Lattice Green's function for crystals containing a planar interface

Flexible boundary condition methods couple an isolated defect to a harmonically responding medium through the bulk lattice Green's function; in the case of an interface, interfacial lattice Green's functions. We present a method to compute the lattice Green's function for a planar interface with arbitrary atomic interactions suited for the study of line defect/interface interactions. The interface is coupled to two different semi-infinite bulk regions, and the Green's function for interface-interface, bulk-interface and bulk-bulk interactions are computed individually. The elastic bicrystal Green's function and the bulk lattice Green's function give the interaction between bulk regions. We make use of partial Fourier transforms to treat in-plane periodicity. Direct inversion of the force constant matrix in the partial Fourier space provides the interface terms. The general method makes no assumptions about the atomic interactions or crystal orientations. We simulate a screw dislocation interacting with a $(10\bar{1}2)$ twin boundary in Ti using flexible boundary conditions and compare with traditional fixed boundary conditions results. Flexible boundary conditions give the correct core structure with significantly less atoms required to relax by energy minimization. This highlights the applicability of flexible boundary conditions methods to modeling defect/interface interactions by \textit{ab initio} methods

Thermal Stabilization of the HCP Phase in Titanium

We have used a tight-binding model that is fit to first-principles electronic-structure calculations for titanium to calculate quasi-harmonic phonons and the Gibbs free energy of the hexagonal close-packed (hcp) and omega crystal structures. We show that the true zero-temperature ground-state is the omega structure, although this has never been observed experimentally at normal pressure, and that it is the entropy from the thermal population of phonon states which stabilizes the hcp structure at room temperature. We present the first completely theoretical prediction of the temperature- and pressure-dependence of the hcp-omega phase transformation and show that it is in good agreement with experiment. The quasi-harmonic approximation fails to adequately treat the bcc phase because the zero-temperature phonons of this structure are not all stable

Au/TiO2(110) interfacial reconstruction stability from ab initio

We determine the stability and properties of interfaces of low-index Au surfaces adhered to TiO2(110), using density functional theory energy density calculations. We consider Au(100) and Au(111) epitaxies on rutile TiO2(110) surface, as observed in experiments. For each epitaxy, we consider several different interfaces: Au(111)//TiO2(110) and Au(100)//TiO2(110), with and without bridging oxygen, Au(111) on 1x2 added-row TiO2(110) reconstruction, and Au(111) on a proposed 1x2 TiO reconstruction. The density functional theory energy density method computes the energy changes on each of the atoms while forming the interface, and evaluates the work of adhesion to determine the equilibrium interfacial structure.Comment: 20 pages, 11 figure

Targeted knock-down of miR21 primary transcripts using snoMEN vectors induces apoptosis in human cancer cell lines

We have previously reported an antisense technology, 'snoMEN vectors', for targeted knock-down of protein coding mRNAs using human snoRNAs manipulated to contain short regions of sequence complementarity with the mRNA target. Here we characterise the use of snoMEN vectors to target the knock-down of micro RNA primary transcripts. We document the specific knock-down of miR21 in HeLa cells using plasmid vectors expressing miR21-targeted snoMEN RNAs and show this induces apoptosis. Knock-down is dependent on the presence of complementary sequences in the snoMEN vector and the induction of apoptosis can be suppressed by over-expression of miR21. Furthermore, we have also developed lentiviral vectors for delivery of snoMEN RNAs and show this increases the efficiency of vector transduction in many human cell lines that are difficult to transfect with plasmid vectors. Transduction of lentiviral vectors expressing snoMEN targeted to pri-miR21 induces apoptosis in human lung adenocarcinoma cells, which express high levels of miR21, but not in human primary cells. We show that snoMEN-mediated suppression of miRNA expression is prevented by siRNA knock-down of Ago2, but not by knock-down of Ago1 or Upf1. snoMEN RNAs colocalise with Ago2 in cell nuclei and nucleoli and can be co-immunoprecipitated from nuclear extracts by antibodies specific for Ago2

High-Risk Deviant Decisions: Does Neutralization Still Play a Role?

Extant research has shown that neutralization processes can enable potential IS security policy violators to justify their behavior and overcome the deterrence effect of sanctions in order to engage in unethical behaviors. However, such sanctions are typically moderate and not career ending. We test the boundary conditions of this theory by evaluating whether neutralization plays a role in overcoming the impact of extreme levels of deterrence. We extend the Siponen and Vance (2010) framework within a professional context that assigns extreme sanctions to violators. Using the scenario-based factorial survey method common in IS security research, we collected data from future auditors who understand these extreme sanctions. We test the reasons that auditors may use to form intentions to falsify information concerning an information security issue with a company’s accounting information system, thereby jeopardizing data integrity and security by modifying working papers to hide irregularities and, by doing so, violating their professional standards, which could result in career-ending sanctions. We empirically validated and tested the theoretical model. Our results show that sanctions play an important role in reducing employees’ intentions to violate policy but that, even under extreme boundary conditions, employees might seek to rationalize their unethical behavior by denying responsibility for their actions through, for example, arguing that their supervisors pressured them into performing the violations. We also establish that messages heightening the awareness and perceptions of the certainty and severity of organizational punishment are likely to attenuate such deviant behaviors. We discuss the implications of these findings and suggest future avenues for research

A parametric study on the dynamic response of planar multibody systems with multiple clearance joints

A general methodology for dynamic modeling and analysis of multibody systems with multiple clearance joints is presented and discussed in this paper. The joint components that constitute a real joint are modeled as colliding bodies, being their behavior influenced by geometric and physical properties of the contacting surfaces. A continuous contact force model, based on the elastic Hertz theory together with a dissipative term, is used to evaluate the intra-joint contact forces. Furthermore, the incorporation of the friction phenomenon, based on the classical Coulomb’s friction law, is also discussed. The suitable contact-impact force models are embedded into the dynamics of multibody systems methodologies. An elementary mechanical system is used to demonstrate the accuracy and efficiency of the presented approach, and to discuss the main assumptions and procedures adopted. Different test scenarios are considered with the purpose of performing a parametric study for quantifying the influence of the clearance size, input crank speed and number of clearance joints on the dynamic response of multibody systems with multiple clearance joints. Additionally, the total computation time consumed in each simulation is evaluated in order to test the computational accuracy and efficiency of the presented approach. From the main results obtained in this study, it can be drawn that clearance size and the operating conditions play a crucial role in predicting accurately the dynamic responses of multibody systems.Fundação para a Ciência e a Tecnologia (FCT

Enhanced snoMEN Vectors Facilitate Establishment of GFP–HIF-1α Protein Replacement Human Cell Lines

The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human nucleolar snoRNAs and assessed their application for gene specific knock-downs to improve the efficiency of snoMEN vectors. We identify and characterise a new snoMEN vector, termed 47snoMEN, that is derived from box C/D snoRNA U47, demonstrating its use for knock-down of both endogenous cellular proteins and G/YFP-fusion proteins. Using multiplex 47snoMEM vectors that co-express multiple 47snoMEN in a single transcript, each of which can target different sites in the same mRNA, we document >3-fold increase in knock-down efficiency when compared with the original HBII-180C based snoMEN. The multiplex 47snoMEM vector allowed the construction of human protein replacement cell lines with improved efficiency, including the establishment of novel GFP–HIF-1α replacement cells. Quantitative mass spectrometry analysis confirmed the enhanced efficiency and specificity of protein replacement using the 47snoMEN-PR vectors. The 47snoMEN vectors expand the potential applications for snoMEN technology in gene expression studies, target validation and gene therapy

On the contact detection for contact-impact analysis in multibody systems

One of the most important and complex parts of the simulation of multibody systems with contact-impact involves the detection of the precise instant of impact. In general, the periods of contact are very small and, therefore, the selection of the time step for the integration of the time derivatives of the state variables plays a crucial role in the dynamics of multibody systems. The conservative approach is to use very small time steps throughout the analysis. However, this solution is not efficient from the computational view point. When variable time step integration algorithms are used and the pre-impact dynamics does not involve high-frequencies the integration algorithms may use larger time steps and the contact between two surfaces may start with initial penetrations that are artificially high. This fact leads either to a stall of the integration algorithm or to contact forces that are physically impossible which, in turn, lead to post-impact dynamics that is unrelated to the physical problem. The main purpose of this work is to present a general and comprehensive approach to automatically adjust the time step, in variable time step integration algorithms, in the vicinity of contact of multibody systems. The proposed methodology ensures that for any impact in a multibody system the time step of the integration is such that any initial penetration is below any prescribed threshold. In the case of the start of contact, and after a time step is complete, the numerical error control of the selected integration algorithm is forced to handle the physical criteria to accept/reject time steps in equal terms with the numerical error control that it normally uses. The main features of this approach are the simplicity of its computational implementation, its good computational efficiency and its ability to deal with the transitions between non contact and contact situations in multibody dynamics. A demonstration case provides the results that support the discussion and show the validity of the proposed methodology.Fundação para a Ciência e a Tecnologia (FCT

Elucidation of the ebola virus VP24 cellular interactome and disruption of virus biology through targeted inhibition of host-cell protein function

Viral pathogenesis in the infected cell is a balance between antiviral responses and subversion of host-cell processes. Many viral proteins specifically interact with host-cell proteins to promote virus biology. Understanding these interactions can lead to knowledge gains about infection and provide potential targets for antiviral therapy. One such virus is Ebola, which has profound consequences for human health and causes viral hemorrhagic fever where case fatality rates can approach 90%. The Ebola virus VP24 protein plays a critical role in the evasion of the host immune response and is likely to interact with multiple cellular proteins. To map these interactions and better understand the potential functions of VP24, label-free quantitative proteomics was used to identify cellular proteins that had a high probability of forming the VP24 cellular interactome. Several known interactions were confirmed, thus placing confidence in the technique, but new interactions were also discovered including one with ATP1A1, which is involved in osmoregulation and cell signaling. Disrupting the activity of ATP1A1 in Ebola-virus-infected cells with a small molecule inhibitor resulted in a decrease in progeny virus, thus illustrating how quantitative proteomics can be used to identify potential therapeutic targets