Self-Interactions of Strands and Sheets

Physical strands or sheets that can be modelled as curves or surfaces embedded in three dimensions are ubiquitous in nature, and are of fundamental importance in mathematics, physics, biology, and engineering. Often the physical interpretation dictates that self-avoidance should be enforced in the continuum model, i.e., finite energy configurations should not self-intersect. Current continuum models with self-avoidance frequently employ pairwise repulsive potentials, which are of necessity singular. Moreover the potentials do not have an intrinsic length scale appropriate for modelling the finite thickness of the physical systems. Here we develop a framework for modelling self-avoiding strands and sheets which avoids singularities, and which provides a way to introduce a thickness length scale. In our approach pairwise interaction potentials are replaced by many-body potentials involving three or more points, and the radii of certain associated circles or spheres. Self-interaction energies based on these many-body potentials can be used to describe the statistical mechanics of self-interacting strands and sheets of finite thickness.     

Study of fiber optic sugar sensor

Over the last two decades, the fiber optic technology has passed through many analytical stages. Some commercially available fiber optic sensors, though in a small way, are being used for automation in mechanical and industrial environments. They are also used for instrumentation and controls. In the present work, an intensity-modulated intrinsic fiber optic sugar sensor is presented. This type of sensor, with slight modification, can be used for on-line determination of the concentration of sugar content in sugarcane juice in sugar industry. In the present set-up, a plastic fiber made of polymethylmethacrylate is used. A portion of the cladding (1 cm, 2 cm, 3 cm) at the mid-point along the length of the fiber is removed. This portion is immersed in sugar solution of known concentration and refractive index. At one end of the fiber an 850 nm source is used and at the other end a power meter is connected. By varying the concentration of sugar solution, the output power is noted. These studies are made due to the change in refractive index of the fluid. The device was found to be very sensitive which is free from EMI and shock hazards, stable and repeatable and they can be remotely interfaced with a computer to give on-line measurements and thus become useful for application in sugar industries.     

Palladium-catalyzed [2 + 2 + 2] cocyclotrimerization of benzynes with bicyclic alkenes: an efficient route to anellated 9,10-dihydrophenanthrene derivatives and polyaromatic compounds

An efficient method for the cocyclotrimerization of bicyclic alkenes and benzynes catalyzed by palladium phosphine complexes to give the corresponding norbornane anellated 9,10-dihydrophenanthrene derivatives is described. Bicyclic alkenes 1a-i undergo [2 + 2 + 2] cocyclotrimerization with benzynes generated from precursors 2a-d [2-(trimethylsilyl)phenyl triflate (2a), 4,5-dimethyl-2-(trimethylsilyl)phenyl triflate (2b), 6-(trimethylsilyl)-2,3-dihydro-1H-5-indenyl triflate (2c), 4-methyl-2-(trimethylsilyl)phenyl triflate (2d)] in the presence of PdCl(2)(PPh(3))(2) in acetonitrile at ambient temperature to yield anellated 9,10-dihydrophenanthrene products 3a-r in moderate to excellent yields. The [2 + 2 + 2] cocyclotrimerization products from oxa- and azabicyclic alkenes can be applied for the synthesis of polyaromatics, substituted benzo[b]triphenylenes (8a-f), via a simple Lewis acid mediated deoxyaromatization in good yields. In addition the [2 + 2 + 2] products undergo retro Diels-Alder reaction readily, providing a new method for the synthesis of substituted phenanthrenes and for generating isobenzofurans. A plausible mechanism is proposed to account for the catalytic [2 + 2 + 2] cycloaddition reaction.     

Design and Development of a Non-Enzymatic Electrochemical Biosensor for the Detection of Glutathione

Glutathione (GSH-reduced form) is a tripeptide that plays a vital role as an antioxidant to remove xenobiotics in the human body and changes in GSH levels are a marker for the progression of various diseases. In this context, a highly sensitive non-enzymatic electrochemical biosensor for the detection of GSH has been developed using reduced graphene oxide Manganese oxide (rGMnO) nanocomposite as the nano-interface. Initially, graphene oxide was synthesized by Hummer's method and then thermally reduced in the presence of MnO₂ in a blast furnace to obtain rGMnO nanocomposite. The nanocomposite was characterized to validate its structure and morphological properties via Scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman, and X-ray photoelectron spectroscopy (XPS). Cyclic voltammetry and amperometry studies showed that upon the addition of GSH, the Pt/rGMnO modified working electrode exhibited a linear response in the range of 1–100 μM at an input voltage of −0.62 V. The developed sensor was found to have a sensitivity of 0.3256 μA μM⁻¹ and LOD of 970 nM with a recovery of 92–104 % in real blood serum samples.     

Influence of redox potential on product distribution in Clostridium thermosuccinogenes

Clostridium thermosuccinogenes are the only known anaerobic thermophilic bacteria that ferment inulin to succinate and acetate as major products and formate, lactate, and ethanol as minor products. In this study, organic acid production in 2-L fermentations having an initially low (−300 to −330 mV) or high (−220 to −250 mV) redox potential was compared for two strains of C. thermosuccinogenes (DSM 5808 and DSM 5809). Although DSM 5809 consistently provided higher succinate yield, high variability in results was attributed to the absence of redox control during the fermentations, and, therefore, fermentations at three controlled redox potentials (−240, −275, and −310 mV) were conducted. At an intermediate redox potential (−275 mV), the succinate yield was the greatest (0.36 g of succinate/g of hexose unit), whereas ethanol yield was the least (0.02 g/g). Redox potential did not significantly affect acetate or lactate formation. At controlled redox potential of −275 mV, the growth of DSM 5809 on three substrates was also compared: inulin, fructose, and glucose. DSM 5809 had similar growth rates when inulin (0.20/h) or glucose (0.21/h) was the carbon source but grew more slowly when fructose (0.16/h) was the carbon source. Also, the specific rate of utilization of fructose by DSM 5809 was higher (0.89 g of fructose/[g of biomass·h]) compared to glucose (0.53 g/[g·h]) or inulin (0.55 g/[g·h]). Succinate was the major product formed by DSM 5809 fermenting inulin (0.50 g/[g·h]) or glucose (0.36 g/[g·h]), and ethanol was the principal product when DSM 5809 fermented fructose (0.54 g/[g·h]).     

On network form and function

Moving from the observation that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review theoretical and observational evidence on river patterns and their scale-invariant structure. Exact results complemented by numerical annealing of the basic equation in the presence of additive noise suggest that configurations at (or very close to) the global minimum of energy dissipation differ from dynamically accessible states, which have rather different scaling properties and conform much better to natural forms. Thus we argue that, at least in the fluvial landscape, Nature works through imperfect searches for dynamically accessible optimal configurations. We also show that optimal networks are spanning loopless configurations only under precise physical requirements. This is stated in a form applicable to generic networks, suggesting that other branching structures occurring in Nature (e.g. scale-free and looping) may possibly arise through optimality to selective pressures. Indeed, we show that this is the case.     

Scaling, Optimality, and Landscape Evolution

A nonlinear model is studied which describes the evolution of a landscape under the effects of erosion and regeneration by geologic uplift by mean of a simple differential equation. The equation, already in wide use among geomorphologists and in that context obtained phenomenologically, is here derived by reparametrization invariance arguments and exactly solved in dimension d=1. Results of numerical simulations in d=2 show that the model is able to reproduce the critical scaling characterizing landscapes associated with natural river basins. We show that configurations minimizing the rate of energy dissipation (optimal channel networks) are stationary solutions of the equation describing the landscape evolution. Numerical simulations show that a careful annealing of the equation in the presence of additive noise leads to configurations very close to the global minimum of the dissipated energy, characterized by mean field exponents. We further show that if one considers generalized river network configurations in which splitting of the flow (i.e., braiding) and loops are allowed, the minimization of the dissipated energy results in spanning loopless configurations, under the constraints imposed by the continuity equations. This is stated in the form of a general theorem applicable to generic networks, suggesting that other branching structures occurring in nature may possibly arise as optimal structures minimizing a cost function.     

Metabolic flux analysis of clostridium thermosuccinogenes

Clostridium thermosuccinogenes are anaerobic thermophilic bacteria that ferment various carbohydrates to succinate and acetate as major products and formate, lactate, and ethanol as minor products. Metabolic carbon flux analysis was used to evaluate the effect of pH and redox potential on the batch fermentation of C. thermosuccinogenes. In a first study, the effects of four pH values (6.50, 6.75, 7.00, and 7.25) on intracellular carbon flux at a constant redox potential of -275 mV were compared. The flux of carbon toward succinate and formate increased whereas the flux to lactate decreased significantly with a pH increase from 6.50 to 7.25. Both specific growth rate and specific rate of glucose consumption were unaffected by changes in pH. The fraction of carbon flux at the phosphoenolpyruvate (PEP) node flowing to oxaloacetate increased with an increase in pH. At the pyruvate node, the fraction of flux to formate increased with increasing pH. At the acetyl CoA node, the fraction of flux to acetate increased significantly with an increase in pH. A second study elucidated the effect of four controlled culture redox potentials (-225, -250, -275, and -310 mV) on metabolic carbon flux at a constant pH of 7.25. Lower values of culture redox potential were correlated with increased succinate, acetate, and formate fluxes and decreased ethanol and hydrogen fluxes in C. thermosuccinogenes. Lactate formation was not significantly influenced by redox potential. At the PEP node, the fraction of carbon to oxaloacetate increased with a decrease in redox potential. At the pyruvate node, the fraction of carbon to formate increased, while at the acetyl CoA node, the fraction of carbon flux to acetate increased with reduced redox potential. The presence of hydrogen in the headspace or the addition of nicotinic acid to the growth media resulted in increased hydrogen and ethanol fluxes and decreased succinate, acetate, formate, and lactate fluxes.     

Strategies for protein folding and design

Fundamental challenges in molecular biology can be addressed by using simple models on a lattice, where statistical mechanics and combinatoric techniques can be employed. The basic premise is that it is sensible to test any proposed method on the simplest of models in order to assess their validity before launching a full-scale attack on realistic problems. In this paper we follow this strategy and we present different efficient schemes to perform protein design and to extract effective amino acid interaction potentials.This work was supported in part by INFM, INFN sez. di Trieste, NASA and NATO.