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A remarkable property of certain covalent glasses and their melts is intermediate range order, manifested as the first sharp diffraction peak (FSDP) in neutron-scattering experiments, as was exhaustively investigated by Price, Saboungi, and collaborators. Atomistic simulations thus far have relied on either quantum molecular dynamics (QMD), with systems too small to resolve FSDP, or classical molecular dynamics, without quantum-mechanical accuracy. We investigate prototypical FSDP in GeSe2 glass and melt using neural-network quantum molecular dynamics (NNQMD) based on machine learning, which allows large simulation sizes with validated quantum mechanical accuracy to make quantitative comparisons with neutron data. The system-size dependence of the FSDP height is determined by comparing QMD and NNQMD simulations with experimental data. Partial pair distribution functions, bond-angle distributions, partial and neutron structure factors, and ring-size distributions are presented. Calculated FSDP heights agree quantitatively with neutron scattering data for GeSe2 glass at 10 K and melt at 1100 K.

The surface free energy of solids, γ, plays a crucial role in all physical and chemical processes involving material surfaces. For the first time, we obtained γ directly from molecular dynamics simulations using a crystal cleavage method. The approach was successfully realized in a Lennard-Jones system by inserting two movable external walls, each consisting of a single crystal layer, into a bulk crystal to create flat, defect-free surfaces. The cleavage technique designed allowed us to calculate the surface free energy according to its definition and avoid surface premelting. The temperature dependence of γ was determined for the (100) and (110) crystal planes along the whole sublimation line and its metastable extension, up to T = 1.02 · Tm, where Tm is the melting point. Good agreement with indirect values of γ(T) was found. The proposed computational cleavage method can be applied to other solids of interest, providing valuable insight into the understanding of chemical and physical surface processes, and demonstrates the successful import of the cleavage method, traditionally used in technical preparation and study of crystal surfaces, into a modern atomistic simulation.

A systematic comparison of structural, thermodynamical and kinetic properties of silicon by molecular dynamics simulation was done using five interatomic potentials, namely the Stillinger-Weber (SW) model, the environment-dependent interatomic potential (EDIP), two versions of the modified embedded-atom method (MEAM-1 and MEAM-2) and the angular dependent potential (ADP). This benchmark allows us to determine which interatomic potential is the most adequate to simulate this material. Structural properties and the vibrational density of states (VDOS) for diamond-structure crystal and amorphous phases were studied. We also obtained the diffusion coefficient for the liquid phase. For the models able to describe crystallization from the melt, the interfacial free-energy was also computed. Results show that the SW potential outperforms the remaining models in several aspects including the structure factor and the coordination number distribution of the liquid and the melting temperature. MEAM-2 follows as the second best model due to its ability to reproduce the crystal-liquid interfacial free-energy and the structure factor and the VDOS for the amorphous phase. EDIP, MEAM-1 and ADP models can reproduce some physical properties but they lack transferability, which is a key aspect of a good interatomic potential.

In this work, we study the structural phase transitions of gallium phosphide (GaP), witha combination of molecular dynamics simulations (MD) and ab initio calculations based on density functional theory (DFT) with vibrational corrections within the harmonic approximation, for pressures up to 50 GPa. We show that the transition sequence depends on temperature for both cases. For low temperatures, our MD simulations predict a transition sequence zinc blende → β -tin → Immm → NaCl, while DFT predicts the sequence zinc blende → Sc16 → β -tin → Immm. Our DFT calculations with vibrational corrections also indicate that, for high temperatures, the Sc16 phase gradually loses stability and other structures such as Cmcm, β -tin and NaCl become more stable. The kinetic effects are also studied by dynamically changing the pressure in MD simulations up to 200 GPa. We show that, as we increase the pressure, a transition to the β -tin structure should not occur at room temperature due a large energy barrier. For higher temperatures, we show that the first transition is zinc blende → NaCl. The differences in the observed transition sequence at low and high temperatures indicate that the vibrational corrections included in the DFT calculations are fundamental to the description of the stability of higher pressure structures, as also observed on other semiconductors. Moreover, the good agreement between DFT and MD shows the suitability of the classical effective many-body interaction potential, used to describe the different high-pressure phases of GaP.

We used a recently developed two-body interatomic potential for barium sulfide (BaS), and performed molecular dynamics (MD) simulations with 36,000 particles to determine the kinetics of spontaneous, homogeneous nucleation and growth of BaS crystals in the supercooled liquid. Isothermal-isobaric MD simulations were accomplished at three temperatures. The calculated pair correlation function, along with several snapshots, allowed us to quantify the nucleation times, their crystal growth rates, and the time evolution of overall crystallization. Nucleation was spontaneously achieved in the supercooled liquid state; therefore, we computed the average birth times of the critical nuclei (also known as average onset time of the first nucleus) from 15 samples at each temperature, from which we computed the steady-state nucleation rates, MD Jss(T). Then, we independently obtained by MD the diffusion coefficients, D(T), the melting point, Tm, and the enthalpy of melting, ΔHm. Thus, the MD Jss could be compared with the predictions of the Classical Nucleation Theory (CNT) for homogeneous nucleation using only one fitting parameter, the nucleus/liquid interfacial free energy, σ. The calculated critical nucleus is made of only 2 to 3-unit cells, which is consistent with the critical size observed in the simulations, approximately 10–15 atoms. Using a constant (fitted value of) σ, and the D(T) and thermodynamic parameters from the simulations, we found that the MD pre-exponential factor has the same order of magnitude as the theoretical value predicted by the CNT. To the best of our knowledge, this agreement of the predictions of CNT and MD simulations has seldom been reported. Therefore, our results corroborate the validity of the CNT for simple supercooled liquids.

Herein we report the synthesis, characterization, and photophysical and biological evaluation of the complexes Ln(DBM)3(RPhen) (Ln = Sm, R = H; Ln = Sm, Eu, Tb, R = 5-NH2) stabilized by three β-diketonate units (DBM) and a phenanthroline (RPhen) derivative, with the aim of contributing to the development of lanthanide-based compounds with potential application as anticancer agents. The UV-vis spectra of [Sm(DBM)3(Phen)], [Sm(DBM)3(NH2Phen)], [Eu(DBM)3(NH2Phen)] and [Tb(DBM)3(NH2Phen)] measured in DMSO and PBS showed a strong absorption band centered at ca. 350 nm in both solvents. In DMSO, all lanthanide compounds except [Sm(DBM)3(Phen)] show a ligand centered emission band at ca. 520 nm. In PBS only sharp emission peaks are detected. The complexes show similar cytotoxic effects in A2780 ovarian cancer cells, presenting IC50 values at 24 h in the range 16-27 μM. The measurement of the cellular uptake of the complexes in the A2780 cells by inductively coupled plasma mass spectrometry (ICP-MS) revealed preferential accumulation at the membrane and cytoskeleton, with the exception of [Sm(DBM)3(Phen)] that presented higher accumulation in the cytosol than in the cell membranes. All the evaluated lanthanide complexes showed low nuclear uptake, although not negligible. Spectroscopic studies on the interaction of the complexes with calf thymus DNA (ctDNA) revealed a moderate affinity with apparent binding constants in the 104 M-1 range. Complexes bind DNA not by intercalation but probably by electrostatic interactions. A morphological evaluation of the cells treated with the different complexes by electron microscopy (TEM/SEM) proved that all of them induce mitochondrial alterations, which seemed more pronounced for the NH2Phen complexes. In addition, the complex [Eu(DBM)3(NH2Phen)] presented lysosomal uptake that might explain its augmented cytotoxicity.

The validity of the classical nucleation theory (CNT), the most important tool to describe and predict nucleation kinetics in supercooled liquids, has been at stake for almost a century. Here, we carried out comprehensive molecular dynamics simulations of the nucleation kinetics of a fast quenched supercooled germanium using the Stillinger-Weber potential at six temperatures, covering a supercooling range of

Coelomocytes is a generic name for a collection of cellular morphotypes, present in many coelomate animals, that has been reported as highly variable across echinoderm classes. The roles attributed to the major types of the free circulating cells present in the coelomic fluid of echinoderms include immune response, phagocytic digestion and clotting. The main aim of the present study is the thorough characterization of coelomocytes present in the coelomic fluid ofMarthasterias glacialis(class Asteroidea) through the combined use of flow cytometry (FC) and fluorescence plus transmission electron microscopy. Two coelomocyte populations (here named P1 and P2) were identified by flow cytometry and subsequently studied in terms of abundance, morphology, ultrastructure, cell viability and cell cycle profiles. Ultrastructurally, P2 diploid cells showed two main morphotypes, similar to phagocytes and vertebrate thrombocytes, whereas the small P1 haploid cellular population was characterized by a low mitotic activity, relatively undifferentiated cytotype and a high nucleus/cytoplasm ratio. These last cells resemble stem-cell types present in other animals. P1 and P2 cells differ also in cell viability and cell cycle profiles. Additionally, two other morphotypes were only detected by fluorescence microscopy and a third one when using a combined microscopy/FC approach.

Low doses of ionizing radiation (LDIR) activate endothelial cells inducing angiogenesis. In zebrafish, LDIR induce vessel formation in the sub-intestinal vessels during post-embryonic development and enhance the inter-ray vessel density in adult fin regeneration. Since angiogenesis is a crucial process involved in both post-embryonic development and regeneration, herein we aimed to understand whether LDIR accelerate these physiological conditions. Our data show that LDIR upregulate the gene expression of several pro-angiogenic molecules, such as flt1, kdr, angpt2a, tgfb2, fgf2 and cyr61in sorted endothelial cells from zebrafish larvae and this effect was abrogated by using a vascular endothelial growth factor receptor (VEGFR)-2 tyrosine kinase inhibitor. Irradiated zebrafish present normal indicators of developmental progress but, importantly LDIR accelerate post-embryonic development in a VEGFR-2 dependent signaling. Furthermore, our data show that LDIR do not accelerate regeneration after caudal fin amputation and the gene expression of the early stages markers of regeneration are not modulated by LDIR. Even though regeneration is considered as a recapitulation of embryonic development and LDIR induce angiogenesis in both conditions, our findings show that LDIR accelerate post-embryonic development but not regeneration. This highlights the importance of the physiological context for a specific phenotype promoted by LDIR.

We carried out extensive molecular dynamics simulations of seeded crystallization in a Lennard-Jones liquid in a wide range of supercoolings under zero external pressure. The number of particles in...

A well-designed study of the relationship between crystal nucleation and relaxation in supercooled liquids could clarify some critical issues in condensed matter science. In this article, we dwell on the kinetic spinodal temperature, T K S – where the times of first critical nucleus formation and structural relaxation curves cross over – and the Kauzmann temperature, T K – where the entropy of the supercooled liquid and crystal equalize. Germanium liquid was used as a model system, for which a reliable Stillinger-Weber potential and crystal nucleation kinetics are available. Using molecular dynamics (MD) simulations, we obtained the self-diffusion coefficient, D ( T ) , and the shear viscosity, η ( T ) , down to T = 0.7 · T m , where T m is the equilibrium melting temperature. In this way, three relaxation times were determined in the supercooled liquid: (i) via the shear viscosity, τ η ; (ii) the incoherent intermediate scattering function, τ α ; and (iii) the self-diffusion coefficient, τ D . We found that τ α ( T ) ≈ τ D ( T ) and τ η ( T ) τ α ( T ) , corroborating the findings of recent experimental and computational studies conducted with other four substances. Hence, the viscosity only gives a lower bound to the intrinsic structural relaxation times, τ α ( T ) . We also compared the MD values of the atomic transport coefficient across the supercooled liquid/critical nucleus interface, D * , with those obtained by the classical nucleation theory (CNT) and found that the activation energies of D ( T ) , η ( T ) , and D * ( T ) are similar. The birth times of the first critical crystal nucleus at steady-state conditions, τ 1 ( T ) , obtained in our previous study for the same material, were extrapolated to lower temperatures using the CNT for different sample sizes. We found that τ 1 ( T ) is much longer than the nucleation time-lags, confirming the establishment of the steady-state nucleation regime. A relevant finding is that the τ α ( T ) and τ 1 ( T ) curves indeed cross over, confirming the existence of a kinetic spinodal for this liquid. Finally, we demonstrate that if the Kauzmann temperature existed for germanium, it would be located well below the T K S ; hence, crystallization would intervene in the cooling path before the supercooled germanium liquid could reach T K , thus averting the entropy paradox, posed by Kauzmann in 1948. These findings shed light on several fundamental questions related to supercooled liquids.

Crystallization of supercooled liquids and glasses is of gargantuan scientific and industrial importance. However, investigating its early stages is experimentally very challenging because of the nanometric size and very short lifetime of the critical nuclei; therefore, computer simulations can substantially assist in unveiling the nucleation mechanism and dynamics. In this work, we determined the critical nucleus sizes, the transport coefficient at the nucleus/liquid interface, and the interfacial free energy employing the seeding approach at shallow supercoolings combined with spontaneous homogeneous nucleation rates ( J ss ) at deep supercoolings in barium sulfide liquid. The nucleation rates were calculated using the MD results for the relevant physical properties and theoretical values of the driving force without any adjustable parameter, and agree quite well with the J ss obtained directly by MD simulations. The results confirm the ability of the seeding method to estimate nucleation parameters. They not only corroborate recent findings for mW water, hard spheres, Lennard-Jones, and zinc selenide models, but also show the best simulations-CNT calculations agreement ever. As this set of relevant outcomes is dispersed for other substances; here we combined and discussed them together to reinforce and generalize the soundness of the Classical Nucleation Theory in describing and predicting crystal nucleation rates for various supercooled liquids.

Structural relaxation and crystallization are crucial phenomena in physics, chemistry, and materials science. A thorough study of their relationship could clarify some critical open questions. In this article, we focus on thermodynamic and kinetic properties: the Kauzmann temperature, T K (where the excess entropy tends to zero), the kinetic spinodal temperature, T ks (where the relaxation and crystal nucleation curves cross), and the glass transition temperature, T g . We used zinc selenide (ZnSe) as a model system for which a reliable potential is available and obtained the self-diffusion coefficient, viscosity, critical nucleus birth times, relaxation times, entropy, T g , T ks and T K by molecular dynamics (MD) simulations. We confirmed that the Stokes-Einstein equation breaks down in the moderate supercooled regime, impacting the relationships between the dynamic and thermodynamic properties. Two relaxation times were determined in the supercooled liquid (SCL) state: i) using the shear viscosity and the Maxwell equation, τ η , and ii) from the self-intermediate scattering function and the Kohlrausch equation, τ R . We found that in the whole supercooling regime, τ η ≪ τ R confirming two recent experimental studies for other substances. The nucleus birth times, τ N , were also obtained for two system sizes. The τ R T and τ N T curves indeed crossover, confirming the existence of a kinetic spinodal temperature for this system. Hence, for temperatures somewhat above and below the T ks , crystallization of the SCL could be affected by structural relaxation. Finally, our results demonstrate that if the Kauzmann temperature existed, it would be well below the T ks . Hence, crystal nucleation intervenes on the cooling path, and SCL ZnSe cannot reach this temperature, thus averting the paradoxical entropic situation. These findings shed light on some central problems related to supercooled liquids.

Copyright: Pereira et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited., We propose a novel single-deoxynucleoside-based assay that is easy to perform and provides accurate values for the absolute length (in units of time) of each of the cell cycle stages (G1, S and G2/M). This flow-cytometric assay takes advantage of the excellent stoichiometric properties of azide-fluorochrome detection of DNA substituted with 5-ethynyl-2'-deoxyuridine (EdU). We show that by pulsing cells with EdU for incremental periods of time maximal EdU-coupled fluorescence is reached when pulsing times match the length of S phase. These pulsing times, allowing labelling for a full S phase of a fraction of cells in asynchronous populations, provide accurate values for the absolute length of S phase. We characterized additional, lower intensity signals that allowed quantification of the absolute durations of G1 and G2 phases.Importantly, using this novel assay data on the lengths of G1, S and G2/M phases are obtained in parallel. Therefore, these parameters can be estimated within a time frame that is shorter than a full cell cycle. This method, which we designate as EdU-Coupled Fluorescence Intensity (E-CFI) analysis, was successfully applied to cell types with distinctive cell cycle features and shows excellent agreement with established methodologies for analysis of cell cycle kinetics., João A. Ferreira received support from a Calouste Gulbenkian Foundation grant (96526) and Pedro Pereira is an FCT fellow (SFRH/BD/45502/2008). Evguenia Bekman is the recipient of an IMM-Lisbon fellowship (iMM/BPD/60-2016; project PTDC/BEXBCM/5899/2014).

In this work we study the finite size effects on bulk properties of an atomistic model of ferroelectric barium titanate. The interaction potential is based on the core-shell model, which confers polarizability to ions, and a long range electrostatic potential. Results show that finite size effects are dependent on the property analyzed. Structural and static properties such as elastic constants and spontaneous polarization show minor deviation with chosen system size, while the transition temperatures and the coercive field are largely affected by it. The dielectric susceptibility, a static property commonly reported as being very sensitive to finite size effects, presents no deviations with system size in our study. The computation of the long range electrostatic energy contribution is not related to the finite size effects found in this model. We believe that the appearance of finite size effects for a subset of bulk properties is the strong dependence of the energy barriers in the potential energy landscape with the chosen system size.

Details of the microscopic mechanisms and dynamics of most processes in supercooled liquids (SCL) and glasses remain blurred due to their complexity and the extraordinarily long or inaccessibly short timescales, depending on the supercooling degree. In this paper, we determined the structural relaxation times in an intermediate supercooling window (0.67–0.78 Tm, Tm = melting point) of barium sulfide liquid, used as a model material, through molecular dynamics (MD) simulations based on a reliable two-body interatomic potential. We also inferred these dynamics in the glassy state using extrapolated data and well-accepted models. The average structural α-relaxation times, , were determined via the intermediate scattering function. Relaxation kinetics were also estimated by the Maxwell relation via the equilibrium shear viscosity and shear modulus, obtained by MD. We found that the viscosity derived (Maxwell) relaxation times are significantly shorter than the intrinsic α -relaxation times, corroborating two recent experimental studies of other substances. For the simulated system, with 36,000 particles and average volume of 1.4x103 nm3, the structural relaxation and nucleus birth time curves cross at the kinetic spinodal temperature, TKS (=0.33 Tm), which is significantly below the glass transition temperature, Tg (=0.44 Tm). However, for larger sample sizes, the TKS occurs at higher temperatures. As for temperatures above TKS, crystal nucleation starts after structural relaxation, and vice-versa, to understand and describe crystal nucleation one must necessarily take the relaxation process into account, however, this is not included in nucleation theories. These discoveries shed light on some obscure aspects of supercooled liquids, i.e., they challenge a critical assumption of nucleation theories (that crystal nucleation always occurs in a fully relaxed SCL), and show that crystallization is BaS ultimate fate, corroborating studies with other substances.

The structural, thermodynamic, and dynamical properties of zinc selenide, as well as the structural phase transformation induced by pressure, based on a many-body interatomic potential that considers two- and three-body interactions, were studied using molecular dynamics simulations. The potential was able to describe the energetics of the zinc-blende, wurtzite, and rock-salt structures of ZnSe. The effective interatomic potential was parameterized using experimental values of the bulk modulus and cohesive energy at an experimental density. Other properties, not used in the parameterization of the potential, such as the vibrational density of states, were correctly described. Cooling from the liquid, an amorphous phase or a re-crystallized material could be obtained. Pair distribution function, coordination number, volume change, and bond angle distributions are presented and compared with available experimental data. The structural phase transition from zinc-blend to rock-salt induced by hydrostatic pressure was obtained at ∼21 GPa for monocrystals and ∼16 GPa for polycrystals.

Understanding and controlling the liquid to crystal transformation is a central topic for numerous natural phenomena and technological applications. However, the microscopic mechanism of crystal nucleation is still elusive, which leads to strong controversies regarding the ability of the most used model, the Classical Nucleation Theory (CNT), to describe nucleation rates in supercooled liquids. In this work, we were able to deeply supercool Zinc Selenide (ZnSe), and determine spontaneous homogeneous steady-state nucleation rates, J MD , by MD simulations using the mean lifetime method. At moderate supercoolings, where the nucleation rates are much smaller, we used the seeding method to compute the nucleation rates by the CNT formalism, J CNT , without any fitting parameter, using the physical properties obtained by MD simulations: the melting temperature, T m , density, melting enthalpy, diffusion coefficient, D + , and the critical nucleus size, N ∗ , combined with two expressions for the thermodynamic driving force, Δ μ . The values of interfacial free energy, γ , calculated by the CNT expression using the MD simulation data, via both the seeding method and the mean lifetime method at moderate and deep supercoolings show a weak temperature dependence, which is in line with the Diffuse Interface Theory. The extrapolated values of γ , from the spontaneous nucleation regime to the seeding nucleation region cover the range of values of γ calculated via the seeding method and the CNT formalism. Finally, the J CNT extrapolated from moderate supercoolings to deep supercoolings are in good agreement with the J MD . These results confirm the validity of the CNT.

In this presentation by employing a combination of calculations based on Density Functional Theory (DFT) and Molecular Dynamics simulations (MD), we show that temperature has an unquestionable role in the behavior of Gallium Phosphide under pressure, shedding a new light in the controversial interpretation of experimental results. For example, we justify the absence of some structures predicted by early theoretical works, which remained up to now misunderstood. Moreover, we predict transitions to new structures at high temperature that may encourage new experiments. The differences in the observed transition sequences at low and high temperatures indicate that the vibrational corrections we included in the DFT calculations are fundamental to the description of the stability of higher pressure structures, and may be employed on other materials. Additionally, the good agreement between DFT and MD shows the suitability of the classical effective many-body interaction potential used to describe the different high-pressure phases of GaP in the Molecular Dynamics simulations. Finally, we discuss the behavior of GaP under extreme conditions for temperatures up to 1400 K and pressures up to 50 GPa, predicting new phases.

Viral interactions with host nucleus have been thoroughly studied, clarifying molecular mechanisms and providing new antiviral targets. Considering that African swine fever virus (ASFV) intranuclear phase of infection is poorly understood, viral interplay with subnuclear domains and chromatin architecture were addressed. Nuclear speckles, Cajal bodies, and promyelocytic leukaemia nuclear bodies (PML-NBs) were evaluated by immunofluorescence microscopy and Western blot. Further, efficient PML protein knockdown by shRNA lentiviral transduction was used to determine PML-NBs relevance during infection. Nuclear distribution of different histone H3 methylation marks at lysine’s 9, 27 and 36, heterochromatin protein 1 isoforms (HP1α, HPβ and HPγ) and several histone deacetylases (HDACs) were also evaluated to assess chromatin status of the host. Our results reveal morphological disruption of all studied subnuclear domains and severe reduction of viral progeny in PML-knockdown cells. ASFV promotes H3K9me3 and HP1β foci formation from early infection, followed by HP1α and HDAC2 nuclear enrichment, suggesting heterochromatinization of host genome. Finally, closeness between DNA damage response factors, disrupted PML-NBs, and virus-induced heterochromatic regions were identified. In sum, our results demonstrate that ASFV orchestrates spatio-temporal nuclear rearrangements, changing subnuclear domains, relocating Ataxia Telangiectasia Mutated Rad-3 related (ATR)-related factors and promoting heterochromatinization, probably controlling transcription, repressing host gene expression, and favouring viral replication.

Solid-state nuclear magnetic resonance (ssNMR) experimental 27Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.

© 2017. Published by The Company of Biologists Ltd., Spliceostatin A, meayamycin, and pladienolide B are small molecules that target the SF3b subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP). These compounds are attracting much attention as tools to manipulate splicing and for use as potential anti-cancer drugs. We investigated the effects of these inhibitors on mRNA transport and stability in human cells. Upon splicing inhibition, unspliced pre-mRNAs accumulated in the nucleus, particularly within enlarged nuclear speckles. However, a small fraction of the pre-mRNA molecules were exported to the cytoplasm. We identified the export adaptor ALYREF as being associated with intron-containing transcripts and show its requirement for the nucleo-cytoplasmic transport of unspliced pre-mRNA. In contrast, the exon junction complex (EJC) core protein eIF4AIII failed to form a stable complex with intron-containing transcripts. Despite the absence of EJC, unspliced transcripts in the cytoplasm were degraded by nonsense-mediated decay (NMD), suggesting that unspliced transcripts are degraded by an EJC-independent NMD pathway. Collectively, our results indicate that although blocking the function of SF3b elicits a massive accumulation of unspliced pre-mRNAs in the nucleus, intron-containing transcripts can still bind the ALYREF export factor and be transported to the cytoplasm, where they trigger an alternative NMD pathway., This work was supported by Fundação para a Ciência e a Tecnologia (PTDC/BEX-BCM/5899/2014)

Single mRNA molecules can be imaged in living cells by a method that consists in genetically inserting binding sites for a bacteriophage protein in the gene of interest. The resulting reporter transgene is then integrated in the genome of cells that express the phage protein fused to a fluorescent tag. Upon transcription, binding of the fluorescent protein to its target sequence makes the RNA visible. With this approach it is possible to track, in real time, the life cycle of a precursor mRNA at the site of transcription in the nucleus and transport of mature mRNA to the cytoplasm. In order to measure the fluorescence associated with individual RNA molecules over time, we developed a semi-automated quantitative image analysis tool termed STaQTool. We describe in detail the implementation and application of the STaQTool software package, which is a generic tool able to process large 4D datasets allowing quantitative studies of different steps in gene expression.

Structural, dynamical and thermodynamic properties of barium sulfide, as well as the structural transformation induced by pressure, are investigated in a molecular dynamics simulation based on an effective two-body interatomic potential. The two-body interatomic potential proposed for BaS is made up of steric repulsions, Coulomb interactions due to charge transfer, charge-induced dipole attractions due to the electronic polarizability and van der Waals attraction. The stability of the most stable phases of this compound, the vibrational density of states, heat capacity as a function of temperature, melting and recrystallization, as well as the structural phase transformation induced by pressure, are correctly described. It is shown that this phase transformation depends strongly on the temperature and crystallinity of the material. The simulated results are compared with experimental observations and other calculations reported in the literature.

Ferroelectric domain wall is modeled as a stretched membrane. For an electric field E(t) = E 0+ E 1sinωt, with E 1sufficiently weak, the oscillation problem reduces to a linear boundary value problem from which dispersion relationships are calculated. Hysteretic effect is introduced into the model through the effective field. Predicted dependence of permittivity on frequency and electric field agree with experiments. As the domain size is reduced a diminution of the dielectric response and tunability occurs. The same effect is observed experimentally when the grain size is diminished, pointing to domain size reduction as a possible cause of the observed behavior.

The ability to observe protein dynamics in living cells is critical for the mechanistic understanding of highly flexible biological processes such as pre-mRNA splicing by the spliceosome. Splicing relies on intricate RNA and protein networks that are repeatedly rearranged during spliceosome assembly. Here we describe a method based on fluorescence microscopy that has been used by our and other laboratories to study interaction of spliceosomal proteins with nascent pre-mRNA in living cells. The method involves co-expressing in mammalian cells the target pre-mRNA labeled with one color, and the spliceosomal protein tagged with another color. The diffusion coefficient of the protein as well as its association and dissociation rates with the pre-mRNA are estimated by fluorescence recovery after photobleaching (FRAP) or photoactivation.

Herein we present the synthesis and characterization of benzo[b]acridin-12(7H)-ones bearing carboranyl moieties and test their biological effectiveness as boron neutron capture therapy (BNCT) agents in cancer treatment. The cellular uptake of these novel compounds into the U87 human glioblastoma cells was evaluated by boron analysis (ICP-MS) and by fluorescence imaging (confocal microscopy). The compounds enter the U87 cells exhibiting a similar profile, i.e., preferential accumulation in the cytoskeleton and membranes and a low cytotoxic activity (IC50 values higher than 200 μM). The cytotoxic activity and cellular morphological alterations after neutron irradiation in the Portuguese Research Reactor (6.6 × 10(7) neutrons cm(-2) s(-1), 1 MW) were evaluated by the MTT assay and by electron microscopy (TEM). Post-neutron irradiation revealed that BNCT has a higher cytotoxic effect on the cells. Accumulation of membranous whorls in the cytoplasm of cells treated with one of the compounds correlates well with the cytotoxic effect induced by radiation. Results provide a strong rationale for considering one of these compounds as a lead candidate for a new generation of BNCT agents.

At low doses, ionizing radiation activates endothelial cells and promotes angiogenesis. However, it is still unknown if other cells may contribute to this process. In this study, the effect of low-dose ionizing radiation (LDIR) in modulating the pro-angiogenic potential of adipocytes was investigated. Adipocytes are known to secrete multiple angiogenic factors and adipokines that induce angiogenesis. In this work, a confluent monolayer of 3T3-L1 pre-adipocytes was exposed to low doses (0.1 and 0.3 Gy) and to higher doses (0.5, 0.8 and 1.0 Gy), as control. Our data show that the adipocyte-conditioned media (A-CM) from mature adipocytes differentiated from low-dose irradiated pre-adipocytes presented a higher angiogenic potential, compared to mature adipocytes differentiated from sham-irradiated control preadipocytes. The vascular endothelial growth factor (VEGF)-A levels were significantly increased in A-CM from the 0.1 Gy (P < 0.05) and 0.3 Gy (P < 0.01) experimental conditions and a significant increase was found in response to 0.3 Gy dose of radiation for VEGF-C, angiopoietin-2 (ANG-2) and hepatocyte growth factor (HGF). Moreover, 0.3 Gy dose of radiation significantly increased the expression of matrix metalloproteinase (MMP)-2 active forms. In vitro, the A-CM from the 0.1 and 0.3 Gy doses experimental conditions significantly accelerated endothelial cell migration after an in vitro wound healing assay. Importantly, in vivo, the A-CM corresponding to the 0.3 Gy experimental condition significantly induced the growth of more blood vessels towards the inoculation area in the chick embryo chorioallantoic membrane (CAM). In conclusion, this work reveals a new mechanism by which low-dose radiation might promote angiogenesis, enhancing the angiogenic potential of A-CM.

© 2013 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-No Derivative Works License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited., Removal of introns from pre-messenger RNAs (pre-mRNAs) via splicing provides a versatile means of genetic regulation that is often disrupted in human diseases. To decipher how splicing occurs in real time, we directly examined with single-molecule sensitivity the kinetics of intron excision from pre-mRNA in the nucleus of living human cells. By using two different RNA labeling methods, MS2 and λN, we show that β-globin introns are transcribed and excised in 20-30 s. Furthermore, we show that replacing the weak polypyrimidine (Py) tract in mouse immunoglobulin μ (IgM) pre-mRNA by a U-rich Py decreases the intron lifetime, thus providing direct evidence that splice-site strength influences splicing kinetics. We also found that RNA polymerase II transcribes at elongation rates ranging between 3 and 6 kb min(-1) and that transcription can be rate limiting for splicing. These results have important implications for a mechanistic understanding of cotranscriptional splicing regulation in the live-cell context., This work was supported by a grant from Fundação para a Ciência e Tecnologia, Portugal (PTDC/SAU-GMG/118180/2010), and the Harvard Medical School-Portugal Program in Translational Research and Information. R.M.M. was supported by a grant from Fundação para a Ciência e Tecnologia, Portugal (SFRH/BPD/66611/2009), and received an EMBO Short Term Fellowship (ASTF272.00-2011). J.R. holds a Ciência 2008 position from the Portuguese Ministry of Science and Technology. E.M. was supported in part by grants from the National Institutes of Health (NIH U54 AI057159) and the New England Regional Center of Excellence in Biodefense and Emerging Infectious Diseases. T.K. was supported in part by NIH grant GM 075252.

Histone H3 of nucleosomes positioned on active genes is trimethylated at Lys36 (H3K36me3) by the SETD2 (also termed KMT3A/SET2 or HYPB) methyltransferase. Previous studies in yeast indicated that H3K36me3 prevents spurious intragenic transcription initiation through recruitment of a histone deacetylase complex, a mechanism that is not conserved in mammals. Here, we report that downregulation of SETD2 in human cells leads to intragenic transcription initiation in at least 11% of active genes. Reduction of SETD2 prevents normal loading of the FACT (FAcilitates Chromatin Transcription) complex subunits SPT16 and SSRP1, and decreases nucleosome occupancy in active genes. Moreover, co-immunoprecipitation experiments suggest that SPT16 is recruited to active chromatin templates, which contain H3K36me3-modified nucleosomes. Our results further show that within minutes after transcriptional activation, there is a SETD2-dependent reduction in gene body occupancy of histone H2B, but not of histone H3, suggesting that SETD2 coordinates FACT-mediated exchange of histone H2B during transcription-coupled nucleosome displacement. After inhibition of transcription, we observe a SETD2-dependent recruitment of FACT and increased histone H2B occupancy. These data suggest that SETD2 activity modulates FACT recruitment and nucleosome dynamics, thereby repressing cryptic transcription initiation.

The vast majority of human protein-coding genes contain up to 90% of non-coding sequence in the form of introns that must be removed from the primary transcripts or pre-mRNAs. Diverse forms of mRNAs encoded from a single gene are created by the differential use of splice sites and alternative splicing is rapidly evolving. Although the kinetic properties of splicing are thought to be critical for proofreading and regulatory mechanisms, tools for making direct experimental measurements of splicing rates are still limited. We recently developed a strategy that permits real-time imaging of fluorescent-labelled introns in single pre-mRNA molecules. Here we describe the software tool that we created for automatic tracking and quantification of intronic fluorescence at the site of transcription in live human cells.

In this paper we present a large-scale molecular dynamics simulation that describes the deformation mechanism of an ordered intermetallic compound (TiAl) during a nanoindentation procedure. Using a totally rigid spherical indenter we were able to address the question on which mechanism underlies its plastic deformation, namely homogeneous defect nucleation followed by the expansion of dislocation loops. By means of the calculated local pressure, local shear stress and spatial rearrangements of atoms beneath the indenter, it was possible to quantify the indentation damage on the crystalline structure. Our results show that both emission and interaction of dislocations are mediated by expansion of glide loops on the {1 1 1} planes resulting in the formation of prismatic loops. Moreover, through the load-penetration depth response we estimated the elastic modulus and hardness values of the system, which are in good agreement with experimental results.

This work addresses the question on how the glass-forming ability (GFA) of a binary Pd-Ni metallic glass can be enhanced by the alloying effect of Pt. The structural features and slow dynamics of liquid and glassy states on both alloys are investigated by molecular dynamics simulations. Both alloys show typical features of glassy dynamics, namely, the non-Arrhenian behavior of diffusion and relaxation and the fractional Stokes-Einstein relation validity at low temperatures. On the basis of the analysis of the dynamical susceptibilities, we demonstrate that there is a strong influence of the alloying effect on the collective motion of the species, revealing that the GFA of the binary liquid increases with Pt alloying.

Copyright: © 2015 Cascão et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited, Background: Rheumatoid arthritis (RA) is a chronic immune-mediated inflammatory disease characterized by cellular infiltration into the joints, hyperproliferation of synovial cells and bone damage. Available treatments for RA only induce remission in around 30% of the patients, have important adverse effects and its use is limited by their high cost. Therefore, compounds that can control arthritis, with an acceptable safety profile and low production costs are still an unmet need. We have shown, in vitro, that celastrol inhibits both IL-1β and TNF, which play an important role in RA, and, in vivo, that celastrol has significant anti-inflammatory properties. Our main goal in this work was to test the effect of celastrol in the number of sublining CD68 macrophages (a biomarker of therapeutic response for novel RA treatments) and on the overall synovial tissue cellularity and joint structure in the adjuvant-induced rat model of arthritis (AIA). Methods: Celastrol was administered to AIA rats both in the early (4 days after disease induction) and late (11 days after disease induction) phases of arthritis development. The inflammatory score, ankle perimeter and body weight were evaluated during treatment period. Rats were sacrificed after 22 days of disease progression and blood, internal organs and paw samples were collected for toxicological blood parameters and serum proinflammatory cytokine quantification, as well as histopathological and immunohistochemical evaluation, respectively. Results: Here we report that celastrol significantly decreases the number of sublining CD68 macrophages and the overall synovial inflammatory cellularity, and halted joint destruction without side effects. Conclusions: Our results validate celastrol as a promising compound for the treatment of arthritis., RC was supported with a fellowship from Fundação para a Ciência e a Tecnologia (FCT, SFRH/BPD/92860/2013).

In the nucleus of higher eukaryotes, maturation of mRNA precursors involves an orderly sequence of transcription-coupled interdependent steps. Transcription is well known to influence splicing, but how splicing may affect transcription remains unclear. Here we show that a splicing mutation that prevents recruitment of spliceosomal snRNPs to nascent transcripts causes co-transcriptional retention of unprocessed RNAs that remain associated with polymerases stalled predominantly at the 3' end of the gene. In contrast, treatment with spliceostatin A, which allows early spliceosome formation but destabilizes subsequent assembly of the catalytic complex, abolishes 3' end pausing of polymerases and induces leakage of unspliced transcripts to the nucleoplasm. Taken together, the data suggest that recruitment of splicing factors and correct assembly of the spliceosome are coupled to transcription termination, and this might ensure a proofreading mechanism that slows down release of unprocessed transcripts from the transcription site.

Auger-emitting radionuclides such as 99mTc have been the focus of recent studies aiming at finding more selective therapeutic approaches. To explore the potential usefulness of 99mTc as an Auger emitter, we have synthesized and biologically evaluated novel multifunctional structures comprising (1) a pyrazolyl-diamine framework bearing a set of donor atoms to stabilize the [M(CO)3]+ (M is Re, 99mTc) core; (2) a DNA intercalating moiety of the acridine orange type to ensure close proximity of the radionuclide to DNA and to follow the internalization and subcellular trafficking of the compounds by confocal fluorescence microscopy; and (3) a bombesin (BBN) analogue of the type X-BBN[7-14] (where X is SGS, GGG) to provide specificity towards cells expressing the gastrin releasing peptide receptor (GRPr). Of the evaluated 99mTc complexes, Tc 3 containing the GGG-BBN[7-14] peptide showed the highest cellular internalization in GRPr-positive PC3 human prostate tumor cells, presenting a remarkably high nuclear uptake in the same cell line. Live-cell confocal imaging microscopy studies with the congener Re complex, Re 3 , showed a considerable accumulation of fluorescence in the nucleus, with kinetics of uptake similar to that exhibited by Tc 3 . Together, these data show that the acridine orange intercalator and the metal fragment are colocalized in the nucleus, which indicates that they remain connected despite the lysosomal degradation of Tc 3 /Re 3 . These compounds are the first examples of 99mTc bioconjugates that combine specific cell targeting with nuclear internalization, a crucial issue to explore use of 99mTc in Auger therapy. Pyrazolyl-diamine Re/99mTc tricarbonyl complexes bearing an acridine orange intercalator and bombesin peptides internalize and target the nucleus of gastrin releasing peptide receptor positive PC3 human prostate tumor cells.

The structural properties of twin-plane superlattices in InP nanowires are systematically analyzed. First, we employ molecular dynamics simulations to determine the strain fields in nanowires grown in the [111] direction. These fields are produced by the formation of twin-planes and by surface effects. By using the stress tensor obtained from molecular dynamics simulations, we are able to describe changes on the electronic structure of these nanowires. On the basis of the resulting electronic structure, we confirm that a one-dimensional superlattice is indeed formed. Furthermore, we describe the transport properties of both electrons and holes in the twin-plane superlattices. In contrast to the predicted transparency of Γ-electrons in heterolayered III-V semiconductor superlattices, we verify that surface effects in 1D systems open up possibilities of electronic structure engineering and the modulation of their transport and optical responses.

An effective interatomic potential which can be used to describe perovskite-type CaTiO 3 in molecular dynamics (MD) simulations is proposed. The potential proposed consists of two-body interactions, which include steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between particles, and charge-induced dipole interactions due to the electronic polarizability of ions and dipole–dipole (van der Waals) attraction. The energetics of the three crystalline forms of CaTiO 3 were calculated: the orthorhombic- Pbnm structure had the lowest energy, followed by the tetragonal- I4 / mcm and cubic- Pm3m structures. The two phase transitions induced by temperature change were characterized through anomalies in the lattice parameters, elastic constants, bulk modulus, bond-angle distribution and the intensity of the first peak of the partial pair distribution function, g Ca–O ( r ). Analysis of the pair distribution function is a sensitive means of detecting structural transformation in materials caused by small distortions. It is shown that the rise in structural symmetry with temperature is actually due to the tilting of the TiO 6 polyhedra. The response of the system to external pressure was also analyzed. Extremely high pressure, up to 300 GPa, was applied and no significant modification attributable to a major structural change was observed. The proposed interatomic potential is in good agreement with experimental data, predicting the melting point, phonon vibrational density of sates, thermal expansion coefficient and specific heat at constant volume. The recrystallized polycrystalline CaTiO 3 was reproduced in the simulation by cooling the liquid. It is shown that the presence of grain boundaries in the material is essential to reproduce the experimental data correctly.

Non-equilibrium molecular dynamics calculations were performed in order to obtain the thermal conductivity coefficients of InSb nanowires in comparison with the bulk system value. For bulk, the value obtained was 16 ± 2 Wm−1 K−1 which is in very good agreement with experimental value of 15 Wm−1 K−1, and the thermal conductivity of the nanowires were 0.54 ± 0.01 Wm−1 K−1 and 0.50 ± 0.01 Wm−1 K−1 for a 5 and 4 unit cells square cross-sectional nanowires, respectively, which is almost two orders of magnitude smaller. This result is in agreement with other simulations performed for other materials.

An effective interatomic potential is proposed for AlAs. Molecular dynamics technique was used to simulate the energetics of zinc-blende, wurtzite, rocksalt and NiAs crystal structures of AlAs. The calculated cohesive energy, bulk modulus and C11 elastic constant at room temperature and melting temperature agreed very well with experimental values. By constructing a common tangent to the calculated energy versus volume curves for zinc-blende and rocksalt structures of AlAs, the pressure of structural transition between these phases was found to be 10 GPa. Vibrational density of states and specific heat were compared with first-principle calculations, displaying very good agreement. The proposed interatomic potential allows us to predict the temperature dependence of several properties, such as the elastic constants and specific heat.

The dynamic behavior of mono- and nanocrystalline SiC ceramics under plane shock loading is revealed using molecular-dynamics simulations. The generation of shock-induced elastic compression, plastic deformation, and structural phase transformation is characterized at different crystallographic directions as well as on a 5-nm grain size nanostructure at 10 K and 300 K. Shock profiles are calculated in a wide range of particle velocities 0.1–6.0 km/s. The predicted Hugoniot agree well with experimental data. Results indicate the generation of elastic waves for particle velocities below 0.8–1.9 km/s, depending on the crystallographic direction. In the intermediate range of particle velocities between 2 and 5 km/s, the shock wave splits into an elastic precursor and a zinc blende-to-rock salt structural transformation wave, which is triggered by shock pressure over the ∼90 GPa threshold value. A plastic wave, with a strong deformation twinning component, is generated ahead of the transformation wave for shoc...

Using numerical simulations we investigated the dynamic response to an externally driven force of a classical two-dimensional (2D) electron system on a helium film at finite temperatures. A potential barrier located at the center of the system behaves as a pinning center that results in an insulator state below a threshold driving force. We have found that the current-voltage characteristic obeys the scaling relation I=f ξ , with ξ ranging from ∼(1.0–1.7) for different pinning strengths and temperatures. Our results may be used to understand the spread range of ξ in experiments with typical characteristic of plastic depinning.

Equilibrium and non-equilibrium molecular dynamics calculations of thermal conductivity coefficient are presented for bulk systems of InSb, using an effective two- and three-body inter atomic potential which demonstrated to be very transferable. In the calculations, the obtained coefficients were comparable to the experimental data. In the case of equilibrium simulations a Green-Kubo approach was used and the thermal conductivity was calculated for five temperatures between 300 K and 900 K. For the non equilibrium, or direct method, which is based on the Fourier’s law, the thermal conductivity coefficient was determined at a mean temperature of 300K. In this case it was used a pair of reservoirs, placed at a distance L from each other, and with internal temperatures fixed in 250 K, for the cold reservoir, and 350 K for the hot one. In order to obtain an approach to an infinite system coefficient, four different values of L were used, and the data was extrapolated to L→∞.