The Flexible Rare Event Sampling Harness System (FRESHS)

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling (FFS) and Stochastic Process Rare Event Sampling (SPRES) have been implemented. These two methods together make rare event sampling available for both quasi-static and full non-equilibrium regimes. Our framework provides a plugin system for software implementing the underlying physics of the system of interest. At present, example plugins exist for our framework to steer the popular MD packages GROMACS, LAMMPS and ESPResSo, but due to the simple interface of our plugin system, it is also easy to attach other simulation software or self-written code. Use of our framework does not require recompilation of the simulation program. The modular structure allows the flexible implementation of further sampling methods or physics engines and creates a basis for objective comparison of different sampling algorithms.     

Thermal fluid multiphysics optimization of spherical tokamak centerpost

An experimental Fusion Nuclear Science Facility (FNSF) is required that will create the environment that simultaneously achieves high energy neutrons and high ion fluence necessary in order to bridge the gaps from ITER to the realization of a fusion nuclear power plant. One concept for achieving this is a high duty cycle spherical torus. This study will focus on thermal modeling of the spherical torus centerpost using computational fluid dynamics to effectively model the thermal transfer of the cooling fluid to the centerpost. The design of the fluid channels is optimized in order to minimize the temperature in the centerpost. Results indicate the feasibility of water cooling for a long-pulse spherical torus FNSF.     

A case study on software risk analysis and planning in medical device development

Software failures in medical devices can lead to catastrophic situations. Therefore, it is crucial to handle software-related risks when developing medical devices, and there is a need for further analysis of how this type of risk management should be conducted. The objective of this paper is to collect and summarise experiences from conducting risk management with an organisation developing medical devices. Specific focus is put on the first steps of the risk management process, i.e. risk identification, risk analysis, and risk planning. The research is conducted as action research, with the aim of analysing and giving input to the organisation’s introduction of a software risk management process. First, the method was defined based on already available methods and then used. The defined method focuses on user risks, based on scenarios describing the expected use of the medical device in its target environment. During the use of the method, different stakeholders, including intended users, were involved. Results from the case study show that there are challenging problems in the risk management process with respect to definition of the system boundary and system context, the use of scenarios as input to the risk identification, estimation of detectability during risk analysis, and action proposals during risk planning. It can be concluded that the risk management method has potential to be used in the development organisation, although future research is needed with respect to, for example, context limitation and how to allow for flexible updates of the product.     

Microstructure of the HMX‐Based PBX KS32 after Mechanical Loading

Non‐destructive X‐ray diffraction techniques were applied in order to monitor the influence of mechanical and shock‐loading on the microstructure of the plastic‐bonded high explosive KS32. The investigations uncovered damage to embedded coarse HMX crystals and to the binder system HTPB‐IPDI. Damage to the crystals occurred already during the kneading process in terms of deformation twinning. On higher loading between 400 MPa (static) and 480 MPa (dynamic) also crystal fracture was observed. The change in the binder structure was found after both static and dynamic loading, but not in the cured, differently kneaded samples. Moreover, the change in binder structure after dynamic loading was verified by dynamic mechanical analysis, and interpreted as a partial damage of the binder rubber shell around the explosive particles. The results are compared to literature data from imaging techniques.     

Aurora Kinase A Is Involved in Controlling the Localization of Aquaporin-2 in Renal Principal Cells

The cAMP-dependent aquaporin-2 (AQP2) redistribution from intracellular vesicles into the plasma membrane of renal collecting duct principal cells induces water reabsorption and fine-tunes body water homeostasis. However, the mechanisms controlling the localization of AQP2 are not understood in detail. Using immortalized mouse medullary collecting duct (MCD4) and primary rat inner medullary collecting duct (IMCD) cells as model systems, we here discovered a key regulatory role of Aurora kinase A (AURKA) in the control of AQP2. The AURKA-selective inhibitor Aurora-A inhibitor I and novel derivatives as well as a structurally different inhibitor, Alisertib, prevented the cAMP-induced redistribution of AQP2. Aurora-A inhibitor I led to a depolymerization of actin stress fibers, which serve as tracks for the translocation of AQP2-bearing vesicles to the plasma membrane. The phosphorylation of cofilin-1 (CFL1) inactivates the actin-depolymerizing function of CFL1. Aurora-A inhibitor I decreased the CFL1 phosphorylation, accounting for the removal of the actin stress fibers and the inhibition of the redistribution of AQP2. Surprisingly, Alisertib caused an increase in actin stress fibers and did not affect CFL1 phosphorylation, indicating that AURKA exerts its control over AQP2 through different mechanisms. An involvement of AURKA and CFL1 in the control of the localization of AQP2 was hitherto unknown.     

Charaterization of UHMWPE fiber/matrix adhesion by dynamic mechanical spectrometry

The tensile and dynamic mechanical properties of polystyrene and a poly(styrene-co-buty1 acrylate-co-cyclohexy1 methacrylate) statistical terpolymer (terpolymer) reinforced by randomly oriented, discontinuous ultra-high molecular weight polyethylene (UHMWPE) fibers are presented in terms of the fiber/matrix interfacial properties. Using a thermomechanical block model based on the parallel rule of mixtures, the adhesion characteristics of poly(butyl acrylate) (PBA) and poly(cyclohexyl methacrylate) (PCHM) grafted, plasma treated, and untreated fibers were determined. The model successfully predicts the tan δ response of the composites including peak height variations and the development of additional loss dispersions associated with the interphase. Moreover, the model yields a fiber reinforcement efficiency factor, K, which gives a quantitative measure of adhesion. The contact angle of PBA and PCHM grafted high density polyethylene (HDPE) films are also included and are compared to the contact angle of plasma treated fibers. The results indicate that PBA and PCHM grafts enhance adhesion through polymer graft/matrix interactions, not simply by improved wetting.     

Synthesis of magnetic nanocomposite microparticles for binding of chlorinated organics in contaminated water sources

In this work, the development of novel magnetic nanocomposite microparticles (MNMs) via free radical polymerization for their application in the remediation of contaminated water is presented. Acrylated plant-based polyphenols, curcumin multiacrylate (CMA) and quercetin multiacrylate (QMA), were incorporated as functional monomers to create high affinity binding sites for the capture of polychlorinated biphenyls (PCBs), as a model pollutant. The MNMs were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, dynamic light scattering, and UV–visible spectroscopy. The affinity of these novel materials for PCB 126 was evaluated and fitted to the nonlinear Langmuir model to determine binding affinities (K_D). The results suggest the presence of the polyphenolic moieties enhances the binding affinity for PCB 126, with K_D values comparable to that of antibodies. This demonstrates that these nanocomposite materials have promising potential as environmental remediation adsorbents for harmful contaminants.     

Effects of substitution of Thr63 by alanine on the structure and function of Lactobacillus casei dihydrofolate reductase

A mutant of Lactobacillus casei dihydrofolate reductase hasbeen constructed in which Thr63, a residue which interacts withthe 2'-phosphate group of the bound coenzyme, is replaced byalanine. This substitution does not affect k_cat, but producesan 800-fold increase in the K_m for NADPH, which reflects dissociationof NADPH from the enzyme-NADPH-tetrahydrofolate complex, anda 625-fold increase (corresponding to 3.8 kcal/mol) in the dissociationconstant for the enzyme-NADPH complex. The difference in magnitudeof these effects indicates a small effect of the substitutionon the negative cooperativity between NADPH and tetrahydrofolate.Stopped-flow studies of the kinetics of NADPH binding show thatthe weaker binding arises predominantly from a decrease in theassociation rate constant. NMR spectroscopy was used to comparethe structures of the mutant and wild-type enzymes in solution,in their complexes with methotrexate and with methotrexate andNADPH. This showed that only minimal structural changes resultfrom the mutation; a total of 47 residues were monitored fromtheir resolved ¹H resonances, and of these nine in the binarycomplex and six in the ternary differed in chemical shift betweenmutant and wild-type enzyme. These affected residues are confinedto the immediate vicinity of residue 63. There is a substantialdifference in the ³¹P chemical shift of the 2'-phosphate ofthe bound coenzyme, reflecting the loss of the interaction withthe side chain of Thr63. The only changes in nuclear Overhausereffects (NOEs) observed were decreases in the intensity of NOEsbetween protons of the adenine ring of the bound coenzyme andthe nearby residues Leu62 and Ile102, showing that the substitutionof Thr63 does cause a change in the position or orientationof the adenine ring in its binding site.