Early Structure Formation Research Articles

Early structure formation of foam concrete mix containing modifying admixture

Early structure formation of foam concrete mix containing modifying admixture

Fast helix formation in the B domain of protein A revealed by site-specific infrared probes.

Comparison of experimental and computational protein folding studies can be difficult because of differences in structural resolution. Isotope-edited infrared spectroscopy offers a direct measure of structural changes involved in protein folding at the single-residue level. Here we demonstrate the increased resolution of site-specific infrared probes to the peptide backbone in the B domain of staphylococcal protein A (BdpA). (13)C═(18)O-labeled methionine was incorporated into each of the helices using recombinant protein expression. Laser-induced temperature jumps coupled with infrared spectroscopy were used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation kinetics of the buried helices, solvated helices, and labeled positions were measured independently by probing the corresponding bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe a fast nanosecond phase and slower microsecond phase at each position. We find at least partial formation of helices 1-3 in the fast intermediate state that precedes the transition state. These measurements provide direct, time-resolved experimental evidence of the early formation of partial helical structure in helices 1 and 3, supporting folding models proposed by computer simulations.

Primordial star formation under the influence of far ultraviolet radiation: 1540 cosmological haloes and the stellar mass distribution

We perform a large set of cosmological simulations of early structure formation and follow the formation and evolution of 1540 star-forming gas clouds to derive the mass distribution of primordial stars. The star formation in our cosmological simulations is characterized by two distinct populations, the so-called Population III.1 stars and primordial stars formed under the influence of far ultraviolet (FUV) radiation (Population III.2D stars). In this work, we determine the stellar masses by using the dependences on the physical properties of star-forming cloud and/or the external photodissociating intensity from nearby primordial stars, which are derived from the results of two-dimensional radiation hydrodynamic simulations of protostellar feedback. The characteristic mass of the Pop III stars is found to be a few hundred solar masses at z ~ 25, and it gradually shifts to lower masses with decreasing redshift. At high redshifts z > 20, about half of the star-forming gas clouds are exposed to intense FUV radiation and thus give birth to massive Pop III.2D stars. However, the local FUV radiation by nearby Pop III stars becomes weaker at lower redshifts, when typical Pop III stars have smaller masses and the mean physical separation between the stars becomes large owing to cosmic expansion. Therefore, at z < 20, a large fraction of the primordial gas clouds host Pop III.1 stars. At z =< 15, the Pop III.1 stars are formed in relatively cool gas clouds due to efficient radiative cooling by H_2 and HD molecules; such stars have masses of a few x 10 Msun. Since the stellar evolution and the final fate are determined by the stellar mass, Pop III stars formed at different epochs play different roles in the early universe.

Non-Native Structure Appears in Microseconds during the Folding of E. coli RNase H

The folding pathway of Escherichia coli RNase H is one of the best experimentally characterized for any protein. In spite of this, spectroscopic studies have never captured the earliest events. Using continuous-flow microfluidic mixing, we have now observed the first several milliseconds of folding by monitoring the tryptophan fluorescence lifetime (60μs dead time). Two folding intermediates are observed, the second of which is the previously characterized Icore millisecond intermediate. The new earlier intermediate is likely on-pathway and appears to have long-range non-native structure, providing a rare example of such non-native structure formation in a folding pathway. The tryptophan fluorescence lifetimes also suggest a deviation from native packing in the second intermediate, Icore. Similar results from a fragment of RNase H demonstrate that only half of the protein is significantly involved in this early structure formation. These studies give us a view of the formation of tertiary structure on the folding pathway, which complements previous hydrogen-exchange studies that monitored only secondary structure and observed sequential native structure formation. Our results provide detailed folding information on both a timescale and a size-scale accessible to all-atom molecular dynamics simulations of protein folding.

THE FORMATION OF MASSIVE PRIMORDIAL STARS IN THE PRESENCE OF MODERATE UV BACKGROUNDS

Radiative feedback from populations II stars played a vital role in early structure formation. Particularly, photons below the Lyman limit can escape the star forming regions and produce a background ultraviolet (UV) flux which consequently may influence the pristine halos far away from the radiation sources. These photons can quench the formation of molecular hydrogen by photo-detachment of $\rm H^{-}$. In this study, we explore the impact of such UV radiation on fragmentation in massive primordial halos of a few times $\rm 10^{7}$~M${_\odot}$. To accomplish this goal, we perform high resolution cosmological simulations for two distinct halos and vary the strength of the impinging background UV field in units of $\rm J_{21}$. We further make use of sink particles to follow the evolution for 10,000 years after reaching the maximum refinement level. No vigorous fragmentation is observed in UV illuminated halos while the accretion rate changes according to the thermal properties. Our findings show that a few 100-10, 000 solar mass protostars are formed when halos are irradiated by $\rm J_{21}=10-500$ at $\rm z>10$ and suggest a strong relation between the strength of UV flux and mass of a protostar. This mode of star formation is quite different from minihalos, as higher accretion rates of about $\rm 0.01-0.1$ M$_{\odot}$/yr are observed by the end of our simulations. The resulting massive stars are the potential cradles for the formation of intermediate mass black holes at earlier cosmic times and contribute to the formation of a global X-ray background.

The high-z universe confronts warm dark matter: Galaxy counts, reionization and the nature of dark matter

We use $N$-body simulations to show that high-redshift galaxy counts provide an interesting constraint on the nature of dark matter, specifically Warm Dark Matter (WDM), owing to the lack of early structure formation these models. Our simulations include three WDM models with thermal-production masses of 0.8 keV, 1.3 keV, and 2.6 keV, as well as CDM. Assuming a relationship between dark halo mass and galaxy luminosity that is set by the observed luminosity function at bright magnitudes, we find that 0.8 keV WDM is disfavored by direct galaxy counts in the Hubble Ultra Deep Field at $>\!\!10\sigma$. Similarly, 1.3 keV WDM is statistically inconsistent at $2.2\sigma$. Future observations with JWST (and possibly HST via the Frontier Fields) could rule out $1.3$ keV WDM at high significance, and may be sensitive to WDM masses greater than 2.6 keV. We also examine the ability of galaxies in these WDM models to reionize the universe, and find that 0.8 keV and 1.3 keV WDM produce optical depths to the Cosmic Microwave Background (CMB) that are inconsistent at 68% C.L. with current Planck results, even with extremely high ionizing radiation escape fractions, and 2.6 keV WDM requires an optimistic escape fraction to yield an optical depth consistent with Planck data. Although CMB optical depth calculations are model dependent, we find a strong challenge for stellar processes alone to reionize the universe in a 0.8 keV and 1.3 keV WDM cosmology.

Structure formation during an early period of matter domination

In this work we show that modifying the thermal history of the Universe by including an early period of matter domination can lead to the formation of astronomical objects. However, the survival of these objects can only be possible if the dominating matter decays to a daughter particle which is not only almost degenerate with the parent particle but also has an open coannihilation channel. This requirement translates in an upper bound for the coupling of such a channel and makes the early structure formation viable.

Cosmological signatures of tilted isocurvature perturbations: reionization and 21cm fluctuations

We investigate cosmological signatures of uncorrelatedisocurvature perturbations whose power spectrum is blue-tilted withspectral index 2≲p≲4. Such an isocurvature powerspectrum can promote early formation of small-scale structure, notablydark matter halos and galaxies, and may thereby resolve the shortage ofionizing photons suggested by observations of galaxies at high redshifts(z ≃ 7−8) but that are required to reionize the universe at z ∼ 10. We mainly focus on how the formation of dark matter halos can bemodified. Based on the Δχ2 analysis with other cosmologicalparameters being fixed, weexplore the connection between the spectral shape of CMBanisotropies and the reionization optical depth as a powerful probe of ahighly blue-tilted isocurvature primordial power spectrum. We alsostudy the consequences for 21cm line fluctuations due to neutralhydrogens in minihalos.Combination of measurements of the reionizationoptical depth and 21cm line fluctuations will provide complementaryprobes of a highly blue-tilted isocurvature power spectrum.

HYBRID COSMOLOGICAL SIMULATIONS WITH STREAM VELOCITIES

In the early universe, substantial relative "stream" velocities between the gas and dark matter arise due to radiation pressure and persist after recombination. To asses the impact of these velocities on high-redshift structure formation, we carry out a suite of high-resolution Adaptive Mesh Refinement (AMR) cosmological simulations, which use Smoothed Particle Hydrodynamic datasets as initial conditions, converted using a new tool developed for this work. These simulations resolve structures with masses as small as a few 100 M$_\odot$, and we focus on the $10^6$ M$_\odot$ "mini-halos" in which the first stars formed. At $z \approx 17,$ the presence of stream velocities has only a minor effect on the number density of halos below $10^6$ M$_\odot$, but it greatly suppresses gas accretion onto all halos and the dark matter structures around them. Stream velocities lead to significantly lower halo gas fractions, especially for $\approx 10^5$ M$_\odot$ objects, an effect that is likely to depend on the orientation of a halo's accretion lanes. This reduction in gas density leads to colder, more compact radial profiles, and it substantially delays the redshift of collapse of the largest halos, leading to delayed star formation and possibly delayed reionization. These many differences suggest that future simulations of early cosmological structure formation should include stream velocities to properly predict gas evolution, star-formation, and the epoch of reionization.

A cosmic growth spurt in an infant galaxy

One of the most extreme starburst galaxies in the early Universe has been identified and characterized. This system shows the rapid formation of a massive galaxy when the Universe was only 6% of its current age. See Letter p.329 The physical properties of the first massive starburst galaxies in the Universe provide important clues as to patterns of early cosmic structure formation. But as regions of intense star formation tend to be shrouded in dust, the search for such systems at very high redshift has been a major challenge. Now a massive starburst galaxy has been identified at a redshift z = 6.34, just 880 million years after the Big Bang when the Universe was one-sixteenth of its present age. Line-emission data reveal the presence of 100 billion solar masses of gas, equivalent to at least 40% of the galaxy's baryonic (visible matter) mass. The galaxy hosts an intense starburst, converting gas into stars at a rate more than 2,000 times that of the Milky Way. These findings are consistent with the theory that massive galaxies form via extreme starbursts in the early Universe.

PROBING PRIMORDIAL MAGNETIC FIELDS USING Lyα CLOUDS

From previous studies of the effect of primordial magnetic fields on early structure formation, we know that the presence of primordial magnetic fields during early structure formation could induce more perturbations at small scales (at present 1-10 Mpc/h) as compared to the usual LCDM theory. Matter power spectrum over these scales are effectively probed by cosmological observables such as shear correlation and Ly-alpha clouds, In this paper we discuss the implications of primordial magnetic fields on the distribution of Ly-alpha clouds. We simulate the line of sight density fluctuation including the contribution coming from the primordial magnetic fields. We compute the evolution of Ly-alpha opacity for this case and compare our theoretical estimates of Ly-alpha opacity with the existing data to constrain the parameters of the primordial magnetic fields. We also discuss the case when the two density fields are correlated. Our analysis yields an upper bounds of roughly 0.3-0.6 nG on the magnetic field strength for a range of nearly scale invariant models, corresponding to magnetic field power spectrum index n \simeq -3.

Early structure formation from cosmic string loops

We examine the effects of cosmic strings on structure formation and on the ionization history of the universe. While Gaussian perturbations from inflation are known to provide the dominant contribution to the large scale structure of the universe, density perturbations due to strings are highly non-Gaussian and can produce nonlinear structures at very early times. This could lead to early star formation and reionization of the universe. We improve on earlier studies of these effects by accounting for high loop velocities and for the filamentary shape of the resulting halos. We find that for string energy scales Gμ≳10−7, the effect of strings on the CMB temperature and polarization power spectra can be significant and is likely to be detectable by the Planck satellite. We mention shortcomings of the standard cosmological model of galaxy formation which may be remedied with the addition of cosmic strings, and comment on other possible observational implications of early structure formation by strings.

Radiative feedback and cosmic molecular gas: numerical method

We present results from self-consistent 3D numerical simulations of cosmic structure formation with a multi-frequency radiative transfer scheme and non-equilibrium molecular chemistry of 13 primordial species (e-, H, H+, H-, He, He+, He++, H2, H2+, D, D+, HD, HeH+), performed by using the simulation code GADGET. We describe our implementation and show tests for ionized sphere expansion in a static and dynamic density field around a central radiative source, and for cosmological abundance evolution coupled with the cosmic microwave background radiation. As a demonstrative application of radiative feedback on molecular gas, we run also cosmological simulations of early structure formation in a ~1Mpc size box. Our tests agree well with analytical and numerical expectations. Consistently with other works, we find that ionization fronts from central sources can boost H2 fractions in shock-compressed gas. The tight dependence on H2 lead to a corresponding boost of HD fractions, as well. We see a strong lowering of the the typical molecular abundances up to several orders of magnitudes which partially hinders further gas collapse of pristine neutral gas, and clearly suggests the need of re-ionized gas or metal cooling for the formation of the following generation of structures.

Exploring the Role of Topological Frustration in Actin Refolding with Molecular Simulations

Actin plays crucial roles in the life of the cell while being notorious for its inability to reach a functional conformation without the help of assistant proteins. In eukaryotes, for example, the cytosolic chaperonin containing TCP-1 (CCT) and prefoldin (PFD) are required for actin folding assistance and prevention of protein aggregation in the crowded cellular environment. The folding of non-native actin is known to occur in a number of steps, but the reasons underlying its folding difficulty are unknown. Because a full, atomistic-level, investigation of the kinetics and thermodynamics of folding of such a large molecule is beyond computational reach, we focused our investigation on the role of topological frustration on the folding of actin. Namely, we studied the (re)folding of actin using simulations of a variant self-organized polymer model (SOP-DH) starting from a stretched state, leading to results that correlate well with experimentally driven conclusions and allowing us to make a number of testable predictions. Primarily, our simulations reveal that the successful refolding of the C-terminus end of actin occurs through a zipping process in which the α-helices wind up turn by turn upon formation of their native tertiary contacts. In turn, an early formation of the helical structure in this region of the chain has deleterious effects for actin's refolding fitness. Moreover, the C-terminus refolding is a very rare event in our simulations, in agreement with the large activation barrier predicted on the basis of experimental studies of actin unfolding in EDTA. We also discovered that subdomain 4 has a low refolding probability, which can help explain why many of the non-native actin target binding sites for CCT and PFD are located within this subdomain.

Demography of High-Redshift AGN

High-redshift AGN holds the key to understanding early structure formation and to probe the Universe during its infancy. We review the latest searches for high-zAGN in the deepest X-ray field so far, the Chandra Deep Field South (CDFS) 4 Msecond exposure. We do not confirm the positive detection of a signal in the stacked Chandra images at the position ofz~6galaxies recently reported by Treister and collaborators (2011). We presentz&gt;3X-ray sources number counts in the 0.5–2 keV band, obtained joining CDFS faint detections (see Fiore et al. (2011)), with Chandra-COSMOS and XMM-COSMOS detections. We use these number counts to make predictions for surveys with three mission concepts: Athena, WFXT, and a Super-Chandra.

Structure formation with scalar-field dark matter: the fluid approach

The properties of nearby galaxies that can be observed in great detail suggest that a better theory rather than cold dark matter (CDM) would describe in a better way a mechanism by which matter is more rapidly gathered into large-scale structure such as galaxies and groups of galaxies. In this work we develop and simulate a hydrodynamical approach for the early formation of structure in the Universe, this approach is based on the fact that dark matter is on the form of some kind of scalar field (SF) with a potential that goes as $\mu^2\Phi^2/2+\lambda\Phi^4/4$, we expect that the fluctuations coming from the SF will give us some information about the matter distribution we observe these days.

The interplay between chemical and mechanical feedback from the first generation of stars

We study cosmological simulations of early structure formation, including non-equilibrium molecular chemistry, metal pollution from stellar evolution, transition from Population III (PopIII) to Population II (PopII) star formation, regulated by a given critical metallicity, and feedback effects. We perform analyses of the properties of the gas, and use the PopIII and PopII populations as tracers of the metallicity. This allows us to investigate the properties of early metal spreading from the different stellar populations and its interplay with pristine molecular gas, in terms of the initial mass function and critical metallicity. We find that, independently of the details about PopIII modelling, after the onset of star formation, regions enriched below the critical level are mostly found in isolated environments, while PopII star formation regions are much more clumped. Typical star-forming haloes, at z∼ 15–10, with masses between ∼107 and 108 M⊙, show average supernova (SN) driven outflow rates of up to ∼10−4 M⊙ yr−1 in enriched gas, initially leaving the original star formation regions almost devoid of metals. The polluted material, which is gravitationally incorporated in overdense environments on time-scales of ∼107 yr, is mostly coming from external, nearby star-forming sites (‘gravitational enrichment’). In parallel, the pristine-gas inflow rates are some orders of magnitudes larger, between ∼10−3 and 10−1 M⊙ yr−1. However, thermal feedback from SN destroys molecules within the pristine gas hindering its ability to cool and to condense into high-density star-forming regions. Only the polluted material incorporated via gravitational enrichment can continue to cool by atomic fine-structure transitions on short time-scales, short enough to end the initial PopIII regime within less than 108 yr. Moreover, the interplay between the pristine, cold, infalling gas and the ejected, hot, metal-rich gas leads to turbulent Reynolds numbers of the order of ∼108–1010, and contributes to the suppression of pristine inflow rates into the densest, star-forming regions.

The impact of primordial supersonic flows on early structure formation, reionization and the lowest-mass dwarf galaxies

Abstract Tseliakhovich and Hirata recently discovered that higher order corrections to the cosmological linear-perturbation theory lead to supersonic coherent baryonic flows just after recombination (i.e. z ≈ 1020), with rms velocities of ∼30 km s−1 relative to the underlying dark matter distribution, on comoving scales of ≲3 Mpc h−1. To study the impact of these coherent flows, we performed high-resolution N-body plus smoothed particle hydrodynamic simulations in boxes of 5.0 and 0.7 Mpc h−1, for bulk-flow velocities of 0 (as reference), 30 and 60 km s−1. The simulations follow the evolution of cosmic structures by taking into account detailed, primordial, non-equilibrium gas chemistry (i.e. H, He, H2, HD, HeH, etc.), cooling, star formation and feedback effects from stellar evolution. We find that these bulk flows suppress star formation in low-mass haloes (i.e. Mvir≲ 108 M⊙ until z ∼ 13), lower the abundance of the first objects by ∼1–20 per cent and as a consequence delay cosmic star formation history by ∼2 × 107 yr. The gas fractions in individual objects can change by up to a factor of 2 at very early times. Coherent bulk flow therefore has implications for (i) the star formation in the lowest-mass haloes (e.g. dSphs); (ii) the start of reionization by suppressing it in some patches of the Universe; and (iii) the heating (i.e. spin temperature) of neutral hydrogen. We speculate that the patchy nature of reionization and heating on several Mpc scales could lead to enhanced differences in the H i spin temperature, giving rise to stronger variations in the H i brightness temperatures during the late dark ages.

Effects of Temperature on the Performance of Sucrose in Cement Hydration

The performance of sucrose in cement hydration, including both the early structure formation and further development of cement paste under different curing temperatures, was studied by measures of setting time, heat evolution, resistivity evolution, compressive strength, and porosity. The results showed that there was a critical dosage (T0) of sucrose. When the dosage was less than T0, the retarding effect was enhanced by increasing the dosage. Greater than T0, sucrose became less retarding and even became accelerating. Increasing the curing temperature decreased the critical dosage (T0). When the dosage was less than 0.08%, sucrose showed less retarding effect at 40°C than at 20°C, but better retarding effect at the dosage of 0.08–0.2%. The strength development of cement paste after the induction period was accelerated at 40°C than at 20°C, although 0.08% sucrose prolonged the induction period.

Probing early cosmic magnetic fields through pair echoes from high-redshift GRBs

We discuss the expected properties of pair echo emission from gamma-ray bursts (GRBs) at high redshifts ($z \gtrsim 5$), their detectability, and the consequent implications for probing intergalactic magnetic fields (IGMFs) at early epochs. Pair echos comprise inverse Compton emission by secondary electron-positron pairs produced via interactions between primary gamma-rays from the GRB and low-energy photons of the diffuse intergalactic radiation, arriving with a time delay that depends on the nature of the intervening IGMFs. At sufficiently high $z$, the IGMFs are unlikely to have been significantly contaminated by astrophysical outflows, and the relevant intergalactic radiation may be dominated by the well-understood cosmic microwave background (CMB). Pair echoes from luminous GRBs at $z \sim 5-10$ may be detectable by future facilities such as the Cherenkov Telescope Array or the Advanced Gamma-ray Imaging System, as long as the GRB primary emission extends to multi-TeV energies, the comoving IGMFs at these redshifts are $B \sim 10^{-16}-10^{-15}~{\rm Gauss}$, and the non-CMB component of the diffuse intergalactic radiation is relatively low. Observations of pair echos from high-$z$ GRBs can provide a unique, in-situ probe of weak IGMFs during the epochs of early structure formation and cosmic reionization.