ULTRAFAST ELECTRON DYNAMICS IN CORRELATED SYSTEMS PROBED BY TIME-RESOLVED PHOTOEMISSION SPECTROSCOPYTanusree Saha
, 2023, doctoral dissertation
Abstract: Complex systems in condensed matter are characterized by strong coupling
between different degrees of freedom constituting a solid. In materials
described by many-body physics, these interactions may lead to
the formation of new ground states such as excitonic insulators, Mott
insulators, and charge and spin density waves. However, the inherent
complexity in such materials poses a challenge to identifying the
dominant interactions governing these phases using equilibrium studies.
Owing to the distinct timescales associated with the elementary interactions,
such complexities can be readily addressed in the non-equilibrium
regime. Additionally, these materials might also show the emergence
of new, metastable “hidden“ phases under non-equilibrium. The thesis
investigates the ultrafast timescales of fundamental interactions in candidate
systems by employing time-and angle-resolved photoemission spectroscopy
in the femtosecond time domain. In the (supposed) excitonic
insulator model system Ta2NiSe5, the timescale of band gap closure
and the dependence of rise time (of the photoemission signal) on the
photoexcitation strength point to a predominantly electronic origin of
the band gap at the Fermi level. The charge density wave (CDW) -
Mott insulator 1T-TaS2 undergoes photoinduced phase transition to two
different phases. The initial one is a transient phase which resembles
the systems’s high temperature equilibrium phase, followed by a long-lived
“hidden“ phase with a different CDW amplitude and is primarily
driven by the CDW lattice order. For the spin density wave system
CaFe2As2 where multiple bands contribute in the formation of Fermi surfaces,
selective photoexcitation was used to disentangle the role played
by different electron orbitals. By varying the polarization of photoexcitation
pulses, it is observed that dxz/dyz orbitals primarily contribute to
the magnetic ordering while the dxy orbitals have dominant role in the
structural order. The findings of the present study provide deeper perspectives
on the underlying interactions in complex ground phases of
matter, therefore, initiating further experimental and theoretical studies
on such materials.
Keywords: complex systems, charge density wave, excitonic insulator, metastable phase, Mott insulator, non-equilibrium, spin density wave, timescales, time- and angle-resolved photoemission, ultrafast dynamics
Published in RUNG: 01.06.2023; Views: 492; Downloads: 14
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Dynamical interplay between the human high-affinity copper transporter hCtr1 and its cognate metal ionGulshan Walke
, Jana Aupič
, Hadeel Kashoua
, Pavel Janoš
, Shelly Meron
, Yulia Shenberger
, Zena Qasem
, Lada Gevorkyan-Airapetov
, Alessandra Magistrato
, Sharon Ruthstein
, 2022, original scientific article
Abstract: Abnormal cellular copper levels have been clearly implicated in genetic diseases, cancer, and neurodegeneration. Ctr1, a high-affinity copper transporter, is a homotrimeric integral membrane protein that provides the main route for cellular copper uptake. Together with a sophisticated copper transport system, Ctr1 regulates Cu(I) metabolism in eukaryotes. Despite its pivotal role in normal cell function, the molecular mechanism of copper uptake and transport via Ctr1 remains elusive. In this study, electron paramagnetic resonance (EPR), UV-visible spectroscopy, and all-atom simulations were employed to explore Cu(I) binding to full-length human Ctr1 (hCtr1), thereby elucidating how metal binding at multiple distinct sites affects the hCtr1 conformational dynamics. We demonstrate that each hCtr1 monomer binds up to five Cu(I) ions and that progressive Cu(I) binding triggers a marked structural rearrangement in the hCtr1 C-terminal region. The observed Cu(I)-induced conformational remodeling suggests that the C-terminal region may play a dual role, serving both as a channel gate and as a shuttle mediating the delivery of copper ions from the extracellular hCtr1 selectivity filter to intracellular metallochaperones. Our findings thus contribute to a more complete understanding of the mechanism of hCtr1-mediated Cu(I) uptake and provide a conceptual basis for developing mechanism-based therapeutics for treating pathological conditions linked to de-regulated copper metabolism.
Keywords: ctr1, copper, epr, molecular dynamics
Published in RUNG: 15.09.2022; Views: 707; Downloads: 0
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The conformational plasticity of the selectivity filter methionines controls the in-cell Cu(I) uptake through the CTR1 transporterPavel Janoš
, Jana Aupič
, Sharon Ruthstein
, Alessandra Magistrato
, 2022, original scientific article
Abstract: Copper is a trace element vital to many cellular functions. Yet its abnormal levels are toxic to cells, provoking a variety of severe diseases. The high affinity copper transporter 1 (CTR1), being the main in-cell copper [Cu(I)] entry route, tightly regulates its cellular uptake via a still elusive mechanism. Here, all-atoms simulations unlock the molecular terms of Cu(I) transport in eukaryotes disclosing that the two methionine (Met) triads, forming the selectivity filter, play an unprecedented dual role both enabling selective Cu(I) transport and regulating its uptake rate thanks to an intimate coupling between the conformational plasticity of their bulky side chains and the number of bound Cu(I) ions. Namely, the Met residues act as a gate reducing the Cu(I) import rate when two ions simultaneously bind to CTR1. This may represent an elegant autoregulatory mechanism through which CTR1 protects the cells from excessively high, and hence toxic, in-cell Cu(I) levels. Overall, our outcomes resolve fundamental questions in CTR1 biology and open new windows of opportunity to tackle diseases associated with an imbalanced copper uptake.
Keywords: copper, membrane transporter, molecular dynamics, QM/MM, free energy
Published in RUNG: 15.09.2022; Views: 765; Downloads: 0
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Characterization of a karst aquifer in the recharge area of Malenščica and Unica springs based on spatial and temporal variations of natural tracersBlaž Kogovšek
, 2022, doctoral dissertation
Abstract: The aim of the present study is to characterize and improve the still insufficient knowledge of the recharge processes that have an important influence on the flow and solute transport in karst aquifers and thus also on the quantity and quality of karst water sources. A binary karst aquifer in the recharge area of the Malenščica and Unica springs, which covers an area of about 820 km2 in SW Slovenia, was selected as the study area.
A dense monitoring network was established at 20 observation points (six springs, four ponors, seven water-active caves and three surface streams) for simultaneous monitoring of the hydrological characteristics and the physicochemical properties of the water, the so-called natural tracers. Data-loggers were installed to measure water pressure, temperature and conductivity. During selected storm events, samples were taken for chemical and microbiological analyses and discharge measurements were made. The meteorological and hydrological data of the Slovenian Environment Agency complemented the extensive dataset.
Collected data allowed the analysis and comparison of the spatial and temporal variations of the natural tracers under different hydrological conditions. Frequent discharge measurements allowed the generation of rating curves and proved to be a crucial element for understanding the hydraulic processes that determine the functioning of this system. The calculation of the water budget allowed an assessment of the proportion of autogenic and allogenic recharge of the springs and a quantitative estimate of autogenic recharge under different hydrological conditions.
The hydrological analysis, i.e. the flow duration curve, the hydrograph separation techniques and the recession analysis, revealed that the Malenščica spring has a higher storage capacity, a greater proportion of autogenic recharge, especially at low-flow, and a slower recession than the Unica spring. This was also confirmed by correlation and spectral analyses, which were also used to investigate the relationships between discharges at ponors and springs. However, the results of the cross-correlation analysis showed hardly any difference between the two springs and in this case proved to be unsuitable for studying the influence of allogenic recharge. Instead, partial cross-correlation analysis was used to control the input parameters of effective precipitation and discharge of one of the sinking streams to determine the contribution of the other sinking stream to the observed spring. The results confirmed differences in allogenic recharge of the Unica and Malenščica springs.
Hysteresis analysis has been applied as a complementary method to time series analysis and represents an improved approach to the characterization of the karst hydrological system. The hydraulic approach to the construction of hysteresis enabled a detailed analysis of allogenic and autogenic water interaction and its influence on the Malenščica and Unica springs under different hydrological conditions. Narrow shapes of the hysteresis indicate a direct hydraulic connection between the ponor and the spring and thus a well-developed drainage system. Any deviation towards a convex or concave shape indicates a less developed, more matrix-related drainage system or the influence of other recharge sources. Analysis of physicochemical hysteretic function of individual locations confirmed the differences in the recharge characteristics of the two springs. Compared to the Unica spring, the Malenščica spring has specific recharge characteristics that result in lower vulnerability to the effects of the sinking streams. A greater proportion of autogenic recharge in the initial phase of the storm event is important, as it allows for a time delay of the possible negative effects of the sinking stream. However, possible pollution from the area of autogenic recharge can have strong negative effects, as in this initial phase with low discharges the dilution effect is negligible.
Keywords: karst aquifer, dynamics of natural tracers, storm events, discharge measurements, time series analysis, hysteresis, Unica spring, Malenščica spring
Published in RUNG: 01.03.2022; Views: 1476; Downloads: 84
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Testing the predictions of axisymmetric distribution functions of galactic dark matter with hydrodynamical simulationsMihael Petač
, Julien Lavalle
, Arturo Núñez-Castiñeyra
, Emmanuel Nezri
, 2021, original scientific article
Abstract: Signal predictions for galactic dark matter (DM) searches often rely on assumptions regarding the DM phase-space distribution function (DF) in halos. This applies to both particle (e.g. p-wave suppressed or Sommerfeld-enhanced annihilation, scattering off atoms, etc.) and macroscopic DM candidates (e.g. microlensing of primordial black holes). As experiments and observations improve in precision, better assessing theoretical uncertainties becomes pressing in the prospect of deriving reliable constraints on DM candidates or trustworthy hints for detection. Most reliable predictions of DFs in halos are based on solving the steady-state collisionless Boltzmann equation (e.g. Eddington-like inversions, action-angle methods, etc.) consistently with observational constraints. One can do so starting from maximal symmetries and a minimal set of degrees of freedom, and then increasing complexity. Key issues are then whether adding complexity, which is computationally costy, improves predictions, and if so where to stop. Clues can be obtained by making predictions for zoomed-in hydrodynamical cosmological simulations in which one can access the true (coarse-grained) phase-space information. Here, we test an axisymmetric extension of the Eddington inversion to predict the full DM DF from its density profile and the total gravitational potential of the system. This permits to go beyond spherical symmetry, and is a priori well suited for spiral galaxies. We show that axisymmetry does not necessarily improve over spherical symmetry because the (observationally unconstrained) angular momentum of the DM halo is not generically aligned with the baryonic one. Theoretical errors are similar to those of the Eddington inversion though, at the 10-20% level for velocity-dependent predictions related to particle DM searches in spiral galaxies. We extensively describe the approach and comment on the results.
Keywords: galaxy dynamics, dark matter experiments, dark matter simulations, dark matter theory, cosmology, nongalactic astrophysics, astrophysics of galaxies, high energy physics
Published in RUNG: 01.10.2021; Views: 1416; Downloads: 63
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Advantages and disadvantages of experiments with ultrashort two-color pulsesMatija Stupar
, 2020, doctoral dissertation
Abstract: Advances in the development of lasers have led to a new class of radiation sources generating coherent, tunable, ultrashort light pulses in the spectral region ranging from infrared to soft X-rays. This includes high-order harmonics generation in gas (HHG), on which relies the CITIUS facility at University of Nova Gorica (Slovenia), and free-electron lasers (FELs), such as the facility FERMI at Elettra-Sincrotrone Trieste (Italy). The distinctive structure of HHG and FEL radiation paved the way to time-resolved experiments, which are performed to investigate events occurring on a short, or very short, temporal scale, from picoseconds to femtoseconds.
This work focuses on the advantages and disadvantages of some experimental techniques based on using these novel light sources to investigate the microscopic and/or ultrafast dynamics of matter samples, which have been previously driven out of equilibrium.
Advantages rely on the implementation of various applications based on two-color schemes and, more specifically, include the possibility of acquiring two-dimensional frequency maps, measuring electrons’ effective masses, or investigating electronic properties decoupled from the influence of the lattice. Particular focus will be put on experimental methods relying on photoelectric effect and photoelectron spectroscopy. In all experiments, we took advantage of one or more specific properties of HHG and FEL sources, such as controllable chirp, to study laser dressed states in helium, variable polarization, to study electronic properties of iron-based pnictides and ultrashort pulses (< 10 fs) to study the purely electronic dynamics in transition metal dichalcogenides.
On the other hand, the study of the interface between a molecule and a topological insulator revealed some intrinsic limitations and physical drawbacks of the technique, such as spurious effects originating from the high power pulses, like multiphoton absorption and the space charge effect, or the reduction of experimental resolution when pushing for shorter and shorter pulse durations. Some disadvantages are also connected to the current state-of-the-art in the field of ultrashort laser systems, where a trade-off needs to be found between repetition rate and laser power.
Finally, state-of-the-art experiments based on the ability to generate ultrashort pulses carrying orbital angular momentum in visible, near-infrared as well as extreme UV range will be presented. The use of these pulses opens the door to the investigation of new physical phenomena, such as probing magnetic vortices using extreme ultraviolet light from a free-electron laser or imprinting the spatial distribution of an ultrashort infrared pulse carrying orbital angular momentum onto a photoelectron wave packet.
Keywords: ultrafast lasers, two-color experiments, photoemission, high-order harmonic generation, free-electron lasers, hot-electrons dynamics, surface science, pump-probe photoemission, ultraviolet photoemission, orbital angular momentum
Published in RUNG: 02.12.2020; Views: 3034; Downloads: 108
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Bora wind effects on common structures in the Vipava valleyMarija Bervida
, 2020, doctoral dissertation
Abstract: Strong and gusty north-east wind called Bora is common in south-west regions of Slovenia, as well as along the Adriatic coast. Its intermittent behavior, related to variable strength, frequency and duration, has brought out scientific curiosity for decades. Bora affects human life and causes problems for structures built in Bora affected areas. In Slovenia, Bora is the strongest in the Vipava valley. The motivation for this research is the need to evaluate Bora wind effects on structures, commonly found in the Vipava valley region, using a high resolution computational fluid dynamics (CFD) modeling approach. To date, there are several experimental and computational constraints for accurate representation of Bora in a CFD model, therefore, the main aim of this dissertation is to build foundations for Bora wind simulations using CFD and its method of finite
volumes. The dissertation incorporates the analysis of experimental measurements of Bora wind, as well as numerical modeling studies.
Vertical mean wind speed profile characteristics of Bora were analyzed based on experimental measurements at Razdrto just above the Vipava valley. The obtained results contributed to the choice of Bora mean wind profiles applied at the inflow of computational models. Guidelines regarding the choice of the associated wind profile parameters were given and a new relationship between these parameters was found. As orographic barriers to the north of the Vipava valley
are known to give rise to Bora and to define the specific properties of the Bora flow, numerical modeling studies were in the first place focused on the implementation of the real-scale complex terrain into a CFD model. Simulation of wind flow over orographic barrier in Vipava valley was performed using Raynolds averaged Navier-Stokes approach, providing a first estimation of the flow field over a small hill of
As resolving the turbulence characteristics of Bora is very important for the estimation of wind loads on structures, modeling studies converged towards a more appropriate approach - Large eddy simulations (LES). A crucial step in setting up an accurate LES is the generation of appropriate inflow, which was investigated for the case of atmospheric boundary layer (ABL) flow. The synthetic method PRFG^3 for the generation of unsteady inflow was tested and adapted as a source of an ABL flow with desired turbulence flow properties. Based on its performance, in particular on adequate reproduction of target turbulence intensities and length scales, it was found that PRFG^3 method may be used to generate velocity inflow with desired turbulence properties in LES. Finally, simulations of wind flow coming from Bora direction over the Vipava valley were performed with the aim to depict the effects of underlying orography on the flow within and above the valley. Modeling results were found to be comparable with the results of lidar based remote sensing of vertical atmospheric structures within and above the valley.
Keywords: Vipava valley, Bora wind, Wind profile, Orography, Atmospheric boundary layer, Computational fluid dynamics, Numerical simulations
Published in RUNG: 17.06.2020; Views: 4350; Downloads: 46
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