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1.
Advantages and disadvantages of experiments with ultrashort two-color pulses
Matija 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.
Found in: ključnih besedah
Summary of found: ...sources to investigate the microscopic and/or ultrafast dynamics of matter samples, which have been...
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: 02.12.2020; Views: 822; Downloads: 23
.pdf Fulltext (19,78 MB)

2.
Computational design of customised nanobodies for biotechnological applications
Sara Fortuna, Ario de Marco, Miguel Soler, 2016, unpublished conference contribution

Abstract: In silico modeling to improve the biophysical characteristics of recombinant single-domain antibodies
Found in: ključnih besedah
Keywords: nanobodies, modeling, protein stability, antibody humanization, molecular dynamics
Published: 26.04.2016; Views: 2555; Downloads: 0
.pdf Fulltext (2,42 MB)

3.
Distance-based configurational entropy of proteins from molecular dynamics simulations
Federico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, original scientific article

Abstract: 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.
Found in: ključnih besedah
Keywords: entropy, protein, molecular dynamics, simulations, MD
Published: 12.10.2016; Views: 2308; Downloads: 165
.pdf Fulltext (2,40 MB)

4.
Accurate estimation of the entropy of rotation-translation probability distributions
Federico Fogolari, Cedrix Jurgal Dongmo Foumthuim, Sara Fortuna, Miguel Angel Soler, Alessandra Corazza, Gennaro Esposito, 2016, original scientific article

Abstract: The estimation of rotational and translational entropies in the context of ligand binding has been the subject of long-time investigations. The high dimensionality (six) of the problem and the limited amount of sampling often prevent the required resolution to provide accurate estimates by the histogram method. Recently, the nearest-neighbor distance method has been applied to the problem, but the solutions provided either address rotation and translation separately, therefore lacking correlations, or use a heuristic approach. Here we address rotational–translational entropy estimation in the context of nearest-neighbor-based entropy estimation, solve the problem numerically, and provide an exact and an approximate method to estimate the full rotational–translational entropy.
Found in: ključnih besedah
Summary of found: ...entropy, probability distribution, molecular dynamics, nearest-neighbor...
Keywords: entropy, probability distribution, molecular dynamics, nearest-neighbor
Published: 11.10.2016; Views: 2360; Downloads: 0
.pdf Fulltext (1,47 MB)

5.
Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies
Ario de Marco, Miguel Soler, Sara Fortuna, 2016, original scientific article

Abstract: 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
Found in: ključnih besedah
Keywords: nanobodies, molecular dynamics, modeling, antibody solubility
Published: 11.10.2016; Views: 2657; Downloads: 189
.pdf Fulltext (1,95 MB)

6.
Self-amplified photo-induced gap quenching in a correlated electron material
Jurij Urbančič, Eich Steffen, Mathias Stefan, 2016, original scientific article

Abstract: Capturing the dynamic electronic band structure of a correlated material presents a powerful capability for uncovering the complex couplings between the electronic and structural degrees of freedom. When combined with ultrafast laser excitation, new phases of matter can result, since far-from-equilibrium excited states are instantaneously populated. Here, we elucidate a general relation between ultrafast non-equilibrium electron dynamics and the size of the characteristic energy gap in a correlated electron material. We show that carrier multiplication via impact ionization can be one of the most important processes in a gapped material, and that the speed of carrier multiplication critically depends on the size of the energy gap. In the case of the charge-density wave material 1T-TiSe 2 , our data indicate that carrier multiplication and gap dynamics mutually amplify each other, which explains—on a microscopic level—the extremely fast response of this material to ultrafast optical excitation. Self-amplified photo-induced gap quenching in a correlated electron material. Available from: https://www.researchgate.net/publication/308804379_Self-amplified_photo-induced_gap_quenching_in_a_correlated_electron_material [accessed Apr 20, 2017].
Found in: ključnih besedah
Summary of found: ...a general relation between ultrafast non-equilibrium electron dynamics and the size of the characteristic energy...
Keywords: high harmonic generation, charge-density wave material, 1T-TiSe2, non-equilibrium electron dynamics, ultrafast surface science
Published: 20.04.2017; Views: 2975; Downloads: 0
.pdf Fulltext (1,10 MB)

7.
Heart rate variability and nonlinear dynamic analysis in patients with stress-induced cardiomyopathy
Antonija Krstačić, Paolo Castiglioni, Dragan Gamberger, Gianfranco Parati, Goran Krstačić, Robert Steiner, 2012, original scientific article

Abstract: 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.
Found in: ključnih besedah
Summary of found: ...Heart rate variability, Nonlinear dynamics, Chaos theory, Stress-induced cardiomyopathy, Takotsubo syndrome...
Keywords: Heart rate variability, Nonlinear dynamics, Chaos theory, Stress-induced cardiomyopathy, Takotsubo syndrome
Published: 13.07.2017; Views: 2403; Downloads: 0
.pdf Fulltext (742,92 KB)

8.
Weak forms of shadowing in topological dynamics
Sergey Kryzhevich, Danila Cherkashin, 2017, original scientific article

Abstract: We consider continuous maps of compact metric spaces. It is proved that every pseudotrajectory with sufficiently small errors contains a subsequence of positive density that is point-wise close to a subsequence of an exact trajectory with the same indices. Also, we study homeomorphisms such that any pseudotrajectory can be shadowed by a finite number of exact orbits. In terms of numerical methods this property (we call it multishadowing) implies possibility to calculate minimal points of the dynamical system. We prove that for the non-wandering case multishadowing is equivalent to density of minimal points. Moreover, it is equivalent to existence of a family of $\varepsilon$-networks ($\varepsilon > 0$) whose iterations are also $\varepsilon$-networks. Relations between multishadowing and some ergodic and topological properties of dynamical systems are discussed.
Found in: ključnih besedah
Keywords: Topological dynamics, minimal points, invariant measure, shadowing, chain recurrence, $\varepsilon$-networks, syndetic sets
Published: 27.07.2017; Views: 2413; Downloads: 0
.pdf Fulltext (499,38 KB)

9.
Sets of Invariant Measures and Cesaro Stability
Sergey Kryzhevich, 2017, original scientific article

Abstract: 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.
Found in: ključnih besedah
Keywords: ergodic theory, invariant measures, shadowing, stability, tolerance stability, topological dynamics
Published: 02.10.2017; Views: 1821; Downloads: 0
.pdf Fulltext (529,51 KB)

10.
Nanobodies: towards rational design of immune-reagents
Ario De Marco, 2017, published scientific conference contribution abstract (invited lecture)

Abstract: Antibodies are irreplaceable reagents in both research and clinical practice. Despite their relevance, the structural complexity of conventional mono- and polyclonal antibodies (IgG) has always been a limit for their engineering towards reagents optimized for specific applications, such as in vivo diagnostics and therapy. Furthermore, their isolation is time consuming, their production expensive, and their functionalization results often in heterogeneous macromolecule populations. These drawbacks promoted the search for both innovative antibody isolation strategies and alternative scaffolds. In vitro panning of pre-immune collections of recombinant antibody fragments allows for the simple and fast recovery of binders. Since they did not undergo somatic maturation, their affinity for targets can be insufficient but on the other hand they can be rapidly mutated by standard molecular biology techniques to generate second-generation antibodies among which to identify clones with improved characteristics. Both stochastic and rational methods have been proposed for the optimization process. Random mutagenesis followed by panning at stringent conditions has been successful used to select binders with improved physical characteristics. Rational methods try to identify in silico key residues involved in the regulation of specific antibody features, such as stability or binding affinity. The accuracy of these methods usually depends on the calculation resources. In this perspective, smaller molecules can be analyzed “better” than larger because of their restricted number of residues. Nanobodies small dimensions have been long appreciated since enable better tissue penetration, shorter clearance time, higher yields. Now it becomes evident that this characteristic makes them also optimal objects for modeling.
Found in: ključnih besedah
Summary of found: ...recombinant antibody modeling, nanobody engineering, molecular dynamics and docking...
Keywords: recombinant antibody modeling, nanobody engineering, molecular dynamics and docking
Published: 21.03.2018; Views: 2288; Downloads: 0
.pdf Fulltext (638,20 KB)

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