• 1985 Ph.D., University of Pretoria, South Africa
• 1981 M.S., University of Pretoria, South Africa
• 1979 B.S., University of Pretoria, South Africa

• Development of new methods for the synthesis and processing of materials
• Analysis of complex engineering systems with the aid of models and simulation
• Application of chemical reaction engineering principles to interdisciplinary problems. The following areas are of particular interest:
  • Mechanical-Chemical interaction in solid phase reactants
  • Cooperative behavior or mesoscale: solitons and solitary wave
  • Thermal stresses and crack development in chemically reacting system
  • Development of high temperature acoustic detection methods
  • Piezoelectric sensors, manufacture and modeling
  • Chemical reaction and natural convection
    
  • Analysis of thermal CVD systems, e.g. - the effect of the flow field on the deposition rate and film homogeneity
  • Dynamic stress development of films during deposition
  • Reaction-induced thermal stresses in consolidated media
  • Mechanical failure of catalytic systems during thermal cycling or transient operation
  • The study of nonlinear dynamical systems, e.g. - existence of temporal chaos and solitary waves
  • Bifurcation analysis of non-catalytic highly exothermic reacting systems
  • Development of fast thermocyclers for polymerase chain reaction (PCR)
  • Theoretical investigation of errors in the polymerase chain reaction process
  • Assembly of DNA structures from synthetic oligonucleotides
  • Strategies for Gene Packaging in Virus-Like Particles

Biomolecular engineering:
The application of reaction engineering principles to molecular biology problems, has led to novel insight and discoveries. Kinetic models have been developed for the polymerase chain reaction (PCR) to describe the editing and proof-reading capabilities of the enzyme, the average mutation frequencies and the effects of dexoynucleotide pool compositions and temperature on elongation and error rates. Quantitave models have been developed to assess the errors which accrue during a PCR reaction. Two sources of errors are associated with the PCR process: (1) editing errors that occur during DNA polymerase-catalyzed enzymatic copying and (2) errors due to DNA thermal damage. The errors which are ascribed to the polymerase depend on the efficiency of its editing and proof-reading functions and are closely related to the kinetic models we have developed. Thermally induced errors stem mostly from three sources: A+G depurination, oxidative damage of guanine to 8-oxoG and cytosine deamination to uracil. The post-PCR modifications of nucleic acids at elevated temperatures are more pronounced if the DNA is in a single-stranded form. Below melting temperatures, the DNA molecules are mostly in the double stranded form and the hydrolytic attack on the DNA bases is sterically hindered. Two hydrolytic damage reactions are prominent at elevated temperatures; C deamination and A+G depurination.

The kinetic and error models are combined to simulate PCR experiments and to provide the following measures: (1) yield (2) error frequency (3) optimum reaction conditions. The software resides on the fast thermocyclers we use in our laboratory. The rapid thermocyclers perform typical PCR experiments in 3 to 5 minutes and lend themselves not only to rapid diagnostics, but also to any PCR application that warrants low thermal damage.

Click image to view video clip of typical temperature-time profiles of our rapid PCR thermocycler. (Windows Media 1.4MB)

The combination of rapid PCR and low thermal damage creates an advantage for assembling synthetic oligonucleotides into large DNA molecules by PCR. The PCR assembly technique has been used to synthesize a large number of genes with exceptional accuracy and speed. All eight genes of the Influenza A virus have been synthesized and together with collaborators from Austria, the genes have been packaged into virus like particles (VLP). The dual approach of experiments and theoretical modeling is also followed in PCR assembly. Theoretical models have led to optimal assembly strategies. Typical assembly times for 2,000 base pair structures are 15 to 20 minutes. The current generation of rapid thermocyclers is modified for PCR assembly to automatically capture synthesized parts and ligate them into final constructs.

Electron microscope picture of VLP that contains synthetic HA gene.

As part of the effort to optimize the expression of synthetic genes in cells, a new theoretical project on codon efficiency has started. It is called the tri-frame coding theory. The genetic code uses all three reading frames to encode for the following information: what must be synthesized, how much of it must be synthesized and how accurately it must be synthesized. The zero reading frame (0RF) encodes for the amino acid sequence. The combination of rare codons in the 0RF and stop codons in the 1RF controls the ribosome transit time of the mRNA and hence the expression level. Rare codons in 0RF causes the ribosome to frame-shift and the incomplete polypeptide chain is tagged and terminated in the -1RF and +1RF with high probability. If the out-of-frame stop frequency is low, termination is delayed and ribosome processing time is extended and vice versa. Entropy is the antithesis of accuracy. Codon definition in the DNA is presumably exact and thus the (information) entropy is zero. Mistranscription causes an increase in the codon's entropy. A further entropy increase follows the translation step. The system's entropy is the weighted sum of codon entropies and the probability distribution of the ribosome's occupancy of the reading frames. The tri-frame coding theory provides exact expressions for: (1) the yield of error-free protein, (2) the fraction of prematurely terminated polypeptides, (3) the percentage mistranscription in proteins, (4) the percentage mistranslation in proteins, (5) the percentage mutations due to frameshifting and (5) the energy and entropy cost to synthesize a protein.

Reaction engineering of heterogeneous systems The research is focused on solid phase reactants. In an effort to increase the rate of reaction of metal/oxide mixtures, the general approach has been to reduce the particle sizes of reactants. It has also been recognized that heating by compression (as in a shock wave) is much faster than thermal conduction and some studies have been undertaken by other investigators to explore the possibility to ignite pyrotechnic mixtures by impact, but in most cases the conversion was not complete and most reaction occurred in the post-shock region with little or no contribution to the shock wave. Research on mechano-chemical reactions is conducted with the use of a Bridgman anvil. The project is multi-disciplinary and the following subdivisions are addressed.

Probability distribution of ribosomal occupancy of the three reading frames of mRNA of the rpsU gene of Escherichia coli. The step-reduction at codon 23 in the zero reading frame (0RF) is associated with the rare codon Cysteine. Out-frame stop codons terminate ribosome occupancy in the +1 and -1 RF

(1) Physical properties of mixtures
(2) Kinetics of metal/oxidizer mixtures
(3) Mechano-chemical reactions
(4) Post-reaction behavior

In 1935, Bridgman reported results of combined hydrostatic pressure and shear for a wide variety of materials. Whilst most substances undergo polymorphic transformation, some react violently: PbO decomposes quiescently to a thin film of lead while PbO2 detonates yielding a residue of Pb. Reactive mixtures Al/Fe2O3 and Al/Bi2O3 produce even stronger mechanical-chemical interaction.

A theory has been developed to determine the contact area between heterogeneous mixtures. The contact area is influenced by the presence of pores and this effect has been included in the model. Based on this theory, more realistic kinetic models have been developed for solid/solid reactants. The theory has also been used to develop more advanced models of transport properties, such as effective thermal conductivity, susceptibility, permeability and electrical resistivity. The contact theory proves to be quite useful to describe heterogeneous effects such as Kapitza resistance and impedance mismatch.

Click image to view video clip of thermite reaction in our Bridgman anvil. (Windows Media 380k)

The kinetics of metal/oxidizer mixtures have been measured with the ETA-100 instrument (developed by Dr. Alexander Shteinberg). The instrument allows the user to register and record transient temperatures based on either the brightness or the color of the sample surface during electro-thermal explosion. After dry mixing the mixture is pressed to obtain a cylindrically-shaped specimen measuring 10-12 mm long and 3 mm in diameter. An electric current is sent through the sample until it reaches a pre-set temperature. The current is switched off at that point and further temperature rise is due to chemical reaction alone. Chemical reaction already starts during the preheating stage, albeit small. The temperature of the electro-thermal analyzer is measured by an array of optical diodes at intervals of 0.625 mm along the length of cylindrical specimen. An array of sixteen optical diodes tracks the temperature on the cylinder surface at a sampling rate 10,000 data points per second for each diode. The data are stored and analyzed to determine the kinetic parameters.

• Whitney, S., R. Agupally, R, M. Nelson, and H.J.Viljoen, "Principles of the Polymerase Chain Reaction: Mathematical Modeling and Experimental Verification" Comp. Biol & Chem. 28 pp195-209 (2004).
• Ebmeier, R., S. Whitney, R. Agupally, G. Gogos, R.M. Nelson, N. Padhye and H.J. Viljoen, "A Ranque-Hilsch Vortex Tube Based Thermocycler for DNA Amplification" Instr. Science & Tech. 32 : 567-571 (2004).
• Ebmeier, R., S. Whitney, R. Agupally, G. Gogos, R.M. Nelson, N. Padhye and H.J. Viljoen, "A Ranque-Hilsch Vortex Tube Based Thermocycler for DNA Amplification" Rev. Sci. Instr. 75 pp5356-5359 (2004).
• Viljoen, S.V., M. Griep, M. Nelson and H.J. Viljoen, "A Macroscopic Kinetic Model for DNA Polymerase Elongation and High Fidelity Nucleotide Selection, " Comp. Biol & Chem 29 pp101-110 (2005).
• Griep M, Whitney S, Nelson M and Viljoen HJ "DNA Polymerase Chain Reaction: A Model of Error Frequencies and Extension Rates" AIChE J. 52 pp384-392 (2006).
• Pienaar, E.M., Theron, M. Nelson and H.J. Viljoen, "A Quantitative Model of Error Accumulation During PCR Amplification," Comp. Biol. & Chem. 30 pp 102-111 (2006.)
• Griep, M.A., Kotera, C.A., Nelson, R.M. and Viljoen, H.J. "Kinetics of the DNA Polymerase Pyrococcus Kodakaraensis." Chem. Eng. Sci. 61 pp 3885-3892 (2006)

• Gordopolov, A., O. Dzenis and H.J. Viljoen, "Compression of Powders in a Bridgman Anvil: Fracture and Reaction", Int. SHS J. 13 (3) pp233-243 (2004).
• Gordopolov, A., H.J. Viljoen and N.F.J. van Rensburg, "Reaction of thermites in a Bridgman anvil Part I: The Pre-Explosion Phase." Chem. Phys. 24 (3), pp60-68 (2005).
• Gordopolov, A. and H.J. Viljoen, "A Study in Mechano-chemistry: Pressure Induced Reactions and Non-equilibrium Phenomena" Int. SHS J. 14 (2005).
• Gordopolov, A., O. Dzenis and H.J. Viljoen "Reaction of thermites in a Bridgman anvil Part II: Fracture and Reaction" Chem. Phys. 24 (4), pp61-65 (2005).
• For additional publications, please click the Digital Commons link in the right column of the page.

• 2005 Multidisciplinary Research Award, University of Nebraska-Lincoln
• 1990 Researcher of the Year Award in the Faculty of Engineering, University of Stellenbosch
• 1989 Presidents Award for excellence in research
• 1980 Silver Medal of South African Institute of Chemical Engineers
• Chair and co-chair of session on combustion synthesis at AIChE annual meetings in 1989 (San Francisco), 1990 (Chicago), 1991 (Los Angeles), 1992 (Miami), and 1993 (St. Louis), 1999 (Dallas), 2000 (Los Angeles)
• Co-Chair of sessions on nano-energetic materials at AIChE annual meetings in 2004 (Austin), 2005 (Cincinnati)
• Chair of session at CHISA 2004, Prague, Czech Republic (micro-reactors), International SHS Conference, Cagliari, Italy (2005) (modeling of solid phase combustion)
• Guest editor of a special issue of Combustion Science Technology {88} (1992)
• Co-Author of the section, "Modeling of Chemical Reactors", for Ullman's Technical Encyclopedia, new edition
• Editorial Board of Computational Biology & Chemistry, from 2006
• Research on rapid polymerase chain reaction reviewed in Nature: Moore, P., (2005) "PCR: Replicating Success." Nature 435; 235-238

• Viljoen, H.J. and Jooste, B.R., "Piezoelectric Sensors/Actuators for use in refractory environments," U.S. Patent 6,057,628, issued May 2, 2000
• Whitney, S., Viljoen, H.J., Padhye, N. and Nelson, M.R., "A gas jet process and apparatus for high-speed amplification of DNA." PCT Patent, issued in 2005 in 22 countries in Europe and Asia

• American Institute of Chemical Engineers
• Materials Research Society
• South African Institute of Chemical Engineers
• Consultant to Naval Surface Warfare Center at Indian head on underwater explosions
• Consultant and expert witness for PCS Nitrogen
• Megabase Research Products