Chemical and biomolecular engineering

The polymerase chain reaction (PCR) has found wide application in biochemistry and molecular biology such as gene expression studies, mutation detection, forensic analysis and pathogen detection. Increasingly quantitative real time PCR is used to assess copy numbers from overall yield. In this study the yield is analyzed as a function of several processes: (1) thermal damage of the template and polymerase occurs during the denaturing step, (2) competition exists between primers and templates to either anneal or form dsDNA, (3) polymerase binding to annealed products (primer/ssDNA) to form ternary complexes and (4) extension of ternary complexes. Explicit expressions are provided for the efficiency of each process, therefore reaction conditions can be directly linked to the overall yield. Examples are provided where different processes play the yield-limiting role. The analysis will give researchers a unique understanding of the factors that control the reaction and will aid in the interpretation of experimental results.

Chondrocytes are mechanosensitive cells that require mechanical stimulation for proper growth and function in in vitro culture systems. Ultrasound (US) has emerged as a technique to deliver mechanical stress; however, the intracellular signaling components of the mechanotransduction pathways that transmit the extracellular mechanical stimulus to gene regulatory mechanisms are not fully defined. We evaluated a possible integrin/ mitogen-activated protein kinase (MAPK) mechanotransduction pathway using Western blotting with antibodies targeting specific phosphorylation sites on intracellular signaling proteins. US stimulation of chondrocytes induced phosphorylation of focal adhesion kinase (FAK), Src, p130 Crk-associated substrate (p130Cas), CrkII and extracellular-regulated kinase (Erk). Furthermore, pre-incubation with inhibitors of integrin receptors, Src and MAPK/Erk kinase (MEK) reduced US-induced Erk phosphorylation levels, indicating integrins and Src are upstream of Erk in an US-mediated mechanotransduction pathway. These findings suggest US signals through integrin receptors to the MAPK/Erk pathway via a mechanotransduction pathway involving FAK, Src, p130Cas and CrkII. (E-mail: [email protected]) Published by Elsevier Inc. on behalf of World Federation for Ultrasound in Medicine & Biology

Recently a theoretical analysis of PCR efficiency has been published by . The PCR yield is the product of three efficiencies: (i) the annealing efficiency is the fraction of templates that form binary complexes with primers during annealing, (ii)the polymerase binding efficiency is the fraction of binary complexes that bind to polymerase to form ternary complexes and (iii)the elongation efficiency is the fraction of ternary complexes that extend fully. Yield is controlled by the smallest of the three efficiencies and control could shift from one type of efficiency to another over the course of a PCR experiment. Experiments have been designed that are specifically controlled by each one of the efficiencies and the results are consistent with the mathematical model. The experimental data has also been used to quantify six key parameters of the theoretical model. An important application of the fully characterized model is to calculate initial template concentration from real-time PCR data. Given the PCR protocol, the midpoint cycle number (where the template concentration is half that of the final concentration) can be theoretically determined and graphed for a variety of initial DNA concentrations. Real-time results can be used to calculate the midpoint cycle number and consequently the initial DNA concentration, using this graph. The application becomes particularly simple if a conservative PCR protocol is followed where only the annealing efficiency is controlling.

A d'Alembert-based solution of forced wave motion with internal and boundary damping is presented with the specific intention of investigating the transient response. The dynamic boundary condition is a convenient method to model the absorption and reflection effects of an interface without considering coupled PDE's. Problems with boundary condition of the form @w @z þã @w @t ¼ 0 are not self-adjoint which greatly complicates solution by spectral analysis. However, exact solutions are found with d'Alembert's method. Solutions are also derived for a time-harmonically forced problem with internal damping and are used to investigate the effect of ultrasound in a bioreactor, particularly the amount of energy delivered to cultured cells. The concise form of the solution simplifies the analysis of acoustic field problems.

This study provides evidence that low intensity ultrasound directly affects nuclear processes and the 2 magnitude of the effect varies with frequency. In particular, we show that the transcriptional induction of 3 first load-inducible genes, which is independent of new protein synthesis, is frequency dependent. Bovine 4 chondrocytes were exposed to low intensity (below the cavitational threshold) ultrasound at 2MHz, 5MHz 5 and 8MHz. Ultrasound elevated the expression of early response genes c-Fos, c-Jun and c-Myc, 6 maximized at 5MHz. The phosphorylated ERK inhibitor PD98059 abrogated any increase in c-series gene 7 expression, suggesting that signaling occurs via the MAPPK/ERK pathway. However, phosphorylated 8 ERK levels did not change with ultrasound frequency, indicating that processes downstream of ERK 9 phosphorylation (such as nuclear transport or chromatin reorganization) respond to ultrasound with 10 frequency dependence. A quantitative, biphasic mathematical model based on Biot theory predicted that 11 cytoplasmic and nuclear stress is maximized at 5.2 0.8MHz for a chondrocyte, confirming experimental 12 measurements. 13 14

Chemical looping technology for capturing and hydrothermal processes for conversion of carbon are discussed with focused and critical assessments. The fluidized and stationary reactor systems using solid, including biomass, and gaseous fuels are considered in chemical looping combustion, gasification, and reforming processes. Sustainability is emphasized generally in energy technology and in two chemical looping simulation case studies using coal and natural gas. Conversion of captured carbon to formic acid, methanol, and other chemicals is also discussed in circulating and stationary reactors in hydrothermal processes. This review provides analyses of the major chemical looping technologies for CO 2 capture and hydrothermal processes for carbon conversion so that the appropriate clean energy technology can be selected for a particular process. Combined chemical looping and hydrothermal processes may be feasible and sustainable in carbon capture and conversion and may lead to clean energy technologies using coal, natural gas, and biomass.

Thermochemical gasification is one of the most promising technologies for converting biomass into power, fuels and chemicals. The objectives of this study were to maximize the net energy efficiency for biomass gasification, and to estimate the cost of producing industrial gas and combined heat and power (CHP) at a feedrate of 2000 kg/h. Aspen Plus-based model for gasification was combined with a CHP generation model, and optimized using corn stover and dried distillers grains with solubles (DDGS) as the biomass feedstocks. The cold gas efficiencies for gas production were 57% and 52%, respectively, for corn stover and DDGS. The selling price of gas was estimated to be $11.49 and $13.08/GJ, respectively, for corn stover and DDGS. For CHP generation, the electrical and net efficiencies were as high as 37% and 88%, respectively, for corn stover and 34% and 78%, respectively, for DDGS. The selling price of electricity was estimated to be $0.1351 and $0.1287/kW h for corn stover and DDGS, respectively. Overall, high net energy efficiencies for gas and CHP production from biomass gasification can be achieved with optimized processing conditions. However, the economical feasibility of these conversion processes will depend on the relative local prices of fossil fuels.

In this research, solar energy has been stored using the paraffin with the latent heat technique for heating the plastic greenhouse of 180 m*. Energy and exergy analyses were applied for evaluation of the system efficiency, An average values of the rates of heat and thermal exergy stored into the HSU were 1 740 W and 60 W for the charging periods. It was determined that the average values of the net energy and exergy efficiencies of the system were 4 I .9 % and 3.3 %, respectively.

A combination of the ®rst and second law of thermodynamics has been utilized in analyzing the convective heat transfer in an annular packed bed. The bed was heated asymmetrically by constant heat¯uxes. Introduction of the packing enhances wall to¯uid heat transfer considerably, hence reduces the entropy generation due to heat transfer across a ®nite temperature dierence. However, the entropy generation due to¯uid-¯ow friction increases. The net entropy generations resulting from the above eects provide a new criterion in analysing the system. Using the modi®ed Ergun equation for pressure drop estimation and a heat transfer coecient correlation for an annular packed bed, an expression for the volumetric entropy generation rate has been derived and displayed graphically. In the packed annulus, the fully developed temperature pro®le and the plug¯ow conditions have been assumed and veri®ed with experimental data. The volumetric entropy generation map shows the regions with excessive entropy generation due to operating conditions or design parameters for a required task, and leads to a better understanding of the behavior of the system. Ó

The entropy generation due to heat transfer and friction has been calculated for fully developed, forced convection flow in a large rectangular duct. packed with spherical particles, with constant heat fluxes applied to both the top (heated) and bottom (cooled) wall. An approximate analytical expression for the velocity profile developed for packed bed with t-l/cJ, > 5 has been used together \vith the energy equation of fully developed flow to calculate the nonisothermal temperature profiles along the flow passage. The velocity prolile takes into account the increase in the velocity near the wall due to the higher voidage in this region of the bed. The effect of the asylnmetric heating on the velocity profile is neglected under the thermal conditions considered. The volulnetric entropy generation rate and the irreversibility distribution ratios have been calculated and displayed graphically for the values of tT/cll, = 5 and 20. It was found that the irreversibility distributions are not continnous through the wall and core regions. hence the optimality criterion of equipartition of entropy generations should be considered separately for these regions of the packed duct. $3 1999 Elsevier Science Ltd. All rights reserved. Norl~enclature u velocity [m s-' 1 0017-9310/99/$ -see front mailer : (; 1999 Elseuier Science Ltd. All rights reserved Pli: SO01 7 93 l 0 ( 9 8 ) 0 0 3 2 4 X AP finite pressure AT finite temperature

A combination of the ®rst and second law of thermodynamics has been utilized in analyzing the convective heat transfer in an annular packed bed. The bed was heated asymmetrically by constant heat¯uxes. Introduction of the packing enhances wall to¯uid heat transfer considerably, hence reduces the entropy generation due to heat transfer across a ®nite temperature dierence. However, the entropy generation due to¯uid-¯ow friction increases. The net entropy generations resulting from the above eects provide a new criterion in analysing the system. Using the modi®ed Ergun equation for pressure drop estimation and a heat transfer coecient correlation for an annular packed bed, an expression for the volumetric entropy generation rate has been derived and displayed graphically. In the packed annulus, the fully developed temperature pro®le and the plug¯ow conditions have been assumed and veri®ed with experimental data. The volumetric entropy generation map shows the regions with excessive entropy generation due to operating conditions or design parameters for a required task, and leads to a better understanding of the behavior of the system. Ó

An experimental and numerical investigation of fully developed forced convection in large rectangular packed ducts is presented. The horizontally oriented ducts have the length-to-separation distance ratio of L/H=16 with two aspect ratios of W/H=8 and 4. A constant heat¯ux is supplied to the top wall, while the bottom and side walls are insulated. Packing of hard polyvinyl chloride Raschig rings with outside diameters of 48 and 34 mm, and expanded polystyrene spheres with diameters of 48, 38 and 29 mm are used in the air¯ow passage. The experiments are carried out for 200 < (Re p =ud p /n f ) < 1450, and 4.5 < d e /d p < 9.0. The pressure drop, the heat¯ux, axial and transverse temperature pro®les of air¯ow inside the ducts are measured at the steady state. Similar experiments have also been carried out with empty ducts. Numerical predictions of two-dimensional quasi-homogeneous model are found to be in agreement with the experimental results of the packed ducts. The correlation equations for the Nusselt number are obtained. It is found that the introduction of packing into the air¯ow passage yields about a three times increase in the wall-to-air heat-transfer rate compared with that of the empty duct. #

An experimental study is made into the process of heat transfer from a pulse-superheated probe to a solidified polymer system at probe temperatures above the temperature T d∞ of the beginning of thermal destruction of matter in a quasi-static process. Use is made of the procedures of thermal stabilization of the pulse-superheated probe (with the characteristic time of constancy of superheated probe temperature of 1 ms) and of shock heating (with the characteristic time of increasing the probe temperature of 1 μs and that of monitoring its cooling-down of 1 ms). The effect of short-term thermal stability of polymers in the region of T > T d∞ is revealed. A procedure is developed for identifying the signs of thermal destruction of polymers in the pulsed process. The maximal values are estimated of the density of heat flux through samples without their thermal destruction.

Linear-nonequilibrium thermodynamics (LNET) has been used to express the entropy generation and dissipation functions representing the true forces and¯ows for heat and mass transport in a multicomponent¯uid. These forces and¯ows are introduced into the phenomenological equations to formulate the coupling phenomenon between heat and mass¯ows. The degree of the coupling is also discussed. In the literature such coupling has been formulated incompletely and sometimes in a confusing manner. The reason for this is the lack of a proper combination of LNET theory with the phenomenological theory. The LNET theory involves identifying the conjugated¯ows and forces that are related to each other with the phenomenological coecients that obey the Onsager relations. In doing so, the theory utilizes the dissipation function or the entropy generation equation derived from the Gibbs relation. This derivation assumes that local thermodynamic equilibrium holds for processes not far away from the equilibrium. With this assumption we have used the phenomenological equations relating the conjugated¯ows and forces de®ned by the dissipation function of the irreversible transport and rate process. We have expressed the phenomenological equations with the resistance coecients that are capable of re¯ecting the extent of the interactions between heat and mass¯ows. We call this the dissipation-phenomenological equation (DPE) approach, which leads to correct expression for coupled processes, and for the second law analysis. Ó

Using published experimental data on the thermal conductivity, mutual diffusivity, and heats of transport, the degree of coupling between heat and mass flows has been calculated for binary and ternary nonideal liquid mixtures. The binary mixtures consist of two types: the first is six systems of six-to-eight-carbon straight and branched chain alkanes in chloroform and in carbon tetrachloride; and the second is mixtures of carbon tetrachloride with benzene. toluene, 2-propanone, n-hexane, and 11-octane. The ternary mixture considered is toluene-chlorobenzene-bromobenzene. The published data are available at 25 o C, 30°C, 35 o C and ambient pressure. Using the linear nonequilibrium thermodynamics ( LNET) and the dissipation-phenomenological equation (DPE) approach, the effects of concentration, temperature, molecular weight, chain-length, solute, solvent, and branching on the degree of coupling are examined. The extent of coupling and the thermal diffusion ratio are expressed in terms of the transport coefficients to obtain a better understanding of the interactions between heat and mass flows in liquid mixtures. I t is found that the composition of the heavy component bromobenzene changes the direction and magnitude of the two-flow coupling in the ternary mixture.

Bioenergetics is concerned with the energy conservation and conversion processes in a living cell, particularly in the inner membrane of the mitochondrion. This review summarizes the role of thermodynamics in understanding the coupling between the chemical reactions and the transport of substances in bioenergetics. Thermodynamics has the advantages of identifying possible pathways, providing a measure of the efficiency of energy conversion, and of the coupling between various processes without requiring a detailed knowledge of the underlying mechanisms. In the last five decades, various new approaches in thermodynamics, nonequilibrium thermodynamics and network thermodynamics have been developed to understand the transport and rate processes in physical and biological systems. For systems not far from equilibrium the theory of linear non-equilibrium thermodynamics is used, while extended nonequilibrium thermodynamics is used for systems far away from equilibrium. All these approaches are based on the irreversible character of flows and forces of an open system. Here, linear non-equilibrium thermodynamics is mostly discussed as it is the most advanced. We also review attempts to incorporate the mechanisms of a process into some formulations of nonequilibrium thermodynamics. The formulation of linear non-equilibrium thermodynamics for facilitated transport and active transport, which represent the key processes of coupled phenomena of transport and chemical reactions, is also presented. The purpose of this review is to present an overview of the application of non-equilibrium thermodynamics to bioenergetics, and introduce the basic methods and equations that are used. However, the reader will have to consult the literature reference to see the details of the specific applications.

Linear-nonequilibrium thermodynamics (LNET) has been used to express the entropy generation and dissipation functions representing the true forces and ¯ows for heat and mass transport in a multicomponent ¯uid. These forces and ¯ows are introduced into the phenomenological equations to formulate the coupling phenomenon between heat and mass ¯ows. The degree of the coupling is also discussed. In the literature such coupling has been formulated incompletely and sometimes in a confusing manner. The reason for this is the lack of a proper combination of LNET theory with the phenomenological theory. The LNET theory involves identifying the conjugated ¯ows and forces that are related to each other with the phenomenological coecients that obey the Onsager relations. In doing so, the theory utilizes the dissipation function or the entropy generation equation derived from the Gibbs relation. This derivation assumes that local thermodynamic equilibrium holds for processes not far away from the equilibrium. With this assumption we have used the phenomenological equations relating the conjugated ¯ows and forces de®ned by the dis-sipation function of the irreversible transport and rate process. We have expressed the phenomenological equations with the resistance coecients that are capable of re¯ecting the extent of the interactions between heat and mass ¯ows. We call this the dissipation-phenomenological equation (DPE) approach, which leads to correct expression for coupled processes, and for the second law analysis.