Search

Suppl Table 2

Supplementary Figure legends

Suppl Table 1

Supplementary figures

With the advent of OMICs technologies, both individual research groups and consortia have spear-headed the characterization of human samples of multiple pathophysiologic origins, resulting in thousands of archived genomes and transcriptomes. Although a variety of web tools are now available to extract information from OMICs data, their utility has been limited by the capacity of nonbioinformatician researchers to exploit the information. To address this problem, we have developed CANCERTOOL, a web-based interface that aims to overcome the major limitations of public transcriptomics dataset analysis for highly prevalent types of cancer (breast, prostate, lung, and colorectal). CANCERTOOL provides rapid and comprehensive visualization of gene expression data for the gene(s) of interest in well-annotated cancer datasets. This visualization is accompanied by generation of reports customized to the interest of the researcher (e.g., editable figures, detailed statistical analyses, and access to raw data for reanalysis). It also carries out gene-to-gene correlations in multiple datasets at the same time or using preset patient groups. Finally, this new tool solves the time-consuming task of performing functional enrichment analysis with gene sets of interest using up to 11 different databases at the same time. Collectively, CANCERTOOL represents a simple and freely accessible interface to interrogate well-annotated datasets and obtain publishable representations that can contribute to refinement and guidance of cancer-related investigations at all levels of hypotheses and design.Significance: In order to facilitate access of research groups without bioinformatics support to public transcriptomics data, we have developed a free online tool with an easy-to-use interface that allows researchers to obtain quality information in a readily publishable format. Cancer Res; 78(21); 6320–8. ©2018 AACR.

PDF file - 180K

PDF file - 78K

Nanoporous gold (np-Au) has unique properties due to its high surface-to-volume ratio; in particular, it displays different degrees of radiation sensitivity, from radiation tolerance to significant radiation-induced hardening. However, its thermal instability and propensity to coarsening limit practical applications. It is known that oxide functionalization of np-Au surface improves thermal stability and increases both hardness and elastic modulus of the metallic foam. Nevertheless, the changes in the material properties under irradiation have not been investigated yet. In this work, we address the questions of radiation sensitivity of atomic layer deposition (ALD)-coated np-Au, and how its mechanical properties change after irradiation. ALD Al2O3-coated gold nanofoams were synthetized and irradiated with Ne++ ions and their mechanical behavior was evaluated by nanoindentation. It is concluded that the as-prepared functionalized np-Au hardens and stiffens after ion irradiation depending on the dose, without losing toughness and wear resistance.

A set of embedded atom model (EAM) interatomic potentials was developed to represent highly idealized face-centered cubic (FCC) mixtures of Fe–Ni–Cr–Co–Al at near-equiatomic compositions. Potential functions for the transition metals and their crossed interactions are taken from our previous work for Fe–Ni–Cr–Co–Cu [D. Farkas and A. Caro: J. Mater. Res. 33 (19), 3218–3225, 2018], while cross-pair interactions involving Al were developed using a mix of the component pair functions fitted to known intermetallic properties. The resulting heats of mixing of all binary equiatomic random FCC mixtures not containing Al is low, but significant short-range ordering appears in those containing Al, driven by a large atomic size difference. The potentials are utilized to predict the relative stability of FCC quinary mixtures, as well as ordered L12 and B2 phases as a function of Al content. These predictions are in qualitative agreement with experiments. This interatomic potential set is developed to resemble but not model precisely the properties of this complex system, aiming at providing a tool to explore the consequences of the addition of a large size-misfit component into a high entropy mixture that develops multiphase microstructures.

We have used molecular dynamics and Monte Carlo methods to simulate the structure and phase stability of a Pd crystal in thermodynamic equilibrium with molecular hydrogen gas at temperature T and pressure $$ P_{g}^{H2} $$. The pressure–composition–temperature (PCT) curves were deduced under the extreme conditions of an open system (Pd crystal in equilibrium with a large-volume H2 gas reservoir) and a closed system (Pd crystal in equilibrium with H2 gas reservoir of infinitesimal volume). The PCT curves from the open simulations reproduce the experimental observations, including the ubiquitous hysteresis. The PCT curves from the closed-system simulations are continuous curves. Below a tri-critical point, the Pd–H system decomposes into two coherent phases. We find excellent agreement between the present simulation results and the predictions of the Schwarz–Khachaturyan theory for the decomposition of a Pd–H alloy into two coherent hydride phases.

In this work we examine the driving force for edge dislocations to climb in α -Fe from atomistic and mesoscale viewpoints. We study the bias for the climb process depending on the dislocation orientation and the applied stress due to both the gradient of the chemical potential and the transport coefficients. Both terms are modified by the applied stress and therefore contribute to climb. Surprisingly, even though the vacancy migration barrier distribution is modified by the external stress as obtained by nudged-elastic band calculations, the mobilities resulting from a kinetic Monte Carlo model applied on the obtained energy landscape are indistinguishable, independently of the stress. Moreover, an object kinetic Monte Carlo (OKMC) model including the effect of the dislocation strain field to first order shows indeed a slight anisotropic component in the diffusion in more complex dislocation configurations. However, the OKMC results highlight the fact that the thermodynamic component is the dominant driving force. We conclude that in α -Fe under thermal conditions, the main source of bias is given by the difference in vacancy chemical potentials, which is small enough to hinder the process for dynamic atomistic simulations.

To better understand the mechanisms at the basis of neutrophil functions during SARS-CoV-2, we studied patients with severe COVID-19 pneumonia. They had high blood proportion of degranulated neutrophils and elevated plasma levels of myeloperoxidase (MPO), elastase, and MPO-DNA complexes, which are typical markers of neutrophil extracellular traps (NET). Their neutrophils display dysfunctional mitochondria, defective oxidative burst, increased glycolysis, glycogen accumulation in the cytoplasm, and increase glycogenolysis. Hypoxia-inducible factor 1α (ΗΙF-1α) is stabilized in such cells, and it controls the level of glycogen phosphorylase L (PYGL), a key enzyme in glycogenolysis. Inhibiting PYGL abolishes the ability of neutrophils to produce NET. Patients displayed significant increases of plasma levels of molecules involved in the regulation of neutrophils' function including CCL2, CXCL10, CCL20, IL-18, IL-3, IL-6, G-CSF, GM-CSF, IFN-γ. Our data suggest that metabolic remodelling is vital for the formation of NET and for boosting neutrophil inflammatory response, thus, suggesting that modulating ΗΙF-1α or PYGL could represent a novel approach for innovative therapies.

With the advent of OMICs technologies, both individual research groups and consortia have spear-headed the characterization of human samples of multiple pathophysiologic origins, resulting in thousands of archived genomes and transcriptomes. Although a variety of web tools are now available to extract information from OMICs data, their utility has been limited by the capacity of nonbioinformatician researchers to exploit the information. To address this problem, we have developed CANCERTOOL, a web-based interface that aims to overcome the major limitations of public transcriptomics dataset analysis for highly prevalent types of cancer (breast, prostate, lung, and colorectal). CANCERTOOL provides rapid and comprehensive visualization of gene expression data for the gene(s) of interest in well-annotated cancer datasets. This visualization is accompanied by generation of reports customized to the interest of the researcher (e.g., editable figures, detailed statistical analyses, and access to raw data for reanalysis). It also carries out gene-to-gene correlations in multiple datasets at the same time or using preset patient groups. Finally, this new tool solves the time-consuming task of performing functional enrichment analysis with gene sets of interest using up to 11 different databases at the same time. Collectively, CANCERTOOL represents a simple and freely accessible interface to interrogate well-annotated datasets and obtain publishable representations that can contribute to refinement and guidance of cancer-related investigations at all levels of hypotheses and design., We are grateful to Iñaki Lazaro for the design of the tumor type logos, Evarist Planet and Antoni Berenguer for insightful discussions, and the Carracedo lab for valuable input. V. Torrano is funded by Fundación Vasca de Innovación e Investigación Sanitarias, BIOEF (BIO15/CA/052), the AECC J.P. Bizkaia and the Basque Department of Health (2016111109). The work of A. Carracedo is supported by the Basque Department of Industry, Tourism and Trade (Etortek) and the Department of Education (IKERTALDE IT1106-16, also participated by A. Gomez-Muñoz), the BBVA Foundation, the MINECO [SAF2016-79381-R (FEDER/EU)]; Severo Ochoa Excellence Accreditation SEV-2016-0644; Excellence Networks (SAF2016-81975-REDT), European Training Networks Project (H2020-MSCA-ITN-308 2016 721532), the AECC IDEAS16 (IDEAS175CARR), and the European Research Council (Starting Grant 336343, PoC 754627). CIBERONC was cofunded with FEDER funds. The work of A. Aransay is supported by the Basque Department of Industry, Tourism and Trade (Etortek and Elkartek Programs), the Innovation Technology Department of Bizkaia County, CIBERehd Network, and Spanish MINECO the Severo Ochoa Excellence Accreditation (SEV-2016-0644). I. Apaolaza is funded by a Basque Government predoctoral grant (PRE_2017_2_0028). X.R. Bustelo is supported by grants from the Castilla-León Government (BIO/SA01/15, CSI049U16), Spanish Ministry of Economy and Competitiveness (MINECO; SAF2015-64556-R), Worldwide Cancer Research (14-1248), Ramón Areces Foundation, and the Spanish Society against Cancer (GC16173472GARC). Funding from MINECO to X.R. Bustelo is partially contributed by the European Regional Development Fund. The work of F.J. Planes is supported by the MINECO (BIO2016-77998-R) and ELKARTEK Programme of the Basque Government (KK-2016/00026).

A set of embedded atom method model interatomic potentials is presented to represent a high-entropy alloy with five components. The set is developed to resemble but not model precisely face-centered cubic (fcc) near-equiatomic mixtures of Fe–Ni–Cr–Co–Cu. The individual components have atomic sizes deviating up to 3%. With the heats of mixing of all binary equiatomic random fcc mixtures being less than 0.7 kJ/mol and the corresponding value for the quinary being −0.0002 kJ/mol, the potentials predict the random equiatomic fcc quinary mixture to be stable with respect to phase separation or ordering and with respect to bcc and hcp random mixtures. The details of lattice distortion, strain, and stress states in this phase are reported. The standard deviation in the individual nearest neighbor bond lengths was found to be in the range of 2%. Most importantly, individual atoms in the alloy were found to be under atomic strains up to 0.5%, corresponding to individual atomic stresses up to several GPa.

We use time-dependent density functional theory to calculate the electronic stopping S e in binary Ni-Ni atomic collisions and for a Ni projectile along channeling directions in a Ni crystal. Our results show that when S e is reported as a function of the ground state target electronic density ρ 0 the stopping is not a single-valued function of the local density, as assumed in formalisms that date back to the origins of quantum mechanics, but shows loops, suggesting that it is inaccurate to model stopping as a dissipative force of the type F = β ( ρ 0 ) v , as it is customarily done in non-adiabatic molecular dynamics simulations of ion-solid interactions. We compare our results with S e in a uniform electron gas where the above definition for the force holds, and conclude on the validity of using jellium as a crude approximation for more realistic inhomogeneous electron gases.

Background and aims Cholangiocarcinoma (CCA) is an aggressive tumor type affecting cholangiocytes. CCAs frequently arise under certain cholestatic liver conditions. Intrahepatic accumulation of bile acids may facilitate cocarcinogenic effects by triggering an inflammatory response and cholangiocyte proliferation. Here, the role of bile acid receptors FXR and TGR5 in CCA progression was evaluated. Methods FXR and TGR5 expression was determined in human CCA tissues and cell lines. An orthotopic model of CCA was established in immunodeficient mice and tumor volume was monitored by magnetic resonance imaging under chronic administration of the specific FXR or TGR5 agonists, obeticholic acid (OCA) or INT-777 (0,03% in chow; Intercept Pharmaceuticals), respectively. Functional effects of FXR or TGR5 activation were evaluated on CCA cells in vitro. Results FXR was downregulated whereas TGR5 was upregulated in human CCA tissues compared to surrounding normal liver tissue. FXR expression correlated with tumor differentiation and TGR5 correlated with perineural invasion. TGR5 expression was higher in perihilar than in intrahepatic CCAs. In vitro, FXR was downregulated and TGR5 was upregulated in human CCA cells compared to normal human cholangiocytes. OCA halted CCA growth in vivo, whereas INT-777 showed no effect. In vitro, OCA inhibited CCA cell proliferation and migration which was associated with decreased mitochondrial energy metabolism. INT-777, by contrast, stimulated CCA cell proliferation and migration, linked to increased mitochondrial energy metabolism. Conclusion Activation of FXR inhibits, whereas TGR5 activation may promote, CCA progression by regulating proliferation, migration and mitochondrial energy metabolism. Modulation of FXR or TGR5 activities may represent potential therapeutic strategies for CCA.

Salp15, a salivary protein of Ixodes ticks, inhibits the activation of naïve CD4 T cells. Treatment with Salp15 results in the inhibition of early signaling events and the production of the autocrine growth factor, interleukin-2. The fate of the CD4 T cells activated in the presence of Salp15 or its long-term effects are, however, unknown. We now show that Salp15 binding to CD4 is persistent and induces a long-lasting immunomodulatory effect. The activity of Salp15 results in sustained diminished cross-antigenic antibody production even after interruption of the treatment with the protein. Transcriptionally, the salivary protein provokes an acute effect that includes known activation markers, such as Il2 or Cd44, and that fades over time. The long-term effects exerted by Salp15 do not involve the induction of either anergy traits nor increased populations of regulatory T cells. Similarly, the treatment with Salp15 does not result in B cell anergy or the generation of myeloid suppressor cells. However, Salp15 induces the increased expression of the ectoenzyme, CD73, in regulatory T cells and increased production of adenosine. Our study provides a profound characterization of the immunomodulatory activity of Salp15 and suggests that its long-term effects are due to the specific regulation of CD73. Introduction, Supported by grants from the Department of Education of the Basque Government (PI2013-49 to JA and PI2012-42 to RB). JA is funded by the European Union (Grant Agreement number 602272). AMA and JLL’s work was supported by the Basque Department of Industry, Tourism and Trade (Etortek and Elkartek Programs), the Innovation Technology Department of Bizkaia and the CIBERehd Network. The work of AC is supported by a Ramón y Cajal award, the Basque Department of Industry, Tourism and Trade (Etortek), ISCIII (PI13/00031), FERO VIII Fellowship, the BBVA foundation, MINECO (SAF2016-79381-R) and the European Research Council Starting Grant (336343). CIBERonc was co-funded with FEDER funds. AC-M was funded by a Juan de la Cierva program award and the European Union MSCA program (CIG 660191). RB was funded by MINECO grants BFU2011-25986 and BFU2014-52282-P and the Consolider Program (BFU2014-57703-REDC). FJB was funded by a MINECO grant (CTQ2014-56966-R). D.B. is funded by a MINECO FPI fellowship. We thank the MINECO for the Severo Ochoa Excellence accreditation (SEV-2016-0644).

This study unravels an unprecedented murine model of lethal metastatic prostate cancer, based on the combined deletion of Pten and Lkb1. Importantly, minimal activity of LKB1 is sufficient to hamper prostate cancer cell aggressiveness, thus redefining the relationship between gene dosage and tumor suppression., Gene dosage is a key defining factor to understand cancer pathogenesis and progression, which requires the development of experimental models that aid better deconstruction of the disease. Here, we model an aggressive form of prostate cancer and show the unconventional association of LKB1 dosage to prostate tumorigenesis. Whereas loss of Lkb1 alone in the murine prostate epithelium was inconsequential for tumorigenesis, its combination with an oncogenic insult, illustrated by Pten heterozygosity, elicited lethal metastatic prostate cancer. Despite the low frequency of LKB1 deletion in patients, this event was significantly enriched in lung metastasis. Modeling the role of LKB1 in cellular systems revealed that the residual activity retained in a reported kinase-dead form, LKB1K78I, was sufficient to hamper tumor aggressiveness and metastatic dissemination. Our data suggest that prostate cells can function normally with low activity of LKB1, whereas its complete absence influences prostate cancer pathogenesis and dissemination.

We present a detailed model for the nonadiabatic coupling between ions and electrons in energetic ion-solid interactions over a wide range of energies in concentrated solid-solution fcc alloys of the $3d$ transition metals Ni, Co, Fe, and Cr. The model is based on general statistical mechanical principles and results in a stochastic modification of the classical nuclei motion which is parameterized by the first-principles calculation of a dissipation function produced by explicit time-dependent electronic evolution. This model provides a full picture of an entire collision process, from the ballistic to the thermal phases of a cascade, giving a detailed description of the energy exchange between ions and electrons till their final thermalization, removing in this way some ad hoc assumptions used in the state-of-the-art atomistic two-temperature models. This work is separated in two papers; in the present Part I, we report on the ab initio methodology used to translate stopping power and electron-phonon interaction into a parameterized dissipation function; Part II, to be published, addresses the nonadiabatic ion dynamics using our modified Langevin dynamics [Tamm et al. Phys. Rev. Lett. 120, 185501 (2018)] applying the dissipation functions developed here to specific collision cascade events.

We present a model for the role of electrons in collision cascades in solids in which the coupling between ions and electrons is calculated using first-principles models and introduced into the classical ion equations of motion using our modified Langevin dynamics [A. Tamm et al., Phys. Rev. Lett. 120, 185501 (2018)]. This model gives a full picture of the entire collision process, from the ballistic to the thermal phases of a cascade, giving a detailed representation of the energy exchange between ions and electrons until their final thermalization, removing in this way some ad hoc assumptions used in the state-of-the-art two-temperature model. This work is separated into two papers: Part I [M. Caro et al., Phys. Rev. B 99, 174301 (2019)] reports on the ab initio methodology used to translate stopping power into the parametrized dissipation function. Part II applies the nonadiabatic ion dynamics using the dissipation functions developed in Part I to specific collision cascade events.

International audience; Ni-based alloys are used in nuclear applications, including as a window material at isotope production facilities, withstanding high fluxes of different energetic particles like protons. Irradiation disorders the γ′ precipitates that in large extent confer the mechanical properties characterizing these materials. Upon disordering, the γ′ phase transforms into oversaturated γ, degrading the materials properties. Experimentally it is observed that disordering might take place at fairly low irradiation doses. Once the particles are disordered, a competition between dissolution, due to strong concentration gradients in an oversaturated solid solution, and reordering appears. Here, we examine this competition in a model Ni-Al alloy under thermal conditions for different precipitates sizes and temperatures. We observe Al interdiffusion from the supersaturated particle to the matrix. Also, stochasticity appears as an important factor in to where precipitates locate. Stress relaxation seems to modify the precipitation process, with a stronger interface effect compared to rigid lattice simulations.

Historically, alloy development with better radiation performance has been focused on traditional alloys with one or two principal element(s) and minor alloying elements, where enhanced radiation resistance depends on microstructural or nanoscale features to mitigate displacement damage. In sharp contrast to traditional alloys, recent advances of single-phase concentrated solid solution alloys (SP-CSAs) have opened up new frontiers in materials research. In these alloys, a random arrangement of multiple elemental species on a crystalline lattice results in disordered local chemical environments and unique site-to-site lattice distortions. Based on closely integrated computational and experimental studies using a novel set of SP-CSAs in a face-centered cubic structure, we have explicitly demonstrated that increasing chemical disorder can lead to a substantial reduction in electron mean free paths, as well as electrical and thermal conductivity, which results in slower heat dissipation in SP-CSAs. The chemical disorder also has a significant impact on defect evolution under ion irradiation. Considerable improvement in radiation resistance is observed with increasing chemical disorder at electronic and atomic levels. The insights into defect dynamics may provide a basis for understanding elemental effects on evolution of radiation damage in irradiated materials and may inspire new design principles of radiation-tolerant structural alloys for advanced energy systems.

We present empirical potential and Density Functional Theory results of interstitials in FeCr and pure Cr. Results show that potentials for the original and revised two-band model, a recently introduced third two-band model, and for the revised concentration-dependent model produce errors of up to multiple eV in formation and binding energies for Fe-containing interstitials in pure Cr. Fe-interstitial binding in Cr is much stronger than Cr-interstitial binding in Fe according to Density Functional Theory, but all four potentials still strongly overestimate the binding strength. At the Fe-rich end errors in empirical potentials are smaller and most of the errors are not a linear extrapolation in concentration of the larger errors in pure Cr. Interstitial formation energies in Fe-rich FeCr are underestimated by all four empirical potentials, but much less so than in pure Cr. In Fe-rich FeCr the revised concentration-dependent model produces Cr-interstitial binding energies quite similar to Density Functional Theory values, while all three two-band models show almost no binding or repulsion.

Primary radiation damage formation in solid materials typically involves collisions between atoms that have up to a few hundred keV of kinetic energy. During these collisions, the distance between two colliding atoms can approach 0.05 nm. At such small atomic separations, force fields fitted to equilibrium properties tend to significantly underestimate the potential energy of the colliding dimer. To enable molecular dynamics simulations of high-energy collisions, it is common practice to use a screened Coulomb force field to describe the interactions and to smoothly join this to the equilibrium force field at a suitable interatomic spacing. However, there is no accepted standard method for choosing the parameters used in the joining process, and our results prove that defect production is sensitive to how the force fields are linked. A new procedure is presented that involves the use of ab initio calculations to determine the magnitude and spatial dependence of the pair interactions at intermediate distances, along with systematic criteria for choosing the joining parameters. Results are presented for the case of nickel, which demonstrate the use and validity of the procedure.

Cellular transformation and cancer progression is accompanied by changes in the metabolic landscape. Master co-regulators of metabolism orchestrate the modulation of multiple metabolic pathways through transcriptional programs, and hence constitute a probabilistically parsimonious mechanism for general metabolic rewiring. Here we show that the transcriptional co-activator peroxisome proliferator-activated receptor gamma co-activator 1α (PGC1α) suppresses prostate cancer progression and metastasis. A metabolic co-regulator data mining analysis unveiled that PGC1α is downregulated in prostate cancer and associated with disease progression. Using genetically engineered mouse models and xenografts, we demonstrated that PGC1α opposes prostate cancer progression and metastasis. Mechanistically, the use of integrative metabolomics and transcriptomics revealed that PGC1α activates an oestrogen-related receptor alpha (ERRα)-dependent transcriptional program to elicit a catabolic state and metastasis suppression. Importantly, a signature based on the PGC1α–ERRα pathway exhibited prognostic potential in prostate cancer, thus uncovering the relevance of monitoring and manipulating this pathway for prostate cancer stratification and treatment.

Helium(He) produced by transmutation process inside structural material due to neutron irradiation plays a vital role in the degradation of material properties. We have carried out Molecular dynamics(MD) simulations to study the growth of He bubble in Iron-Chromium alloy. Simulations are carried out at two different temperatures, viz. 0.1 K and 800 K, upto He bubble radius of 2.5 nm. An equation for variation of volume of He bubbles with the number of He atoms is obtained at both the temperatures. Bubble pressure and potential energy variation is obtained with increasing bubble radius. Dislocations are also found to be emitted after the bubble reaches a critical radius of 0.39 nm at 800 K. Separate MD simulations of He with pre-created voids are also carried out to study the binding energies of He and Vacancy (V) to Hem-Vn cluster. Binding energies are found to be in the range of 1–5.5 eV.

We report the results of compressive tests for a model bi-continuous nanoporous gold structure using atomistic simulations focusing on the densification regime and the plasticity mechanisms taking place. The stress – strain response follows a logarithmic evolution proportional to the inverse of strain and we provide a simple scaling law for this behavior. Hardening is correlated to the dislocation density and an exponential dependence is revealed. The plasticity mechanisms were inspected revealing the presence of Hirth and Frank partials contributing to the hardening of the sample. Lomer–Cottrel locks, perfect dislocations, and twinning were also found.

Spinodal decomposition in thermally aged Fe–Cr alloys leads to significant hardening, which is the direct cause of the so-called 475 ∘ C-embrittlement. To illustrate how spinodal decomposition induces hardening by atomistic interactions, we conducted a series of numerical simulations as well as reference experiments. The numerical results indicated that the hardness scales linearly with the short-range order (SRO) parameter, while the experimental result reproduced this relationship within statistical error. Both seemingly suggest that neighboring Cr–Cr atomic pairs essentially cause hardening, because SRO is by definition uniquely dependent on the appearance probability of such pairs. A further numerical investigation supported this notion, as it suggests that the dominant cause of hardening is the pinning effect of dislocations passing over such Cr–Cr pairs. Moreover, this finding has a practical merit, that is, the SRO parameter can serve as a good index of hardening of steels, which is critical for evaluating their lifetime.

Strengthening of metals through nanoscale grain boundaries and coherent twin boundaries is manifested by a maximum strength—a phenomenon known as Hall–Petch breakdown. Different softening mechanisms are considered to occur for nanocrystalline and nanotwinned materials. Here, we report nanocrystalline-nanotwinned Ag materials that exhibit two strength transitions dissimilar from the above mechanisms. Atomistic simulations show three distinct strength regions as twin spacing decreases, delineated by positive Hall–Petch strengthening to grain-boundary-dictated (near-zero Hall–Petch slope) mechanisms and to softening (negative Hall–Petch slope) induced by twin-boundary defects. An ideal maximum strength is reached for a range of twin spacings below 7 nm. We synthesized nanocrystalline-nanotwinned Ag with hardness 3.05 GPa—42% higher than the current record, by segregating trace concentrations of Cu impurity (

Stochastic Langevin dynamics has been traditionally used as a tool to describe non-equilibrium processes. When utilized in systems with collective modes, traditional Langevin dynamics relaxes all modes indiscriminately, regardless of their wavelength. We propose a generalization of Langevin dynamics that can capture a differential coupling between collective modes and the bath, by introducing spatial correlations in the random forces. This allows modeling the electronic subsystem in a metal as a generalized Langevin bath endowed with a concept of locality, greatly improving the capabilities of the two-temperature model. The specific form proposed here for the spatial correlations produces physical wavevector- and polarization-dependency of the relaxation produced by the electron-phonon coupling in a solid. We show that the resulting model can be used for describing the path to equilibration of ions and electrons, and also as a thermostat to sample the equilibrium canonical ensemble. By extension, the family of models presented here can be applied in general to any dense system, solids, alloys and dense plasmas. As an example, we apply the model to study the non-equilibrium dynamics of an electron-ion two-temperature Ni crystal., 6 pages, 3 figures

This paper addresses the role of misfit dislocations in the nucleation and growth of nanoscale He bubbles at interfaces. In a recent work, we studied the nanoscale effects on the capillarity equation and on equilibrium conditions. We proposed an expression for surface energy and for the equation of state, EOS, for He in bubbles, which have a size dependence that captures the role of the interface forces, which become relevant at the nanoscale. Here we determine the EOS for several twist grain boundaries in Fe and Cu and incorporate these results into the rate equation that determines the bubble-to-void transition, focusing on the influence of interface dislocations on the evaporation rate of vacancies. We find a significant effect of the magnitude of the Burgers vector of the dislocations on the critical radius for the transition. These results give a quantitative way to characterize grain boundaries in their ability to capture He and alter the onset of swelling.

High entropy alloys (HEA) have unique properties including the potential to be radiation tolerant. These materials with extreme disorder could resist damage because disorder, stabilized by entropy, is the equilibrium thermodynamic state. Disorder also reduces electron and phonon conductivity keeping the damage energy longer at the deposition locations, eventually favoring defect recombination. In the short time-scales related to thermal spikes induced by collision cascades, phonons become the relevant energy carrier. In this work, we perform a systematic study of phonon thermal conductivity in multiple component solid solutions represented by Lennard-Jones (LJ) potentials. We explore the conditions that minimize phonon mean free path via extreme alloy complexity, by varying the composition and the elements (differing in mass, atomic radii, and cohesive energy). We show that alloy complexity can be tailored to modify the scattering mechanisms that control energy transport in the phonon subsystem. Our analysis provides a qualitative guidance for the selection criteria used in the design of HEA alloys with low phonon thermal conductivity.

The aim of this study is to characterize some atomic-scale properties of Ni-based FCC multicomponent alloys. For this purpose, we use Monte Carlo method combined with density functional theory calculations to study short-range order (SRO), atomic displacements, electronic density of states, and magnetic moments in equimolar ternary NiCrCo, and quaternary NiCrCoFe alloys. According to our study, the salient features for the ternary alloy are a negative SRO parameter between Ni–Cr and a positive between Cr–Cr pairs as well as a weakly magnetic state. For the quaternary alloy we predict negative SRO parameter for Ni–Cr and Ni–Fe pairs and positive for Cr–Cr and Fe–Fe pairs. Atomic displacements for both ternary and quaternary alloys are negligible. In contrast to the ternary, the quaternary alloy shows a complex magnetic structure. The electronic structure of the ternary and quaternary alloys shows differences near the Fermi energy between a random solid solution and the predicted structure with SRO. Despite that, the calculated EXAFS spectra does not show enough contrast to discriminate between random and ordered structures. The predicted SRO has an impact on point-defect energetics, electron–phonon coupling and thermodynamic functions and thus, SRO should not be neglected when studying properties of these two alloys.

Designing radiation tolerant materials is one of the primary challenges associated with advanced nuclear energy systems. One attractive route that has received much attention world-wide is to introduce a high density of sinks, often in the form of interfaces or secondary phases. Here, we develop a simple model of such nanocomposites and examine the ramifications of various factors on the overall radiation stability of the material. In particular, we determine how the distribution of secondary phases, the relative sink strength of those phases, and the irradiation temperature influence the radiation tolerance of the matrix. We find that the best scenario is one in which the sinks have intermediate strength, transiently trapping defects before releasing them back into the matrix. Neither perfect sinks nor the complete absence of sinks perform as well. This provides new insight into the optimal properties of nanocomposites for radiation damage environments.

We investigate the modifications to the Young–Laplace capillarity equation needed to describe nanoscale gas bubbles embedded in metals, scale at which the finite width of the interface region cannot be neglected. We focus in particular on the case of He in Fe. Using both, the concept of Tolman’s length that provides a curvature dependence for the interface energy, and a new equation of state for He at the nanoscale that accounts for interface effects (see Caro et al., 2013), we derive an expression to predict pressure, and from it density and the amount of He in nanoscale bubbles. We find that conditions for equilibrium are found for values of pressure or density at variance by a factor of ∼ 2 compared to the traditional way of using the capillarity equation and a bulk He EOS.

Prostate cancer is among the most frequent cancers in men, and despite its high rate of cure, the high number of cases results in an elevated mortality worldwide. Importantly, prostate cancer incidence is dramatically increasing in western societies in the past decades, suggesting that this type of tumor is exquisitely sensitive to lifestyle changes. Prostate cancer frequently exhibits alterations in the PTEN gene (inactivating mutations or gene deletions) or at the protein level (reduced protein expression or altered sub-cellular compartmentalization). The relevance of PTEN in this type of cancer is further supported by the fact that the sole deletion of PTEN in the murine prostate epithelium recapitulates many of the features of the human disease. In order to study the molecular alterations in prostate cancer, we need to overcome the methodological challenges that this tissue imposes. In this review we present protocols and methods, using PTEN as proof of concept, to study different molecular characteristics of prostate cancer.

By exploiting Monte Carlo methodology and molecular dynamics, we computationally simulate the spinodal decomposition of iron–chromium binary alloys and analyze the relationship between the increase of yield strength induced by the phase separation phenomenon, and statistical parameters of the atomistic configuration. We successfully model the experimentally-discovered proportional relationship between the hardness and the variation parameter (or V), and also found that the adequacy of the parameter V as an empirical indicator of hardening is limited, because it does not properly capture short-range atomistic configurations that influence the hardening. We suggest that the short-range-order parameter has more potential to become universal descriptor of the phenomenon.

Nature 547, 109–113 (2017); doi:10.1038/nature22964 In this Letter, there are errors in Extended Data Figs 5, 8 and 9, and the affiliation of an author. The affiliations for author Violeta Serra should include number 2 (CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellon 11, Planta 0, 28029 Madrid, Spain).

L12-ordered γ′ precipitates embedded in a fcc γ matrix impart excellent mechanical properties to nickel-base superalloys. However, these enhanced mechanical properties are lost under irradiation, which causes the γ′ precipitates to disorder and dissolve. We conduct an atomic-level study of radiation-induced disordering and dissolution at a coherent (100) facet of an initially ordered γ′ Ni3Al precipitate neighboring a pure Ni γ matrix. Using molecular dynamics, we simulate collision-induced events by sequentially introducing 10 keV primary knock-on atoms with random positions and directions. In the absence of thermally assisted recovery processes, the ordered Ni3Al layer disorders rapidly within 0.1–0.2 dpa and then gradually dissolves into the adjacent Ni layer at higher doses. Both the disordering efficiency and mixing parameter calculated from the simulations lie within the range of values found by experiments carried out at room temperature, where thermally activated diffusion is insignificant.

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role of interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. This model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.

We present results of a molecular dynamics simulation study of the effect of electron-ion interactions on the dynamics of the thermal spike in Cu. Interatomic forces are described with a modified embedded atom method potential. We show that the electron-ion interaction acts to reduce the lifetime of the thermal spike and therefore the amount of atomic rearrangement that takes place in energetic displacement cascades in Cu. The results point toward the important effect that inelastic energy losses might have on the dynamics of displacement cascades in the subcascade energy regime where the lifetime of the thermal spike is expected to exceed the electron-phonon coupling time.

We present a description of the thermal behavior of cascades in Cu and Ag over a large energy range and irradiation temperatures. For this purpose the binary collision approximation, which gives the profile of the energy deposition, is coupled to a simplified version of the heat equation. In the present calculations, the original liquid drop model [M. Alurralde, A. Caro, and M. Victoria, J. Nucl. Mater. 183, 33 (1991)] has been extended to the case where the lattice is at finite temperatures. The resulting evolution of the liquid cascade is analyzed for PKA energies up to 1 MeV, and the results are compared to experimental observations of mixing rates. We obtain a temperature dependence that adds to the traditional Radiation Enhanced Diffusion, RED, in very good qualitative agreement with experiments on materials showing thermal spikes.

Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms Activation of the PTEN-PI3K-mTORC1 pathway consolidates metabolic programs that sustain cancer cell growth and proliferation,. Here we show that mTORC1 regulates polyamine dynamics, a metabolic route that is essential for oncogenicity. Through the use of integrative metabolomics in a mouse model and human biopsies of prostate cancer, we identified alterations in tumours impacting on the production of decarboxylated S-adenosylmethionine (dcSAM) and polyamine synthesis. Mechanistically, this metabolic rewiring stems from mTORC1-dependent regulation of S-adenosylmethionine decarboxylase 1 (AMD1) stability. This novel molecular regulation was validated in murine and human cancer specimens. AMD1 was upregulated in prostate cancer specimens with activated mTORC1. Conversely, samples from a clinical trial with the mTORC1 inhibitor everolimus exhibited a predominant decrease in AMD1 immunoreactivity that was associated to a decrease in proliferation, in line with the requirement of dcSAM production for oncogenicity. These findings provide fundamental information about the complex regulatory landscape controlled by mTORC1 to integrate and translate growth signals into an oncogenic metabolic program.

Energetic ions traveling in solids deposit energy in a variety of ways, being nuclear and electronic stopping the two avenues in which dissipation is usually treated. This separation between electrons and ions relies on the adiabatic approximation in which ions interact via forces derived from the instantaneous electronic ground state. In a more detailed view, in which non-adiabatic effects are explicitly considered, electronic excitations alter the atomic bonding, which translates into changes in the interatomic forces. In this work, we use time dependent density functional theory and forces derived from the equations of Ehrenfest dynamics that depend instantaneously on the time-dependent electronic density. With them we analyze how the inter-ionic forces are affected by electronic excitations in a model of a Ni projectile interacting with a Ni target, a metallic system with strong electronic stopping and shallow core level states. We find that the electronic excitations induce substantial modifications to the inter-ionic forces, which translate into nuclear stopping power well above the adiabatic prediction. In particular, we observe that most of the alteration of the adiabatic potential in early times comes from the ionization of the core levels of the target ions, not readily screened by the valence electrons. Energy Dissipation to Defect Evolution Center (EDDE), Energy Frontier Research Center - US Department of Energy, Office of Science, Basic Energy Sciences [2014ORNL1026]; European Commission through the Electron Stopping grant within the Marie Curie CIG program; US DOE [DE-AC52-06NA25396]; US Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Donostia International Physics Center, Donostia-San Sebastian, Spain [20018]; CIC nanoGUNE, Donostia-San Sebastian, Spain [20018] Work performed by M.C., A.A.C., and A.C. was supported as part of the Energy Dissipation to Defect Evolution Center (EDDE), an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Basic Energy Sciences (Award Number 2014ORNL1026). E.A. acknowledges financial support from European Commission through the Electron Stopping grant within the Marie Curie CIG program. This research used resources provided by the LANL Institutional Computing Program. LANL, an affirmative action/equal opportunity employer, is operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the US DOE under contract DE-AC52-06NA25396. Work by A.A.C. performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344, and acknowledges computing support from the Lawrence Livermore National Laboratory Institutional Computing Grand Challenge program. A.C. acknowledges hospitality and financial support from Donostia International Physics Center, 20018 Donostia-San Sebastian, Spain, and CIC nanoGUNE, 20018 Donostia-San Sebastian, Spain. A.C. acknowledges fruitful discussions with J. Ferron.

We have developed a thermodynamically and mechanically reliable concentration dependent embedded atom method interatomic potential for the Mg–Li system using first principles and experimental inputs. Pure elemental potentials from first principles theory and heat of mixing from the experiments are the inputs to the cross pair interaction. This simple potential is able to predict various properties of the Mg–Li alloy such as lattice parameter, heat of mixing, stacking fault energy and bulk modulus as a function of composition and temperature, in good agreement with literature data. Most importantly, it can reproduce experimental Mg–Li phase diagram. We demonstrate its transferability for thermal and mechanical behavior studies across entire concentration range in large-scale atomistic simulations.