Free energy and molecular dynamics calculations for the cubic-tetragonal phase transition in zirconia

The high-temperature cubic-tetragonal phase transition of pure stoichiometric zirconia is studied by molecular dynamics (MD) simulations and within the framework of the Landau theory of phase transformations. The interatomic forces are calculated using an empirical, self-consistent, orthogonal tight-binding model, which includes atomic polarizabilities up to the quadrupolar level. A first set of standard MD calculations shows that, on increasing temperature, one particular vibrational frequency softens. The temperature evolution of the free-energy surfaces around the phase transition is then studied with a second set of calculations. These combine the thermodynamic integration technique with constrained MD simulations. The results seem to support the thesis of a second-order phase transition but with unusual, very anharmonic behavior above the transition temperature.

Molecular detection of exercise-induced free radicals following ascorbate prophylaxis in type 1 diabetes mellitus: a randomised controlled trial

Aims/hypothesis: Patients with type 1 diabetes mellitus are more susceptible than healthy individuals to exercise-induced oxidative stress and vascular endothelial dysfunction, which has important implications for the progression of disease. Thus, in the present study, we designed a randomised double-blind, placebo-controlled trial to test the original hypothesis that oral prophylaxis with vitamin C attenuates rest and exercise-induced free radical-mediated lipid peroxidation in type 1 diabetes mellitus. Methods: All data were collected from hospitalised diabetic patients. The electron paramagnetic resonance spectroscopic detection of spin-trapped a-phenyl-tert-butylnitrone (PBN) adducts was combined with the use of supporting markers of lipid peroxidation and non-enzymatic antioxidants to assess exercise-induced oxidative stress in male patients with type 1 diabetes (HbA1c 7.9±1%, n=12) and healthy controls (HbA1c 4.6±0.5%, n=14). Following participant randomisation using numbers in a sealed envelope, venous blood samples were obtained at rest, after a maximal exercise challenge and before and 2 h after oral ingestion of 1 g ascorbate or placebo. Participants and lead investigators were blinded to the administration of either placebo or ascorbate treatments. Primary outcome was the difference in changes in free radicals following ascorbate ingestion. Resuts: Six diabetic patients and seven healthy control participants were randomised to each of the placebo and ascorbate groups. Diabetic patients (n=12) exhibited an elevated concentration of PBN adducts (p<0.05 vs healthy, n=14), which were confirmed as secondary, lipid-derived oxygen-centred alkoxyl (RO•) radicals (a nitrogen=1.37 mT and aßhydrogen=0.18 mT). Lipid hydroperoxides were also selectively elevated and associated with a depression of retinol and lycopene (p<0.05 vs healthy). Vitamin C supplementation increased plasma vitamin C concentration to a similar degree in both groups (p<0.05 vs pre-supplementation) and attenuated the exercise-induced oxidative stress response (p<0.05 vs healthy). There were no selective treatment differences between groups in the primary outcome variable. Conclusions/ interpretation: These findings are the first to suggest that oral vitamin C supplementation provides an effective prophylaxis against exercise-induced free radical-mediated lipid peroxidation in human diabetic blood.

Defining the molecular basis for the first potent and selective orthosteric agonists of the FFA2 free fatty acid receptor

FFA2 is a G protein-coupled receptor that responds to short chain fatty acids (SCFAs) and has generated interest as a therapeutic target for metabolic and inflammatory conditions. However, definition of its functions has been slowed by a dearth of selective ligands that can distinguish it from the closely related FFA3. At present, the only selective ligands described for FFA2 suffer from either poor potency, altered signaling due to allosteric modes of action, or a lack of function at non-human orthologs of the receptor. To address the need for novel selective ligands, we synthesized two compounds potentially having FFA2 activity and examined the molecular basis of their function. These compounds were confirmed to be potent and selective FFA2 agonists that interact with the orthosteric binding site. A combination of ligand structure-activity relationship, pharmacological analysis, homology modeling, species ortholog comparisons and mutagenesis studies were then employed to define the molecular basis of selectivity and function of these ligands. From this, we identified key residues within both extracellular loop 2 (ECL2) and the transmembrane domain (TM) regions of FFA2 critical for ligand function. One of these ligands was active with reasonable potency at rodent orthologs of FFA2 and demonstrated the role of FFA2 in the regulation of lipolysis in murine 3T3-L1 adipocytes. Together, these findings describe the first potent and selective FFA2 orthosteric agonists and demonstrate key aspects of ligand interaction within the orthosteric binding site of FFA2 that will be invaluable in future ligand development at this receptor.

Metamaterials Nanosensor for Label-free Analysis of Conformation and Molecular Interaction of Biomolecules

Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding of their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors indeed are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. Here, we show that plasmonic metamaterials can offer two transducing channels for parallel acquisition of optical transmission and sensitive SERS spectra at the biointerface, simultaneously probing the conformational states and binding affinity of biomolecules, e.g. G-quadruplexes, in different environments (Fig. 1). We further demonstrate the use of the metamaterials for fingerprinting and detection of arginine-glycine-glycine domain of nucleolin, a cancer biomarker which specifically binds to a G-quadruplex, with the picomolar sensitivity. The dual-mode nanosensor will significantly contribute to unraveling the complexes of the conformational dynamics of biomolecules as well as to improving specificity of biodetection assays.

Label-free Analysis of Conformational Dynamics and Molecular Interaction of Biomolecules by Vis-NIR Metasensor

Analysis of binding recognition and conformation of biomolecules is of paramount important in understanding of their vital functions in complex biological systems. By enabling sub-wavelength light localization and strong local field enhancement, plasmonic biosensors have become dominant tools used for such analysis owing to their label-free and real-time attributes1,2. However, the plasmonic biosensors are not well-suited to provide information regarding conformation or chemical fingerprint of biomolecules. Here, we show that plasmonic metamaterials, consisting of periodic arrays of artificial split-ring resonators (SRRs)3, can enable capabilities of both sensing and fingerprinting of biomolecules. We demonstrate that by engineering geometry of individual SRRs, localized surface plasmon resonance (LSPR) frequency of the metamaterials could be tuned to visible-near infrared regimes (Vis-NIR) such that they possess high local field enhancement for surface-enhanced Raman scattering spectroscopy (SERS). This will provide the basis for the development of a dual mode label-free conformational-resolving and quantitative detection platform. We present here the ability of each sensing mode to independently detect binding adsorption and to identify different conformational states of Guanine (G)-rich DNA monolayers in different environment milieu. Also shown is the use of the nanosensor for fingerprinting and detection of Arginine-Glycine-Glycine (RGG) peptide binding to the G-quadruplex aptamer. The dual-mode nanosensor will significantly contribute to unraveling the complexes of the conformational dynamics of biomolecules as well as to improving specificity of biodetection assays that the conventional, population-averaged plasmonic biosensors cannot achieve.

The Influence of Inert Packaging on the shelf Ageing of Gamma-Irradiation Sterilised ultra-high molecular weight polyethylene

Ultra-high molecular weight polyethylene (UHMWPE) is used for wear applications in total hip prostheses and total knee prostheses. Sterilisation of these prostheses is commonly by gamma-irradiation. This process creates reactive free radicals in the UHMWPE, greatly increasing its susceptibility to oxidative degradation. This study has investigated the influence of air and vacuum packaging on the properties of gamma-irradiated UHMWPE (GUR1050) following 3 years of shelf ageing. The findings indicate that vacuum packaging minimises oxidative degradation reactions that occur for UHMWPE during shelf ageing. However, gamma-irradiation of vacuum-packaged UHMWPE promotes a degree of cross-linking. It is proposed that this may enhance the wear performance of UHMWPE. Accelerated ageing studies indicate that 3 years of shelf ageing would also seem to reduce the susceptibility of gamma-irradiated UHMWPE to oxidative degradation upon removal from its vacuum packaging.

Judging where a ball will go: the case of curved free kicks in football

This study examined whether adding spin to a ball in the free kick situation in football affects a professional footballer's perception of the ball's future arrival position. Using a virtual reality set-up, participants observed the flight paths of aerodynamically realistic free kicks with (+/- 600 rpm) and without sidespin. With the viewpoint being fixed in the centre of the goal, participants had to judge whether the ball would have ended up in the goal or not. Results show that trajectories influenced by the Magnus force caused by sidespin gave rise to a significant shift in the percentage of goal responses. The resulting acceleration that causes the ball to continually change its heading direction as the trajectory unfolds does not seem to be taken into account by the participants when making goal judgments. We conclude that the visual system is not attuned to such accelerated motion, which may explain why goalkeepers appear to misjudge the future arrival point of such curved free kicks.

Kinetics of phase transformations in a model with metastable fluid-fluid separation: A molecular dynamics study

By molecular dynamics (MD) simulations we study the crystallization process in a model system whose particles interact by a spherical pair potential with a narrow and deep attractive well adjacent to a hard repulsive core. The phase diagram of the model displays a solid-fluid equilibrium, with a metastable fluid-fluid separation. Our computations are restricted to fairly small systems (from 2592 to 10368 particles) and cover long simulation times, with constant energy trajectories extending up to 76x10(6) MD steps. By progressively reducing the system temperature below the solid-fluid line, we first observe the metastable fluid-fluid separation, occurring readily and almost reversibly upon crossing the corresponding line in the phase diagram. The nucleation of the crystal phase takes place when the system is in the two-fluid metastable region. Analysis of the temperature dependence of the nucleation time allows us to estimate directly the nucleation free energy barrier. The results are compared with the predictions of classical nucleation theory. The critical nucleus is identified, and its structure is found to be predominantly fcc. Following nucleation, the solid phase grows steadily across the system, incorporating a large number of localized and extended defects. We discuss the relaxation processes taking place both during and after the crystallization stage. The relevance of our simulation for the kinetics of protein crystallization under normal experimental conditions is discussed. (C) 2002 American Institute of Physics.

A dielectric continuum molecular dynamics method

We introduce a novel method to simulate hydrated macromolecules with a dielectric continuum representation of the surrounding solvent. In our approach, the interaction between the solvent and the molecular degrees of freedom is described by means of a polarization density free energy functional which is minimum at electrostatic equilibrium. After a pseudospectral expansion of the polarization and a discretization of the functional, we construct the equations of motion for the system based on a Car-Parrinello technique. In the limit of the adiabatic evolution of the polarization field variables, our method provides the solution of the dielectric continuum problem "on the fly," while the molecular coordinates are propagated. In this first study, we show how our dielectric continuum molecular dynamics method can be successfully applied to hydrated biomolecules, with low cost compared to free energy simulations with explicit solvent. To our knowledge, this is the first time that stable and conservative molecular dynamic simulations of solutes can be performed for a dielectric continuum model of the solvent. (C) 2001 American Institute of Physics.

Beyond Ehrenfest: correlated non-adiabatic molecular dynamics

A method for introducing correlations between electrons and ions that is computationally affordable is described. The central assumption is that the ionic wavefunctions are narrow, which makes possible a moment expansion for the full density matrix. To make the problem tractable we reduce the remaining many-electron problem to a single-electron problem by performing a trace over all electronic degrees of freedom except one. This introduces both one- and two-electron quantities into the equations of motion. Quantities depending on more than one electron are removed by making a Hartree-Fock approximation. Using the first-moment approximation, we perform a number of tight binding simulations of the effect of an electric current on a mobile atom. The classical contribution to the ionic kinetic energy exhibits cooling and is independent of the bias. The quantum contribution exhibits strong heating, with the heating rate proportional to the bias. However, increased scattering of electrons with increasing ionic kinetic energy is not observed. This effect requires the introduction of the second moment.

Conventional free radical polymerization in room temperature ionic liquids: a green approach to commodity polymers with practical advantages

Free-radical polymerization of methyl methacrylate and styrene using conventional organic initiators in the room temperature ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([ C(4)mim][PF6]) is rapid and produces polymers with molecular weights up to 10x higher than from benzene; both polymerization and isolation of products were achieved without using VOCs, offering economic as well as environmental advantages.