Dynamical and transport properties of liquid gallium at high pressures.

Quantum molecular dynamics (QMD) simulations are used to calculate the equation of state, structure, and transport properties of liquid gallium along the principal shock Hugoniot. The calculated Hugoniot is in very good agreement with experimental data up to a pressure of 150 GPa as well as with our earlier classical molecular dynamics calculations using a modified embedded atom method (MEAM) potential. The self-diffusion and viscosity calculated using QMD agree with experimental measurements better than the MEAM results, which we attribute to capturing the complexity of the electronic structure at elevated temperatures. Calculations of the DC conductivity were performed around the Hugoniot. Above a density of 7.5 g/cm(3), the temperature increases rapidly along the Hugoniot, and the optical conductivity decreases, indicating simple liquid metal behavior.

Site-selective electronic correlation in α-plutonium metal.

An understanding of the phase diagram of elemental plutonium (Pu) must include both, the effects of the strong directional bonding and the high density of states of the Pu 5f electrons, as well as how that bonding weakens under the influence of strong electronic correlations. Here we present electronic-structure calculations of the full 16-atom per unit cell α-phase structure within the framework of density functional theory together with dynamical mean-field theory. Our calculations demonstrate that Pu atoms sitting on different sites within the α-Pu crystal structure have a strongly varying site dependence of the localization-delocalization correlation effects of their 5f electrons and a corresponding effect on the bonding and electronic properties of this complicated metal. In short, α-Pu has the capacity to simultaneously have multiple degrees of electron localization/delocalization of Pu 5f electrons within a pure single-element material.

A consideration of biomarkers to be used for evaluation of inflammation in human nutritional studies.

To monitor inflammation in a meaningful way, the markers used must be valid: they must reflect the inflammatory process under study and they must be predictive of future health status. In 2009, the Nutrition and Immunity Task Force of the International Life Sciences Institute, European Branch, organized an expert group to attempt to identify robust and predictive markers, or patterns or clusters of markers, which can be used to assess inflammation in human nutrition studies in the general population. Inflammation is a normal process and there are a number of cells and mediators involved. These markers are involved in, or are produced as a result of, the inflammatory process irrespective of its trigger and its location and are common to all inflammatory situations. Currently, there is no consensus as to which markers of inflammation best represent low-grade inflammation or differentiate between acute and chronic inflammation or between the various phases of inflammatory responses. There are a number of modifying factors that affect the concentration of an inflammatory marker at a given time, including age, diet and body fatness, among others. Measuring the concentration of inflammatory markers in the bloodstream under basal conditions is probably less informative compared with data related to the concentration change in response to a challenge. A number of inflammatory challenges have been described. However, many of these challenges are poorly standardised. Patterns and clusters may be important as robust biomarkers of inflammation. Therefore, it is likely that a combination of multiple inflammatory markers and integrated readouts based upon kinetic analysis following defined challenges will be the most informative biomarker of inflammation.

Superconducting gap structure of the 115s revisited.

Density functional theory calculations of the electronic structure of Ce- and Pu-based heavy fermion superconductors in the so-called 115 family are performed. The gap equation is used to consider which superconducting order parameters are most favorable assuming a pairing interaction that is peaked at (π, π, qz)­the wavevector for the antiferromagnetic ordering found in close proximity. In addition to the commonly accepted dx2−y2 order parameter, there is evidence that an extended s-wave order parameter with nodes is also plausible. We discuss whether these results are consistent with current observations and possible measurements that could help distinguish between these scenarios.

Understanding the complex phase diagram of uranium: the role of electron-phonon coupling.

We report an experimental determination of the dispersion of the soft phonon mode along [100] in uranium as a function of pressure. The energies of these phonons increase rapidly, with conventional behavior found by 20 GPa, as predicted by recent theory. New calculations demonstrate the strong pressure (and momentum) dependence of the electron-phonon coupling, whereas the Fermi-surface nesting is surprisingly independent of pressure. This allows a full understanding of the complex phase diagram of uranium and the interplay between the charge-density wave and superconductivity.

First-principles study of stability of the bcc and ω phases of a low Al concentration Nb1-xAlx alloy.

The phase stability and site occupancy of bcc (body centered cubic) Nb(5)Al and slightly rearranged atomic structures have been examined by means of first-principles calculations. In order to use first-principles methods, a periodic cell is required and we used ordered Nb(5)Al compounds as a tractable example of a low Al concentration Nb(1 - x)Al(x) alloy (in this case, for about 17 at.% Al). The instability against an ω-structure atomic displacement was also studied, since this structure is detrimental to ductility. Mulliken population analysis was used to provide an understanding of the hybridization between the atoms and the electronic origin of the site occupancy and instability of the underlying bcc structures. By making calculations for several different configurations of the Nb-Al system we estimated the strengths of the Nb-Nb and Nb-Al bonds. It is shown that the stability of the underlying bcc phases is directly related to Nb-Nb and Nb-Al first-nearest-neighbor interactions. The first-principles calculations were extended to finite temperature by including various contributions to the free energy. In particular, the vibrational free energy was calculated within the quasiharmonic approximation, and it is shown that the contribution of the low energy modes to the lattice entropy helps to stabilize ordered bcc phases against ω-type phase transformations. Semi-quasi-random structures were employed to study the stability of the ordered and disordered bcc phases. Our study showed, in agreement with experiment, that the ω, ordered, and disordered phases can coexist in a nonequilibrium state at finite temperature.

Elastic properties of the light actinides at high pressure.

Using density-functional perturbation theory, we have calculated the elastic constants for the ground-state crystal structures of the light actinide metals both at their equilibrium volumes (for Th through Np) and as a function of pressure (for Th through U). As necessary, we take into account the effects of atomic relaxation and show that these can be neglected for α-U, but are crucial for α-Np. The elastic constants of Th and U are compared with experimental measurements near ambient conditions and good agreement is found. Studies of the Born stability criteria in pressure reveal that Th and Pa are mechanically unstable while U remains stable up to 85 GPa, as is observed in diamond anvil cell experiments.

Structural and dynamic determinants of ligand binding and regulation of cyclin-dependent kinase 5 by pathological activator p25 and inhibitory peptide CIP.

The crystal structure of the cdk5/p25 complex has provided information on possible molecular mechanisms of the ligand binding, specificity, and regulation of the kinase. Comparative molecular dynamics simulations are reported here for physiological conditions. This study provides new insight on the mechanisms that modulate such processes, which may be exploited to control pathological activation by p25. The structural changes observed in the kinase are stabilized by a network of interactions involving highly conserved residues within the cyclin-dependent kinase (cdk) family. Collective motions of the proteins (cdk5, p25, and CIP) and their complexes are identified by principal component analysis, revealing two conformational states of the activation loop upon p25 complexation, which are absent in the uncomplexed kinase and not apparent from the crystal. Simulations of the uncomplexed inhibitor CIP show structural rearrangements and increased flexibility of the interfacial loop containing the critical residue E240, which becomes fully hydrated and available for interactions with one of several positively charged residues in the kinase. These changes provide a rationale for the observed high affinity and enhanced inhibitory action of CIP when compared to either p25 or the physiological activators of cdk5.

Evaluation of the interaction of cyclin-dependent kinase 5 with activator p25 and with p25-derived inhibitor CIP.

A high-affinity inhibitor protein called CIP, produced by small truncations of p35, was experimentally identified. P35 is a physiological activator of the cyclin-dependent kinase cdk5. P25 is derived from proteolytic truncation of p35 within "stressed" neurons, and it is associated with the hyperphosphorylation of specific neuronal proteins, typically occurring in neurodegenerative diseases such as Alzheimer's. Here, we report a study of the binding mechanisms of the cdk5-p25 and cdk5-CIP complexes. This provides a better understanding of the source of the inhibitory activity of the protein CIP. We use a geometry-based technique to test the hypothesis that p25's truncation increases the flexibility of CIP and thus prevents cdk5 from reaching its active conformation. Our study is based on a geometry-based alignment algorithm, which aligns two given protein conformations with respect to their interfaces. Our results support the flexibility hypothesis and will be used as a basis for targeted molecular dynamics simulations.

Inflammatory disease processes and interactions with nutrition.

Inflammation is a stereotypical physiological response to infections and tissue injury; it initiates pathogen killing as well as tissue repair processes and helps to restore homeostasis at infected or damaged sites. Acute inflammatory reactions are usually self-limiting and resolve rapidly, due to the involvement of negative feedback mechanisms. Thus, regulated inflammatory responses are essential to remain healthy and maintain homeostasis. However, inflammatory responses that fail to regulate themselves can become chronic and contribute to the perpetuation and progression of disease. Characteristics typical of chronic inflammatory responses underlying the pathophysiology of several disorders include loss of barrier function, responsiveness to a normally benign stimulus, infiltration of inflammatory cells into compartments where they are not normally found in such high numbers, and overproduction of oxidants, cytokines, chemokines, eicosanoids and matrix metalloproteinases. The levels of these mediators amplify the inflammatory response, are destructive and contribute to the clinical symptoms. Various dietary components including long chain omega-3 fatty acids, antioxidant vitamins, plant flavonoids, prebiotics and probiotics have the potential to modulate predisposition to chronic inflammatory conditions and may have a role in their therapy. These components act through a variety of mechanisms including decreasing inflammatory mediator production through effects on cell signaling and gene expression (omega-3 fatty acids, vitamin E, plant flavonoids), reducing the production of damaging oxidants (vitamin E and other antioxidants), and promoting gut barrier function and anti-inflammatory responses (prebiotics and probiotics). However, in general really strong evidence of benefit to human health through anti-inflammatory actions is lacking for most of these dietary components. Thus, further studies addressing efficacy in humans linked to studies providing greater understanding of the mechanisms of action involved are required.

Hubbard-U band-structure methods.

The last decade has seen a large increase in the number of electronic-structure calculations that involve adding a Hubbard term to the local-density approximation band-structure Hamiltonian. The Hubbard term is then determined either at the mean-field level or with sophisticated many-body techniques such as using dynamical mean-field theory. We review the physics underlying these approaches and discuss their strengths and weaknesses in terms of the larger issues of electronic structure that they involve. In particular, we argue that the common assumptions made to justify such calculations are inconsistent with what the calculations actually do. Although many of these calculations are often treated as essentially first-principles calculations, in fact, we argue that they should be viewed from an entirely different point of view, namely, as based on phenomenological many-body corrections to band-structure theory. Alternatively, it may also be considered that they are just based on a Hubbard model that is more complex than the simple one- or few-band models traditionally used in many-body theories of solids.

Phonon mechanisms and transformation paths in Pu.

A long-standing problem in Pu science is the crystallographic mechanism for the delta-->alpha' (fcc-->monoclinic) transformation. Orientation relations between the two structures impose severe restrictions on the possible mechanisms and require the transition to be reconstructive, which we describe as a sequence of three displacive transitions: fcc-->trigonal-->hexagonal-->monoclinic. We predict instabilities along the Lambda and Sigma branches in the phonon dispersion of the delta phase and formulate a free energy to describe the displacement of atoms across the transition. We suggest that the delta-->alpha' transition in Pu lies at the threshold of a change in character of the orientation relationship from lighter to heavier actinides, correlating with changes in electron itinerancy, magnetism, and volume.

Calculations for displacive ω-phase transformations in Ti-Al alloys with Nb additions at finite temperature.

We examine by means of first-principles calculations the bcc-like (bcc: body centered cubic) to ω-like phase transformations in Ti-Al alloys with Nb additions at finite temperature. To simulate the alloy we use different discrete atomic configurations in a six atom unit cell of the stoichiometry Ti(3)Al(2)Nb. Calculated ground state energies show an instability in the ternary Ti(3)Al(2)Nb alloy against the ω structure type atomic displacement. To better understand the role of entropy in the stability/instability of these systems, the first-principles calculations are extended to finite temperature by including various contributions to the free energy. In particular, the vibrational free energy is calculated within a quasiharmonic approximation. It is shown that the bcc structure is stabilized by the contribution of the low energy modes to the lattice entropy against ω type atomic displacements. We find that configurational entropy plays a major role in the ω to B8(2) transformation. Calculated lattice parameters and transition temperatures are found to be in excellent agreement with experiment.

Intermolecular conformational coupling and free energy exchange enhance the catalytic efficiency of cardiac muscle SERCA2a following the relief of phospholamban inhibition.

Activation of cardiac muscle sarcoplasmic reticulum Ca2+-ATPase (SERCA2a) by beta1-agonists involves cAMP- and PKA-dependent phosphorylation of phospholamban (PLB), which relieves the inhibitory effects of PLB on SERCA2a. To investigate the mechanism of SERCA2a activation, we compared the kinetic properties of SERCA2a expressed with (+) and without (-) PLB in High Five insect cell microsomes to those of SERCA1 and SERCA2a in native skeletal and cardiac muscle SR. Both native SERCA1 and expressed SERCA2a without PLB exhibited high-affinity (10-50 microM) activation of pre-steady-state catalytic site dephosphorylation by ATP, steady-state accumulation of the ADP-sensitive phosphoenzyme (E1P), and a rapid phase of EGTA-induced phosphoenzyme (E2P) hydrolysis. In contrast, SERCA2a in native cardiac SR vesicles and expressed SERCA2a with PLB lacked the high-affinity activation by ATP and the rapid phase of E2P hydrolysis, and exhibited low steady-state levels of E1P. The results indicate that the kinetic differences in Ca2+ transport between skeletal and cardiac SR are due to the presence of phospholamban in cardiac SR, and not due to isoform-dependent differences between SERCA1 and SERCA2a. Therefore, the results are discussed in terms of a model in which PLB interferes with SERCA2a oligomeric interactions, which are important for the mechanism of Ca2+ transport in skeletal muscle SERCA1 [Mahaney, J. E., Thomas, D. D., and Froehlich, J. P. (2004) Biochemistry 43, 4400-4416]. We propose that intermolecular coupling of SERCA2a molecules during catalytic cycling is obligatory for the changes in Ca2+ transport activity that accompany the relief of PLB inhibition of the cardiac SR Ca2+-ATPase.

New pseudophase structure for alpha-Pu.

We propose a new pseudophase crystal structure, based on an orthorhombic distortion of the diamond structure, for the ground-state alpha phase of plutonium. Electronic-structure calculations in the generalized-gradient approximation give approximately the same total energy for the two structures. Interestingly, our new pseudophase structure is the same as the gamma-Pu structure except with very different b/a and c/a ratios. We show how the contraction relative to the gamma phase, principally in the z direction, leads to an alpha-like structure in the [0,1,1] plane and reproduces the short range bonds of the alpha phase. This is an important link between two complex structures of Pu and opens new possibilities for exploring the very rich phase diagram of Pu through theoretical calculations.

Extended X-ray absorption fine structure measurements of laser-shocked V and Ti and crystal phase transformation in Ti.

Extended x-ray absorption fine structure (EXAFS), using a laser-imploded target as a source, can yield the properties of laser-shocked metals on a nanosecond time scale. EXAFS measurements of vanadium shocked to approximately 0.4 Mbar yield the compression and temperature in good agreement with hydrodynamic simulations and shock-speed measurements. In laser-shocked titanium at the same pressure, the EXAPS modulation damping is much higher than is warranted by the predicted temperature increase. This is shown to be due to the alpha-Ti to omega-Ti crystal phase transformation, known to occur below approximately 0.1 Mbar for slower shock waves.

New mechanism for the alpha to omega martensitic transformation in pure titanium.

We propose a new direct mechanism for the pressure driven alpha-->omega martensitic transformation in pure titanium. A systematic algorithm enumerates all possible pathways whose energy barriers are evaluated. A new, homogeneous pathway emerges with a barrier at least 4 times lower than other pathways. The pathway is shown to be favorable in any nucleation model.

Effects of cis-9, trans-11 and trans-10, cis-12 conjugated linoleic acid (CLA) isomers on immune function in healthy men.

OBJECTIVES: To study the effects of two different mixtures of the main conjugated linoleic acid (CLA) isomers cis-9, trans-11 CLA and trans-10, cis-12 CLA on human immune function. DESIGN: Double-blind, randomized, parallel, reference-controlled intervention study. SUBJECTS AND INTERVENTION: Seventy-one healthy males aged 31-69 y received one of the following treatments: (1). mixture of 50% c9,t11 CLA and 50% t10,c12 CLA isomers (CLA 50:50); (2). mixture of 80% c9,t11 CLA and 20% t10,c12 CLA isomers (CLA 80:20); and (3). sunflower oil fatty acids (reference). The treatments were given as supplements in softgel capsules providing a total of 1.7 g (c9,t11+t10,c12) CLA fatty acids (50:50) or 1.6 g (c9,t11+t10,c12) CLA glycerides (80:20) per day in treatment groups for 12 weeks. RESULTS: Almost twice as many subjects reached protective antibody levels to hepatitis B when consuming CLA 50:50 fatty acids (15/24, 62%) compared with subjects consuming the reference substance (7/21, 33%, P=0.075). In subjects consuming CLA 80:20 glycerides this was 8/22 (36%). Other aspects of immune function, ie DTH responses, NK cell activity, lymphocyte proliferation and production of TNF-alpha, IL1-beta, IL6, IFN-gamma, IL2, IL4, and PGE(2), were not affected. CONCLUSION: This is the first study that suggests that CLA may beneficially affect the initiation of a specific response to a hepatitis B vaccination. This was seen in the CLA 50:50, but not in the CLA 80:20 group.

Three-dimensional elastic compatibility and varieties of twins in martensites.

We model a cubic-to-tetragonal martensitic transition by a Ginzburg-Landau free energy in the symmetric strain tensor. We show in three dimensions (3D) that solving the St. Venant compatibility relations for strain, treated as independent field equations, generates three anisotropic long-range potentials between the two order parameter components. These potentials encode 3D discrete symmetries, express the energetics of lattice integrity, and determine 3D textures. Simulation predictions include twins with temperature-varying orientation, helical twins, competing metastable states, and compatibility-induced elastic frustration. Our approach also applies to improper ferroelastics.