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Opis: 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...sources to investigate the microscopic and/or ultrafast dynamics of matter samples, which have been...
Ključne besede: 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
Objavljeno: 02.12.2020; Ogledov: 1086; Prenosov: 31
Polno besedilo (19,78 MB)

Opis: Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements; the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state; backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy); the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Najdeno v: ključnih besedah
Ključne besede: entropy, protein, molecular dynamics, simulations, MD
Objavljeno: 12.10.2016; Ogledov: 2485; Prenosov: 171
Polno besedilo (2,40 MB)

Opis: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules
Najdeno v: ključnih besedah
Ključne besede: nanobodies, molecular dynamics, modeling, antibody solubility
Objavljeno: 11.10.2016; Ogledov: 2859; Prenosov: 195
Polno besedilo (1,95 MB)

Opis: Complexity-based analyses may quantify abnormalities in heart rate variability (HRV). The aim of this study was to investigate the clinical and prognostic significances of dynamic HRV changes in patients with stress-induced cardiomyopathy Takotsubo syndrome (TS) by means of linear and nonlinear analysis. Patients with TS were included in study after complete noninvasive and invasive cardiovascular diagnostic evaluation and compared to an age and gender matched control group of healthy subjects. Series of R–R interval and of ST–T interval values were obtained from 24-h ECG recordings after digital sampling. HRV analysis was performed by ‘range rescaled analysis’ to determine the Hurst exponent, by detrended fluctuation analysis to quantify fractal longrange correlation properties, and by approximate entropy to assess time-series predictability. Short- and long-term fractal-scaling exponents were significantly higher in patients with TS in acute phases, opposite to lower approximate entropy and Hurst exponent, but all variables normalized in a few weeks. Dynamic HRV analysis allows assessing changes in complexity features of HRV in TS patients during the acute stage, and to monitor recovery after treatment, thus complementing traditional ECG and clinically analysis.
Najdeno v: ključnih besedah
Povzetek najdenega: ...Heart rate variability, Nonlinear dynamics, Chaos theory, Stress-induced cardiomyopathy, Takotsubo syndrome...
Ključne besede: Heart rate variability, Nonlinear dynamics, Chaos theory, Stress-induced cardiomyopathy, Takotsubo syndrome
Objavljeno: 13.07.2017; Ogledov: 2639; Prenosov: 0
Polno besedilo (742,92 KB)

Opis: We take a space X of dynamical systems that could be: homeomorphisms or continuous maps of a compact metric space K or diffeomorphisms of a smooth manifold or actions of an amenable group. We demonstrate that a typical dynamical system of X is a continuity point for the set of probability invariant measures considered as a function of a map, let Y be the set of all such continuity points. As a corollary we prove that for typical dynamical systems average values of continuous functions calculated along trajectories do not drastically change if the system is perturbed.
Najdeno v: ključnih besedah
Ključne besede: ergodic theory, invariant measures, shadowing, stability, tolerance stability, topological dynamics
Objavljeno: 02.10.2017; Ogledov: 2001; Prenosov: 0
Polno besedilo (529,51 KB)