In Phi-0 Josephson junctions, the spin-orbit interaction in a ferromagnet layer provides a mechanism for direct coupling between the magnetisation and the superconducting current, which makes it possible to control the magnetic properties by means of the Josephson current and the effect of magnetisation on the Josephson current. Recently, the possibility of developing cryogenic memory based on the magnetisation reversal in the Phi-0 junction has been studied [1, 2]. However, when using several Phi-0 junctions in a single chip, it becomes necessary to realise the magnetisation reversal in a selected Phi-0 junction. The authors propose a solution to this problem based on mathematical modelling of the dynamics of a system consisting of three Phi-0 junctions connected via LCR-circuits, which is reduced to solving the Cauchy problem. It is shown that by applying an AC external voltage pulse with a frequency coinciding with the eigenfrequency of the LCR-circuit, it is possible to realise the magnetisation reversal in a selected Phi-0 junction, i.e., the possibility of controlled reversal of magnetisation is demonstrated. The influence of system parameters on the dynamics of magnetisation in each of the Phi-0 junction is studied in detail. The researchers developed a software module for the performed calculations. These materials are publicly available on the ML/DL/HPC ecosystem of the HybriLIT Platform (MLIT JINR) [3] in the form of electronic books Jupyter Book [4, 5].

   The work was performed with the support of the Russian Science Foundation as part of project No. 22-71-10022.

   1. Y. M. Shukrinov, Anomalous Josephson effect, Phys. Usp. 65 317–354 (2022)
   2. C. Guarcello and F.S. Bergeret, Phys. Rev. Applied 13, 034012 (2020)
   3. Ecosystem ML/DL/HPC/
   4. A.R. Rahmonova, O.I. Streltsova, M.I. Zuev, I.R. Rahmonov, Python toolkit for simulating the dynamics of a Josephson junction under the influence of external radiation (2023).
   5. M.V. Bashashin, Y.A. Butenko, K.V. Kulikov, A.V. Nechaevskiy, I.R. Rahmonov, A.R. Rahmonova, O.I. Streltsova, M.I. Zuev, Toolkit for modeling superconductor/magnetic hybrid nanostructures (2022).