Kodiak: An Implementation Framework for Branch and Bound Algorithms

Recursive branch and bound algorithms are often used to refine and isolate solutions to several classes of global optimization problems. A rigorous computation framework for the solution of systems of equations and inequalities involving nonlinear real arithmetic over hyper-rectangular variable and parameter domains is presented. It is derived from a generic branch and bound algorithm that has been formally verified, and utilizes self-validating enclosure methods, namely interval arithmetic and, for polynomials and rational functions, Bernstein expansion. Since bounds computed by these enclosure methods are sound, this approach may be used reliably in software verification tools. Advantage is taken of the partial derivatives of the constraint functions involved in the system, firstly to reduce the branching factor by the use of bisection heuristics and secondly to permit the computation of bifurcation sets for systems of ordinary differential equations. The associated software development, Kodiak, is presented, along with examples of three different branch and bound problem types it implements

Initial Design and Quick Analysis of SAW Ultra–Wideband HFM Transducers

This paper presents techniques for initial design and quick fundamental and harmonic operation analysis of surface acoustic waves ultra–wideband hyperbolically frequency modulated (HFM) interdigital transducer (IDT). The primary analysis is based on the quasi–static method. Quasi–electrostatic charge's density distribution was approximated by Chebyshev polynomials and the method of Green’s function. It assesses the non uniform charge distribution of electrodes, electric field interaction and the end effects of a whole transducer. It was found that numerical integration (e.g. Romberg, Gauss–Chebyshev) requires a lot of machine time for calculation of the Chebyshev polynomial and the Green’s function convolution when integration includes coordinates of a large number of neighboring electrodes. In order to accelerate the charge density calculation, the analytic expressions are derived. Evaluation of HFM transducer fundamental and harmonics' operation amplitude response with simulation single–dispersive interdigital chirp filter structure is presented. Elapsed time of HFM IDT with 589 electrodes simulations and 2000 frequency response point is only 54 seconds (0.027 s/point) on PC with CPU Intel Core I7–4770S. Amplitude response is compared with linear frequency modulated (LFM) IDT response. It was determined that the HFM transducer characteristic is less distorted in comparison with LFM transducer

Trends and sustainability criteria of the production and use of liquid biofuels

Environmental impacts associated with the use of fossil fuels, rising prices, potential limitations in supply and concerns about regional and national security are driving the development and use of biomass for bioenergy, biofuels and bioproducts. However, the use of biomass does not automatically imply that its production, conversion and use are sustainable. Conflicts between various ecosystem services (economic production of food, fodder and fuels, biodiversity, social and cultural values, etc.) that are provided by fertile land are increasing as well. Hence, a developed thinking on how to balance between these services is desirable. There is a significant amount of information available on biofuels and their sustainability. In this paper, different initiatives and sustainability criteria for biofuels are presented and assessed. 35 criteria were found in emerging sustainability assessment frameworks. The majority of 12 criteria were focused on environmental issues, 4 were social and only 1 was economic. Energy balance and greenhouse gas balance were perceived as especially critical, social criteria ranked generally low. Although being perceived as important, food security ranked very low.Bioenergy Biofuel Sustainability criterion

Site-to-site peptide transport on a molecular platform using a small-molecule robotic arm.

From PubMed via Jisc Publications RouterPublication status: epublishPeptides attached to a cysteine hydrazide 'transporter module' are transported selectively in either direction between two chemically similar sites on a molecular platform, enabled by the discovery of new operating methods for a molecular transporter that functions through ratcheting. Substrate repositioning is achieved using a small-molecule robotic arm controlled by a protonation-mediated rotary switch and attachment/release dynamic covalent chemistry. A polar solvent mixtures were found to favour to isomerization of the doubly-protonated switch, transporting cargo in one direction (arbitrarily defined as 'forward') in up to 85% yield, while polar solvent mixtures were unexpectedly found to favour to isomerization enabling transport in the reverse ('backward') direction in >98% yield. Transport of the substrates proceeded in a matter of hours (compared to 6 days even for simple cargoes with the original system) without the peptides at any time dissociating from the machine nor exchanging with others in the bulk. Under the new operating conditions, key intermediates of the switch are sufficiently stabilized within the macrocycle formed between switch, arm, substrate and platform that they can be identified and structurally characterized by H NMR. The size of the peptide cargo has no significant effect on the rate or efficiency of transport in either direction. The new operating conditions allow detailed physical organic chemistry of the ratcheted transport mechanism to be uncovered, improve efficiency, and enable the transport of more complex cargoes than was previously possible. [Abstract copyright: This journal is © The Royal Society of Chemistry.

Lanthanide template synthesis of trefoil knots of single handedness

We report on the assembly of 2,6-pyridinedicarboxamide ligands (1) with point chirality about lanthanide metal ion (Ln3+) templates, in which the helical chirality of the resulting entwined 3:1 ligand:metal complexes is covalently captured by ring-closing olefin metathesis to form topologically chiral molecular trefoil knots of single handedness. The ligands do not self-sort (racemic ligands form a near-statistical mixture of homoleptic and heteroleptic lanthanide complexes), but the use of only (R,R)-1 leads solely to a trefoil knot of Λ-handedness, whereas (S,S)-1 forms the Δ-trefoil knot with complete stereoselectivity. The knots and their isomeric unknot macrocycles were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography and the expression of the chirality that results from the topology of the knots studied by circular dichroism

Lanthanide template synthesis of a molecular trefoil knot

Molecular knots1 and entanglements are featured in cyclic DNA2 and some proteins3 and are thought to play an important role in the chemical and physical properties of both natural and synthetic polymers.4 Sauvage and co-workers prepared the first synthetic molecular trefoil knot by connecting the end-groups of a linear two-metal-ion double helicate.5 However, the earliest published idea for a template synthesis of a trefoil knot is Sokolov’s proposal6 for assembling three ligands around a metal center to generate the three crossings necessary7 in the cyclized product. Several groups have attempted to prepare trefoil knots using this strategy thus far without achieving the ultimate goal,8 although Hunter has succeeded in synthesizing a trefoil knot by folding a single ligand strand around a transition metal ion,9 and Siegel has made a ‘trefoil knotted cyclophane’ 10 using a related triskelion approach featuring a covalently bonded scaffold.1

CCDC 1026538: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures

In silico testing of the semi-closed loop infusion system with a new simulator

Goal directed fluid therapy (GDFT) implies the flow-related parameters guided infusion of fluids. It requires adherence to complex clinical algorithms and fluid protocols, as well as simultaneous monitoring of several parameters and evaluation of their fluid responsiveness or actual response to fluid challenges. Automated clinical decision support systems (ACDSS) are used to ease the task. However, they are based on the flow-related (hemodynamic) parameters – arterial blood pressure, cardiac output, etc. Meanwhile, infusions guided by hemodynamic endpoints may lead to edema. A mini Volume Loading Test (mVLT) may be helpful in detection of imminent edema from changes in hemodilution during stepwise infusion which is conventionally used for hemodynamic optimization. We developed an ACDSS which is based on evaluation of both hemodynamic and hemodilution parameters. It operates on the basis of our unique algorithm which implies interchangeable application of fluid loading, vasopressor injection and red cell transfusion. This ACDSS is used in our PC-based command centre of a prototype semi-closed loop (SCL) infusion system. We developed a simulator – ‘Virtual Patient’ – on the basis of our previous clinical records aiming to test a new controller, as well as train the research team before starting a clinical trial. In silico testing continued for 12 hours on five occasions. Primary endpoint was the compliance of a controller with our clinical algorithm and the stability of operation in a spectrum of arterial hypotension and bleeding scenarios. The prototype SCL infusion system was found ready for clinical validation