Miracle-dz/UniFAR-FTUs huggingface dataset:
Rigidity analysis of protein structures and rapid simulations of protein motion

It is a common goal in biophysics to understand protein structural properties and their relationship to protein function. I investigated protein structural properties using three coarse graining methods: a rigidity analysis method First, a geometric simulation method Froda and normal mode analysis as implemented in Elnemo to identify the protein directions of motion. Furthermore, I also compared the results between the coarse graining methods with the results from molecular dynamics and from experiments that I carried out. The results from the rigidity analysis across a set of protein families presented in chapter 3 highlighted two different patterns of protein rigidity loss, i.e. "sudden" and "gradual". It was found that theses characteristic patterns were in line with the rigidity distribution of glassy networks. The simulations of protein motion by merging flexibility, rigidity and normal mode analyses presented in chapter 4 were able to identify large conformational changes of proteins using minimal computational resources. I investigated the use of RMSD as a measure to characterise protein motion and showed that, despite it is a good measure to identify structural differences when comparing the same protein, the use of extensive RMSD better captures the extend of motion of a protein structure. The in-depth investigation of yeast PDI mobility presented in chapter 5 confirmed former experimental results that predicted a large conformational change for this enzyme. Furthermore, the results predicted: a characteristic rigidity distribution for yeast PDI, a minimum and a maximum active site distance and a relationship between the energy cutoff, i.e. the number of hydrogen bonds part of the network of bonds, and protein mobility. The results obtained were tested against molecular dynamics simulations in chapter 6. The MD simulation also showed a large conformational change for yeast PDI but with a slightly different minimum and maximum inter-cysteine distance. Furthermore, MD was able to reveal new data, i.e. the most likely inter-cysteine distance. In order to test the accuracy of the coarse graining and MD simulations I carried out cross-linking experiments to test the minimum inter-cysteine distance predictions. The results presented in chapter 7 show that human PDI minimum distance is below 12A whereas the yeast PDI minimum distance must be above 12A as no cross-linking structures where found with the available (12A long) cross-linkers.
Baroclinic instability of a midlatitude zonal mean state changing with time

A characteristic frequency equation is formulated for atmospheric Rossby waves embedded in a basic zonal mean state changing periodically with time, based on the two-layer model in the midlatitude ? -plane. The characteristic frequencies are calculated for a truncated set of waves including up to the third higher harmonics of geopotential and temperature, and the results are compared with the classical baroclinic instability theory. The zonal mean thermal wind oscillating around the stationary state is found to be more unstable against small perturbations than the instability predicted by classical theory. The oscillating thermal wind influences the Rossby waves in two ways, firstly by enhancing the growth rate and secondly by modulating the propagation phase speed around the central phase velocity. The relative magnitudes of these two effects depend on the frequency and the amplitude of the changing thermal wind. On the other hand, the changing zonal mean wind mainly affects the phase speed of the Rossby waves with little influence on the growth rate. Using a highly truncated model it is shown that a resonant-type interaction is possible between the geopotential and the temperature wave modes in the perturbation when the zonal mean thermal wind changes periodically with time. It is suggested that the discrepancy often observed between the phase speed of developing Rossby waves on weather maps and classic baroclinic instability theory might be partly due to the changing zonal mean state with time. DOI: 10.1111/j.2153-3490.1982. tb01815.x
Chabazite: Energetics of hydration, enthalpy of formation, and effect of cations on stability

Abstract The stability of synthetic cation-exchanged zeolites having the chabazite framework (CHA) and their cation-water interaction were studied using high-temperature reaction calorimetry. Four cations (K, Na, Li, and Ca) were exchanged into CHA. The enthalpies of formation were determined for all samples, and the partial molar enthalpy of hydration was measured by varying the water content of one Ca-CHA. The enthalpy of formation depends strongly on the exchanged cation, becoming more exothermic in the order Ca, Li, Na, K. The integral hydration enthalpy does not depend strongly on the nature of the cation, but becomes slightly less exothermic with increasing aluminum content. For the one Ca-CHA studied in detail, the average enthalpy of hydration is -34.6 ± 1.2 kJ/mol relative to liquid water. A quadratic fit to the transposed temperature drop data gives Δh̅H₂O = -52.97 (± 4.74) + 2.94 (± 0.68) n (kJ/mol), where Δh̅H₂O is the partial molar enthalpy of hydration and n is the number of water molecules per 24 oxygen formula.
Dose-time dependency of tumor formation by chronic UV exposure.

-An animal experiment is presented which involved a total of 223 albino hairless mice (Skh hr 1). These mice, excluding 24 of them which served as controls, were divided over 6 groups, each of which received a different but constant daily dose of UV radiation from fluorescent sunlamps (Westinghouse FS40TL12). The range of daily doses encompassed a factor of 33. Data on the response of each group as a whole are presented. The group responses are measured in two ways: (1) the proportion of tumor bearing mice (prevalence), and (2) the average number of tumors per survivor (yield). The data provide information on the variation of the group response with time, daily dose and tumor size. The relationship between the daily dose and the duration of the treatment till 50% of the mice have tumors is given for several sizes of tumors. From these results, and from direct measurements of tumor growth, it appears that the growth of tumors is virtually dose-independent and, in consequence, only the initiation of tumors is dose-dependent. This implies that the theoretical model of UV-tumorigenesis presented by Blum (1959). based on UV-accelerated growth, is incorrect. It is pointed out that, in similarity to chemo- and radiotumorigenesis, the total dose delivered to a mouse for the induction of tumors has to be higher if a high daily dose is used than if a low daily dose is used. It seems as though an animal becomes more resistant to the UV-stimuius as the rate at which the stimulus is presented is increased: an adaptive phenomenon.
Perturbations in a scalar field model with virtues of $\Lambda$CDM

In the era of precision cosmology, the cosmological constant $\Lambda$ gives quite an accurate description of the evolution of the Universe, but it is still plagued with the fine-tuning problem and the cosmic coincidence problem. In this work, we investigate the perturbations in a scalar field model that drives the recent acceleration in a similar fashion that the cosmological constant does and has the dark energy (DE) density comparable to the dark matter (DM) energy density at the recent epoch starting from arbitrary initial conditions. The perturbations show that this model, though it keeps the virtues of a $\Lambda$CDM model, has a distinctive qualitative feature, particularly it reduces the amplitude of the matter power spectrum on a scale of $8 h^{-1}\, \mbox{Mpc}$, $\sigma_{8}$ at the present epoch.
Critical phenomena in liquids and liquid crystals

defects in liquid crystals computer simulations theory and experiments PDF cooperative phenomena in jahn teller crystals PDF critical phenomena PDF critical phenomena proc of a conference PDF conformal invariance and critical phenomena PDF critical series phenomena answers PDF conformal invariance and critical phenomena 1st edition PDF critical phenomena in alloys magnets and superconductors PDF critical thinking series phenomena answer guide PDF conformal field theory and critical phenomena in two dimensional systems PDF critical phenomena 1983 brasov school conference progress in physics vol 11 PDF critical scattering theory an introduction phase transition phenomena volume 1 PDF critical phenomena in natural sciences chaos fractals selforganization and disorder concepts and PDF critical phenomena in natural sciences chaos fractals selforganization and disorder concepts and tools PDF critical phenomena italian physical society proceedings of the international school of physics enrico fermi course 51 PDF
Fast and stable algorithm for analytical evaluation of two-center overlap integrals over Slater-type orbitals with integer and noninteger principal quantum numbers

A unified algorithm is presented for analytical evaluation of two-center overlap integrals over Slater-type orbitals with integer and noninteger principal quantum numbers. Two-center overlap integrals are expressed as finite sum of Gaunt coefficients and auxiliary functions S(p, t). Special attention is paid to the efficient calculation of this auxiliary function by introducing analytic and recurrence relations. In order to test the accuracy of the formula for two-center overlap integrals, we performed an extensive study in which quantum numbers, orbital exponents, and internuclear distances were varied over wide ranges. We found that the method presented here for two-center overlap integrals is fully reliable for very high quantum numbers and the computation times are very low. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
PERSISTENCE AND SURVIVAL ASPECTS OF FLUCTUATION PHENOMENA IN SURFACES

Title of dissertation: PERSISTENCE AND SURVIVAL ASPECTS OF FLUCTUATION PHENOMENA IN SURFACES Magdalena Constantin, Doctor of Philosophy, 2005 Dissertation directed by: Professor Sankar Das Sarma Department of Physics Controlling the stability of nanostructures is an important fundamental issue in nanoscience. A key problem in this respect is the random stochastic interface dynamics associated with equilibrium nanometer scale thermal fluctuations, which can be understood by applying first–passage statistical concepts, such as the temporal persistence [survival] probability P (t) [S(t)]. P (t) [S(t)] measures the probability of the step height not returning to the original [average] value within a given time interval. In this study, we measure the persistence exponent θ associated with the power–law decay of P (t) at large time scale and also the survival time scale, τs, describing the exponential decay of S(t) for several nonequilibrium surface growth processes and fluctuating steps on solid surfaces. We show that for growth models in the Molecular Beam Epitaxy universality class, the nonlinearity of the underlying equation is clearly reflected in the difference between the measured values of the positive and negative persistence exponents. We also find that the survival time scale provides useful information about the physical mechanism underlying step fluctuations. An exact relation between long-time behaviors of the survival probability and the autocorrelation function is established and numerically verified. The dependencies of the persistence and survival probabilities on the system size and the sampling time are shown to be described by simple scaling forms. We introduce the generalizations of the persistence and survival probabilities for surface fluctuations. Our measurements of the persistent large deviations probability and associated family of exponents show good agreement with the corresponding quantities measured experimentally using scanning tunneling microscopy dynamical images of step fluctuations. The spatial persistence and survival probabilities are also theoretically analyzed. Finally, we investigate the connection between the generalizations of the spatial and temporal persistence probabilities. PERSISTENCE AND SURVIVAL ASPECTS OF FLUCTUATION PHENOMENA IN SURFACES
Investigation of block depth distribution in PS‐b‐PMMA block copolymer using ultra‐low‐energy cesium sputtering in ToF‐SIMS

Directed self‐assembly of block copolymers (BCPs) is a promising candidate for next generation nanolithography. In order to validate a given pattern, the lateral and in‐depth distributions of the blocks should be well characterized; for the latter, time‐of‐flight (ToF) SIMS is a particularly well‐adapted technique. Here, we use an ION‐TOF ToF‐SIMS V in negative mode to provide qualitative information on the in‐depth organization of polystyrene‐b‐polymethylmethacrylate (PS‐b‐PMMA) BCP thin films. Using low‐energy Cs+ sputtering and Bi3+ as the analysis ions, PS and PMMA homopolymer films are first analyzed in order to identify the characteristic secondary ions for each block. PS‐b‐PMMA BCPs are then characterized showing that self‐assembled nanodomains are clearly observed after annealing. We also demonstrate that the ToF‐SIMS technique is able to distinguish between the different morphologies of BCP investigated in this work (lamellae, spheres or cylinders). ToF‐SIMS characterization on BCP is in good agreement with XPS analysis performed on the same samples. Copyright © 2013 John Wiley & Sons, Ltd.
Frictional influence on internal Kelvin waves

Frictional influence on free internal Kelvin waves is studied theoretically. For continuous stratification the friction enters as an eddy viscosity, and the solutions are written in terms of normal modes. This approach implies a stress-free bottom. To obtain an analytical solution, we have assumed that the vertical variation of the eddy viscosity is inversely proportional to the square of the Brunt-Vaisala frequency. Coastal as well as equatorial Kelvin waves are considered. The effects of bottom friction and frictional drag at an interface are studied explicitly in a vertically integrated two-layer model, taking the shear stress at a boundary to be proportional to the velocity difference across it. Formally, the continuously stratified case and the two-layer model result in the same set of equations. Explicit formulae for the frictional damping in time, the Rossby radius of deformation, the frequency, the phase difference between velocity and elevation, and the tilting of the internal co-phase lines backwards from the coast are given. In particular, the latter effect is shown to be much stronger for baroclinic waves than for the barotropic mode of the same wavelength. DOI: 10.1111/j.2153-3490.1981. tb01763.x
Structure-Dependent 4f-Core-Level Binding Energies for Surface Atoms on Ir(111), Ir(100)-(5×1), AND METASTABLE Ir(100)-(1×1)

Shifts in the core-level binding energies of surface atoms relative to bulk atoms which show a dramatic dependency on surface crystallography have been observed. Surface-atom core-level emission intensities are shown to give direct information on the number of surface atoms, while binding energies give information on the surface-atom coordination number. These data show that the reconstructed Ir(100)-(5\ifmmode\times\else\texttimes\fi{}1) face is described by a compressed hexagonal monolayer.
Crystal and molecular structure of dichlorotris-(1,2-dimethylimidazole)copper(II); a trigonal-bipyramidal complex showing elongation of the equatorial Cu–N bond

The structure of dichlorotris-(1,2-dimethylimidazole)copper(II), CuCl2(C5H8N2)3, has been determined by three-dimensional X-ray structure analysis and refined by least-squares methods using 3018 independent reflections to R= 0·032. The crystals are orthorhombic, with unit-cell dimensions a= 15·205, b= 8·791, c= 29·81 A, space group Pca21, and Z= 8. The complex is monomeric, and there are no chemically significant differences between the two crystallographically independent molecules in the cell. The copper atom has a trigonal-bipyramidal co-ordination, with the equatorial positions occupied by two chlorine atoms and a donor nitrogen atom. The equatorial Cu–N bonds (2·145 A) are appreciably longer than the axial ones (2·005 A). This is discussed in terms of the stereochemical influence of the half-filled dz2 orbital in this type of co-ordination. In all molecules the two Cu–Cl bonds are slightly different, with average lengths of 2·370 and 2·414 A.
Modeling the Motion of Microcapsules on Compliant Polymeric Surfaces

By integrating mesoscale models for hydrodynamics and micromechanics, we examine the fluid-driven motion of microcapsules on compliant surfaces. The capsules, modeled as fluid-filled elastic shells, represent polymeric microcapsules or biological cells. We examine the motion of these capsules on flat, mechanically uniform surfaces, mechanically patterned surfaces that contain alternating regions of hard and soft domains, and topologically patterned surfaces, i.e., a corrugated substrate and a substrate that encompasses a regular array of compliant posts. We isolate conditions where the mechanically and topographically patterned surfaces can transmit “stop” and “go” instructions, causing the capsules to halt at specific locations on the substrate, and with an increase in the imposed flow velocity, to resume moving. In the case of the corrugated surfaces, varying the size of the asperities permits significant control over the translational velocity of a capsule for a given shear rate. For surfaces containin.
Diagnostic Strategies for Recurrent Cervical Cancer: A Cohort Study

Objective The effectiveness of various strategies for the post-treatment monitoring of cervical cancer is unclear. This pilot study was conducted to explore recurrence patterns in and diagnostic strategies for patients with uterine cervical cancer who were meticulously followed using a customized monitoring plan. Methods The epidemiological and clinical data of patients with recurrent cervical cancer treated from March 2012 to April 2018 at a tertiary teaching hospital were retrospectively collected. The diagnostic methods and their reliability were compared across patients with various clinicopathological characteristics and were associated with survival outcomes. Results Two hundred sixty-four patients with recurrent cervical cancer were included in the study, among which recurrence occurred in the first three years after the last primary treatment in 214 patients (81.06%). Half of the recurrence events (50.76%) occurred only within the pelvic cavity, and most lesions (78.41%) were multiple in nature. Among all recurrent cases, approximately half were diagnosed based on clinical manifestations (n=117, 44.32%), followed by imaging examinations (n=76, 28.79%), serum tumor markers (n=34, 12.88%), physical examinations (n=33, 12.50%) and cervical cytology with or without high-risk human papillomavirus (hrHPV) testing (n=4, 1.52%). The reliability of the diagnostic methods was affected by the stage (p<0.001), primary treatment regimen (p=0.001), disease-free survival (p=0.022), recurrence site (p=0.002) and number of recurrence sites (p=0.001). Primary imaging methods (sonography and chest X-ray) were not inferior to secondary imaging methods (computed tomography, magnetic resonance imaging and positron emission tomography-computed tomography) in the detection of recurrence. The chest X-ray examination only detected three cases (1.14%) of recurrence. Patients assessed with various diagnostic strategies had similar progression-free and overall survival outcomes. Conclusions A meticulous evaluation of clinical manifestations might allow recurrence to be discovered in a timely manner in most patients with cervical cancer. Specific diagnostic methods for revealing recurrence were not associated with the survival outcomes.
Plasticity via feedback reduces the cost of developmental instability

Costs of plasticity are thought to have important physiological and evolutionary consequences. A commonly predicted cost to plasticity is that plastic genotypes are likely to suffer from developmental instability. Adaptive plasticity requires that the developing organism can in some way sense what environment it is in or how well it is performing in that environment. These two information pathways—an “environmental signal” or a “performance signal” that indicates how well a developing phenotype matches the optimum in the current environment—can differ in their consequences for the organism and its evolution. Here, we consider how developmental instability might emerge as a side‐effect of these two distinct mechanisms. Because a performance cue allows a regulatory feedback loop connecting a trait to a feedback signal, we hypothesized that plastic genotypes using a performance signal would be more developmentally robust compared to those using a purely environmental signal. Using a numerical model of a network of gene interactions, we show that plasticity comes at a cost of developmental instability when the plastic response is mediated via an environmental signal, but not when it is mediated via a performance signal. We also show that a performance signal mechanism can evolve even in a constant environment, leading to genotypes preadapted for plasticity to novel environments even in populations without a history of environmental heterogeneity.
Recommendations for Implementing Gamification for Mental Health and Wellbeing

Gamification is increasingly being proposed as a strategy to increase engagement for mental health and wellbeing technologies. However, its implementation has been criticized as atheoretical, particularly in relation to behavior change theory and game studies theories. Definitions of the term “gamification” vary, sometimes widely, between and within academic fields and the effectiveness of gamification is yet to be empirically established. Despite this, enthusiasm for developing gamified mental health technologies, such as interventions, continues to grow. There is a need to examine how best to implement gamification in mental health and wellbeing technologies in a way that takes quick production cycles into account while still emphasizing empirical investigation and building a rigorous evidence base. With reference to game studies and the medical (eHealth/mHealth) literature, this article interrogates gamification for mental health and wellbeing by examining core properties of the game form. It then explores how gamification can best be conceptualized and implemented for mental health and wellbeing goals from conceptualization through to iterative co-development and evaluation that accommodates software development schedules. Finally, it summarizes its conceptual analysis into recommendations for researchers and designers looking to do so. These recommendations are: (1) assess suitability, (2) implement to support, (3) assess acceptability, (4) evaluate impact, and (5) document comprehensively. These recommendations aim to encourage clear language, unified terminology, the application and evaluation of theory, comprehensive and constant documentation, and transparent evaluation of outcomes.