Hoài Anh Huỳnh - Academia.edu (original) (raw)

Papers by Hoài Anh Huỳnh

Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to... more Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to study abundant complicated behaviours of systems with nonlinear interactions among many degrees of freedom. These systems can range from a very simple system like one-dimensional map (May R., 1976 Nature 261 459) or a collective system with many (spatial) degrees of freedom like cellular model of sandpile (Bak P.,

Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to... more Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to study abundant complicated behaviours of systems with nonlinear interactions among many degrees of freedom. These systems can range from a very simple system like one-dimensional map (May R., 1976 Nature 261 459) or a collective system with many (spatial) degrees of freedom like cellular model of sandpile (Bak P.,

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lowerdimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an ǫ-expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension , a remarkable relation is observed, satisfied by both regular and fractal lattices.

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lowerdimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an ǫ-expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension , a remarkable relation is observed, satisfied by both regular and fractal lattices.

PLOS ONE, 2015

We study properties of the symbolic sequences extracted from the fractals generated by the arc-fr... more We study properties of the symbolic sequences extracted from the fractals generated by the arc-fractal system introduced earlier by Huynh and Chew. The sequences consist of only a few symbols yet possess several nontrivial properties. First using an operator approach, we show that the sequences are not periodic, even though they are constructed from very simple rules. Second by employing the ε-machine approach developed by Crutchfield and Young, we measure the complexity and randomness of the sequences and show that they are indeed complex, i.e. neither periodic nor random, with the value of complexity measure being significant as compared to the known example of logistic map at the edge of chaos. The complexity and randomness of the sequences are then discussed in relation with the properties of associated fractal objects, such as their fractal dimension, symmetry and orientations of the arcs.

PLOS ONE, 2015

We study properties of the symbolic sequences extracted from the fractals generated by the arc-fr... more We study properties of the symbolic sequences extracted from the fractals generated by the arc-fractal system introduced earlier by Huynh and Chew. The sequences consist of only a few symbols yet possess several nontrivial properties. First using an operator approach, we show that the sequences are not periodic, even though they are constructed from very simple rules. Second by employing the ε-machine approach developed by Crutchfield and Young, we measure the complexity and randomness of the sequences and show that they are indeed complex, i.e. neither periodic nor random, with the value of complexity measure being significant as compared to the known example of logistic map at the edge of chaos. The complexity and randomness of the sequences are then discussed in relation with the properties of associated fractal objects, such as their fractal dimension, symmetry and orientations of the arcs.

Applied Microbiology and Biotechnology, 2014

The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitat... more The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitation, and a recent study has suggested that for recombinant Autographa californica multiple nucleopolyhedrovirus (rAcMNPV)-infected Sf9 cells, a drop in messenger RNA (mRNA) levels may be sufficient to explain the cell density effect for this system. The current study aims to investigate the response in cell-specific yields (viral DNA (vDNA), LacZ mRNA and βgalactosidase (β-Gal) protein) with increasing infection cell density (ICD) for rAcMNPV-infected Hi5 cells, where the rAcMNPV expresses the β-Gal gene under control of the polyhedral promoter. Hi5 cells in suspension culture of Express Five® medium were synchronously infected with a rAcMNPV at multiple ICDs between 0.5 and 6×10 6 cells/ mL and a multiplicity of infection of 10 plaque-forming units (PFU)/cell either in the original or fresh medium conditions. There were negative correlations between the three key virus infection indicators (vDNA, mRNA and β-Gal) and the peak cell density (PCD). However, unlike infected Sf9 cells, the yield decline started at the lowest PCD investigated (0.6×10 6 cells/mL). Generally, the yield decline with increasing PCD was most pronounced for β-Gal followed by mRNA and was more moderate for vDNA. The decline was significantly reduced but not totally arrested when fresh medium replacement was used. The results suggest that the reduction in recombinant protein-specific yields at high PCDs is associated with limitations during the upstream processes of replication and transcription rather than entirely caused by limitations during translation. In addition, low production rates at late infection stages of moderate to high ICDs are a probable cause of the cell density effect.

Applied Microbiology and Biotechnology, 2014

The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitat... more The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitation, and a recent study has suggested that for recombinant Autographa californica multiple nucleopolyhedrovirus (rAcMNPV)-infected Sf9 cells, a drop in messenger RNA (mRNA) levels may be sufficient to explain the cell density effect for this system. The current study aims to investigate the response in cell-specific yields (viral DNA (vDNA), LacZ mRNA and βgalactosidase (β-Gal) protein) with increasing infection cell density (ICD) for rAcMNPV-infected Hi5 cells, where the rAcMNPV expresses the β-Gal gene under control of the polyhedral promoter. Hi5 cells in suspension culture of Express Five® medium were synchronously infected with a rAcMNPV at multiple ICDs between 0.5 and 6×10 6 cells/ mL and a multiplicity of infection of 10 plaque-forming units (PFU)/cell either in the original or fresh medium conditions. There were negative correlations between the three key virus infection indicators (vDNA, mRNA and β-Gal) and the peak cell density (PCD). However, unlike infected Sf9 cells, the yield decline started at the lowest PCD investigated (0.6×10 6 cells/mL). Generally, the yield decline with increasing PCD was most pronounced for β-Gal followed by mRNA and was more moderate for vDNA. The decline was significantly reduced but not totally arrested when fresh medium replacement was used. The results suggest that the reduction in recombinant protein-specific yields at high PCDs is associated with limitations during the upstream processes of replication and transcription rather than entirely caused by limitations during translation. In addition, low production rates at late infection stages of moderate to high ICDs are a probable cause of the cell density effect.

Physical Review E, 2012

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration, and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lower-dimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension, a remarkable relation is observed, satisfied by both regular and fractal lattices.

Physical Review E, 2012

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration, and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lower-dimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension, a remarkable relation is observed, satisfied by both regular and fractal lattices.

Methods, 2012

Metabolomics refer to the global analysis of small molecule metabolites in a biological system, a... more Metabolomics refer to the global analysis of small molecule metabolites in a biological system, and can be a powerful tool to elucidate and optimize cellular processes, particularly when integrated into a systems biology framework. Determining the endometabolome in cultured animal cells is especially challenging, due to the conflicting demands for rapid quenching of metabolism and retention of membrane integrity, while cells are separated from the complex medium. The challenge is magnified in virus infected cells due to increased membrane fragility. This paper describes an effective methodology for quantitative intracellular metabolite analysis of the baculovirus-insect cell expression system, an important platform for the production of heterologous proteins and baculovirus-based biopesticides. These two applications were represented by Spodoptera frugiperda (Sf9) and Helicoverpa zea (HzAM1) cells infected with recombinant Autographa californica and wild-type Helicoverpa armigera nucleopolyhedroviruses (AcMNPV and HaSNPV), respectively. Specifically, an ice-cold quenching solution comprising 1.1% w/v NaCl and 0.2% w/v Pluronic Ò F-68 (NaCl + P) was found to be efficacious in preserving cell viability and minimizing cell leakage during quenching and centrifugation-based washing procedures (prior to extraction using cold 50% v/v acetonitrile). Good recoveries of intracellular adenosine triphosphate, total adenosine phosphates and amino acids were obtained after just one wash step, for both uninfected and infected insect cells. The ability to implement wash steps is critical, as insect cell media are metabolites-rich, while infected insect cells are much more fragile than their uninfected counterparts. Hence, a promising methodology has been developed to facilitate endometabolomic analysis of insect cell-baculovirus systems for bioprocess optimization.

Journal of Statistical Mechanics: Theory and Experiment, 2011

We perform a high-accuracy moment analysis of the avalanche size, duration and area distribution ... more We perform a high-accuracy moment analysis of the avalanche size, duration and area distribution of the Abelian Manna model on eight two-dimensional and four one-dimensional lattices. The results provide strong support to establish universality of exponents and moment ratios across different lattices and a good survey for the strength of corrections to scaling which are notorious in the Manna universality class. The results are compared against previous work done on Manna model, Oslo model and directed percolation. We also confirm hypothesis of various scaling relations.

International Journal of Bifurcation and Chaos, 2010

In this paper, we have explored the bifurcation behavior and chaos of a two-coupled pendulum syst... more In this paper, we have explored the bifurcation behavior and chaos of a two-coupled pendulum system with a coupling energy of the form: κ(θ1 - θ2)2. Using fixed point analysis, we have determined the bifurcation map, which provides a pictorial view of the number and stability properties of the fixed points with respect to the coupling parameter. The bifurcation map shows that the two-coupled pendulum system can exhibit three forms of bifurcation: pitchfork; saddle-node; and a new bifurcation in which a fixed point of the mixed type changes to a center, while a second fixed point of mixed type is born. In order to analyze the chaotic dynamics of the two-coupled pendulum system, we have introduced an equivalent model to the system. This model enables us to investigate the system dynamics in terms of the motion of a particle interacting with a potential landscape. Through analyzing the geometry of the landscape, we are able to determine the dynamical transition points from regular to l...

IEEE Distributed Systems Online, 2006

Using middleware to bridge the gap between applications and low-level constructs is a novel appro... more Using middleware to bridge the gap between applications and low-level constructs is a novel approach to resolving many wireless sensor network issues and enhancing application development. This survey discusses representative WSN middleware, presenting the state of the research.

Fractals, 2011

In this paper, we present an idea of creating fractals by using the geometric arc as the basic el... more In this paper, we present an idea of creating fractals by using the geometric arc as the basic element. This approach of generating fractals, through the tuning of just three parameters, gives a universal way to obtain many novel fractals including the classic ones. Although this arc-fractal system shares similar features with the well-known Lindenmayer system, such as the same set of invariant points and the ability to tile the space, they do have different properties. One of which is the generation of pseudo-random number, which is not available in the Lindenmayer system. Furthermore, by assuming that coastline formation is based purely on the processes of erosion and deposition, the arc-fractal system can also serve as a dynamical model of coastal morphology, with each level of its construction corresponds to the time evolution of the shape of the coastal features. Remarkably, our results indicate that the arc-fractal system can provide an explanation on the origin of fractality ...

Communications in Nonlinear Science and Numerical Simulation, 2013

Abstract By means of two geometrical approaches: (i) the potential landscape, and (ii) the Hamilt... more Abstract By means of two geometrical approaches: (i) the potential landscape, and (ii) the Hamiltonian manifold method, we have found the relations that predict the transition to chaos in a two-coupled pendulum system due to a shift from positive to negative curvature. Our scrutiny from numerical simulations show that the splitting of the KAM island at the symmetric mode is another scenario that hints at the incidence of chaotic behaviour. We have uncovered two regimes on the onset of chaos, depending on whether the coupling parameter is greater or less than a critical point. In the first regime, chaos is observed to first occur after the splitting of the KAM island at the symmetric mode and before the switching of the dynamical curvature. On the other hand, an interchange of scenarios arises in the second regime, with chaos now appears after curvature switching and before KAM island splitting at the symmetric mode.

Biotechnology Progress, 2012

A critical component of an in vitro production process for baculovirus biopesticides is a growth ... more A critical component of an in vitro production process for baculovirus biopesticides is a growth medium that is efficacious, robust, and inexpensive. An in-house low-cost serum-free medium, VPM3, has been shown to be very promising in supporting Helicoverpa armigera nucleopolyhedrovirus (HaSNPV) production in H. zea insect cell suspension cultures, for use as a biopesticide against the Heliothine pest complex. However, VPM3 is composed of a significant number of undefined components, including five different protein hydrolysates, which introduce a challenging lot-to-lot variability to the production process. In this study, an intensive statistical optimization routine was employed to reduce the number of protein hydrolysates in VPM3 medium. Nearly 300 runs (including replicates) were conducted with great efficiency by using 50 mL TubeSpin® bioreactors to propagate insect cell suspension cultures. Fractional factorial experiments were first used to determine the most important of the five default protein hydrolysates, and to screen for seven potential substitutes for the default meat peptone, Primatone RL. Validation studies informed by the screening tests showed that promising alternative media could be formulated based on just two protein hydrolysates, in particular the YST-AMP (Yeast Extract and Amyl Meat Peptone) and YST-POT (Yeast Extract and Lucratone Potato Peptone) combinations. The YST-AMP (meat-based) and YST-POT (meat-free) variants of VPM3 were optimized using response surface methodology, and were shown to be just as good as the default VPM3 and the commercial Sf-900 II media in supporting baculovirus yields, hence providing a means toward a more reproducible and scalable production process for HaSNPV biopesticides.

Applied Microbiology and Biotechnology, 2013

The cell density effect is a well-established constraint in the baculovirus-insect cell expressio... more The cell density effect is a well-established constraint in the baculovirus-insect cell expression platform, in which cell-specific productivity declines with increasing cell density, hence limiting the maximum achievable volumetric yield of protein product. A deeper elucidation of this phenomenon is sought in this study, by tracking the peak production of viral DNA (vDNA), recombinant LacZ mRNA, and β-galactosidase (β-gal) protein, over a wide range of cell densities. Sf9 suspension cell cultures were propagated in Sf-900 III serum-free medium and synchronously infected with rAcMNPV at multiple infection cell densities (ICDs) of between 0.5 and 8×10 6 cells/mL. There was a strong negative linear correlation between the specific β-gal yield and the peak cell density (PCD) post-infection, but contrary to previous reports, the yield decline started at a lower PCD of around 1×10 6 cells/mL. Most interestingly, there also was a corresponding strong negative linear correlation between the specific vDNA or LacZ mRNA yield, and the PCD. Comparing the infections at the highest and lowest PCDs tested, the yield decline was most dramatic for β-gal protein (95 %) and LacZ mRNA (90 %), while it was more moderate for vDNA (50 %). These declines were significantly reduced but not completely arrested, when spent medium was replaced with fresh at the ICD. These findings suggest that protein yield deterioration with increasing cell density originated from limitations during upstream events such as virus gene replication or transcription, rather than during the translational phase. Such limitations may be largely nutritional, but a more complex mechanism may be implicated.

Animal Feed Science and Technology, 2011

A trial was conducted using 275 growing Cherry Valley ducks to determine the apparent (AMEn) and ... more A trial was conducted using 275 growing Cherry Valley ducks to determine the apparent (AMEn) and true (TMEn) metabolizable energy corrected for nitrogen of maize, broken rice, rice bran, wheat bran, cassava meal, soybean meal and two fish meals with 550 g (low protein) and 600 g (high protein) crude protein (CP)/kg. The design was completely randomized with 5 pens replicates of 5 birds each per ingredient. Five extra pens were used to measure endogenous energy loss. Trial was conducted within 14 days with the last 4 days for feeding and excreta collection to measure the AMEn and TMEn. The AMEn were 14.65, 14.63, 12.33, 12.15, 13.38, 11.25, 11.85, and 11.92 MJ/kg dry matter for maize, broken rice, rice bran, wheat bran, cassava meal, soybean meal and low and high CP fish meals, respectively. The TMEn values were 0.76-1.47% higher than the AMEn values.

Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to... more Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to study abundant complicated behaviours of systems with nonlinear interactions among many degrees of freedom. These systems can range from a very simple system like one-dimensional map (May R., 1976 Nature 261 459) or a collective system with many (spatial) degrees of freedom like cellular model of sandpile (Bak P.,

Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to... more Over the past few decades, Complex Systems or Complexity has emerged as a new field of Science to study abundant complicated behaviours of systems with nonlinear interactions among many degrees of freedom. These systems can range from a very simple system like one-dimensional map (May R., 1976 Nature 261 459) or a collective system with many (spatial) degrees of freedom like cellular model of sandpile (Bak P.,

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lowerdimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an ǫ-expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension , a remarkable relation is observed, satisfied by both regular and fractal lattices.

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lowerdimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an ǫ-expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension , a remarkable relation is observed, satisfied by both regular and fractal lattices.

PLOS ONE, 2015

We study properties of the symbolic sequences extracted from the fractals generated by the arc-fr... more We study properties of the symbolic sequences extracted from the fractals generated by the arc-fractal system introduced earlier by Huynh and Chew. The sequences consist of only a few symbols yet possess several nontrivial properties. First using an operator approach, we show that the sequences are not periodic, even though they are constructed from very simple rules. Second by employing the ε-machine approach developed by Crutchfield and Young, we measure the complexity and randomness of the sequences and show that they are indeed complex, i.e. neither periodic nor random, with the value of complexity measure being significant as compared to the known example of logistic map at the edge of chaos. The complexity and randomness of the sequences are then discussed in relation with the properties of associated fractal objects, such as their fractal dimension, symmetry and orientations of the arcs.

PLOS ONE, 2015

We study properties of the symbolic sequences extracted from the fractals generated by the arc-fr... more We study properties of the symbolic sequences extracted from the fractals generated by the arc-fractal system introduced earlier by Huynh and Chew. The sequences consist of only a few symbols yet possess several nontrivial properties. First using an operator approach, we show that the sequences are not periodic, even though they are constructed from very simple rules. Second by employing the ε-machine approach developed by Crutchfield and Young, we measure the complexity and randomness of the sequences and show that they are indeed complex, i.e. neither periodic nor random, with the value of complexity measure being significant as compared to the known example of logistic map at the edge of chaos. The complexity and randomness of the sequences are then discussed in relation with the properties of associated fractal objects, such as their fractal dimension, symmetry and orientations of the arcs.

Applied Microbiology and Biotechnology, 2014

The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitat... more The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitation, and a recent study has suggested that for recombinant Autographa californica multiple nucleopolyhedrovirus (rAcMNPV)-infected Sf9 cells, a drop in messenger RNA (mRNA) levels may be sufficient to explain the cell density effect for this system. The current study aims to investigate the response in cell-specific yields (viral DNA (vDNA), LacZ mRNA and βgalactosidase (β-Gal) protein) with increasing infection cell density (ICD) for rAcMNPV-infected Hi5 cells, where the rAcMNPV expresses the β-Gal gene under control of the polyhedral promoter. Hi5 cells in suspension culture of Express Five® medium were synchronously infected with a rAcMNPV at multiple ICDs between 0.5 and 6×10 6 cells/ mL and a multiplicity of infection of 10 plaque-forming units (PFU)/cell either in the original or fresh medium conditions. There were negative correlations between the three key virus infection indicators (vDNA, mRNA and β-Gal) and the peak cell density (PCD). However, unlike infected Sf9 cells, the yield decline started at the lowest PCD investigated (0.6×10 6 cells/mL). Generally, the yield decline with increasing PCD was most pronounced for β-Gal followed by mRNA and was more moderate for vDNA. The decline was significantly reduced but not totally arrested when fresh medium replacement was used. The results suggest that the reduction in recombinant protein-specific yields at high PCDs is associated with limitations during the upstream processes of replication and transcription rather than entirely caused by limitations during translation. In addition, low production rates at late infection stages of moderate to high ICDs are a probable cause of the cell density effect.

Applied Microbiology and Biotechnology, 2014

The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitat... more The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitation, and a recent study has suggested that for recombinant Autographa californica multiple nucleopolyhedrovirus (rAcMNPV)-infected Sf9 cells, a drop in messenger RNA (mRNA) levels may be sufficient to explain the cell density effect for this system. The current study aims to investigate the response in cell-specific yields (viral DNA (vDNA), LacZ mRNA and βgalactosidase (β-Gal) protein) with increasing infection cell density (ICD) for rAcMNPV-infected Hi5 cells, where the rAcMNPV expresses the β-Gal gene under control of the polyhedral promoter. Hi5 cells in suspension culture of Express Five® medium were synchronously infected with a rAcMNPV at multiple ICDs between 0.5 and 6×10 6 cells/ mL and a multiplicity of infection of 10 plaque-forming units (PFU)/cell either in the original or fresh medium conditions. There were negative correlations between the three key virus infection indicators (vDNA, mRNA and β-Gal) and the peak cell density (PCD). However, unlike infected Sf9 cells, the yield decline started at the lowest PCD investigated (0.6×10 6 cells/mL). Generally, the yield decline with increasing PCD was most pronounced for β-Gal followed by mRNA and was more moderate for vDNA. The decline was significantly reduced but not totally arrested when fresh medium replacement was used. The results suggest that the reduction in recombinant protein-specific yields at high PCDs is associated with limitations during the upstream processes of replication and transcription rather than entirely caused by limitations during translation. In addition, low production rates at late infection stages of moderate to high ICDs are a probable cause of the cell density effect.

Physical Review E, 2012

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration, and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lower-dimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension, a remarkable relation is observed, satisfied by both regular and fractal lattices.

Physical Review E, 2012

The Abelian Manna model of self-organized criticality is studied on various three-dimensional and... more The Abelian Manna model of self-organized criticality is studied on various three-dimensional and fractal lattices. The exponents for avalanche size, duration, and area distribution of the model are obtained by using a high-accuracy moment analysis. Together with earlier results on lower-dimensional lattices, the present results reinforce the notion of universality below the upper critical dimension and allow us to determine the coefficients of an expansion. By rescaling the critical exponents by the lattice dimension and incorporating the random walker dimension, a remarkable relation is observed, satisfied by both regular and fractal lattices.

Methods, 2012

Metabolomics refer to the global analysis of small molecule metabolites in a biological system, a... more Metabolomics refer to the global analysis of small molecule metabolites in a biological system, and can be a powerful tool to elucidate and optimize cellular processes, particularly when integrated into a systems biology framework. Determining the endometabolome in cultured animal cells is especially challenging, due to the conflicting demands for rapid quenching of metabolism and retention of membrane integrity, while cells are separated from the complex medium. The challenge is magnified in virus infected cells due to increased membrane fragility. This paper describes an effective methodology for quantitative intracellular metabolite analysis of the baculovirus-insect cell expression system, an important platform for the production of heterologous proteins and baculovirus-based biopesticides. These two applications were represented by Spodoptera frugiperda (Sf9) and Helicoverpa zea (HzAM1) cells infected with recombinant Autographa californica and wild-type Helicoverpa armigera nucleopolyhedroviruses (AcMNPV and HaSNPV), respectively. Specifically, an ice-cold quenching solution comprising 1.1% w/v NaCl and 0.2% w/v Pluronic Ò F-68 (NaCl + P) was found to be efficacious in preserving cell viability and minimizing cell leakage during quenching and centrifugation-based washing procedures (prior to extraction using cold 50% v/v acetonitrile). Good recoveries of intracellular adenosine triphosphate, total adenosine phosphates and amino acids were obtained after just one wash step, for both uninfected and infected insect cells. The ability to implement wash steps is critical, as insect cell media are metabolites-rich, while infected insect cells are much more fragile than their uninfected counterparts. Hence, a promising methodology has been developed to facilitate endometabolomic analysis of insect cell-baculovirus systems for bioprocess optimization.

Journal of Statistical Mechanics: Theory and Experiment, 2011

We perform a high-accuracy moment analysis of the avalanche size, duration and area distribution ... more We perform a high-accuracy moment analysis of the avalanche size, duration and area distribution of the Abelian Manna model on eight two-dimensional and four one-dimensional lattices. The results provide strong support to establish universality of exponents and moment ratios across different lattices and a good survey for the strength of corrections to scaling which are notorious in the Manna universality class. The results are compared against previous work done on Manna model, Oslo model and directed percolation. We also confirm hypothesis of various scaling relations.

International Journal of Bifurcation and Chaos, 2010

In this paper, we have explored the bifurcation behavior and chaos of a two-coupled pendulum syst... more In this paper, we have explored the bifurcation behavior and chaos of a two-coupled pendulum system with a coupling energy of the form: κ(θ1 - θ2)2. Using fixed point analysis, we have determined the bifurcation map, which provides a pictorial view of the number and stability properties of the fixed points with respect to the coupling parameter. The bifurcation map shows that the two-coupled pendulum system can exhibit three forms of bifurcation: pitchfork; saddle-node; and a new bifurcation in which a fixed point of the mixed type changes to a center, while a second fixed point of mixed type is born. In order to analyze the chaotic dynamics of the two-coupled pendulum system, we have introduced an equivalent model to the system. This model enables us to investigate the system dynamics in terms of the motion of a particle interacting with a potential landscape. Through analyzing the geometry of the landscape, we are able to determine the dynamical transition points from regular to l...

IEEE Distributed Systems Online, 2006

Using middleware to bridge the gap between applications and low-level constructs is a novel appro... more Using middleware to bridge the gap between applications and low-level constructs is a novel approach to resolving many wireless sensor network issues and enhancing application development. This survey discusses representative WSN middleware, presenting the state of the research.

Fractals, 2011

In this paper, we present an idea of creating fractals by using the geometric arc as the basic el... more In this paper, we present an idea of creating fractals by using the geometric arc as the basic element. This approach of generating fractals, through the tuning of just three parameters, gives a universal way to obtain many novel fractals including the classic ones. Although this arc-fractal system shares similar features with the well-known Lindenmayer system, such as the same set of invariant points and the ability to tile the space, they do have different properties. One of which is the generation of pseudo-random number, which is not available in the Lindenmayer system. Furthermore, by assuming that coastline formation is based purely on the processes of erosion and deposition, the arc-fractal system can also serve as a dynamical model of coastal morphology, with each level of its construction corresponds to the time evolution of the shape of the coastal features. Remarkably, our results indicate that the arc-fractal system can provide an explanation on the origin of fractality ...

Communications in Nonlinear Science and Numerical Simulation, 2013

Abstract By means of two geometrical approaches: (i) the potential landscape, and (ii) the Hamilt... more Abstract By means of two geometrical approaches: (i) the potential landscape, and (ii) the Hamiltonian manifold method, we have found the relations that predict the transition to chaos in a two-coupled pendulum system due to a shift from positive to negative curvature. Our scrutiny from numerical simulations show that the splitting of the KAM island at the symmetric mode is another scenario that hints at the incidence of chaotic behaviour. We have uncovered two regimes on the onset of chaos, depending on whether the coupling parameter is greater or less than a critical point. In the first regime, chaos is observed to first occur after the splitting of the KAM island at the symmetric mode and before the switching of the dynamical curvature. On the other hand, an interchange of scenarios arises in the second regime, with chaos now appears after curvature switching and before KAM island splitting at the symmetric mode.

Biotechnology Progress, 2012

A critical component of an in vitro production process for baculovirus biopesticides is a growth ... more A critical component of an in vitro production process for baculovirus biopesticides is a growth medium that is efficacious, robust, and inexpensive. An in-house low-cost serum-free medium, VPM3, has been shown to be very promising in supporting Helicoverpa armigera nucleopolyhedrovirus (HaSNPV) production in H. zea insect cell suspension cultures, for use as a biopesticide against the Heliothine pest complex. However, VPM3 is composed of a significant number of undefined components, including five different protein hydrolysates, which introduce a challenging lot-to-lot variability to the production process. In this study, an intensive statistical optimization routine was employed to reduce the number of protein hydrolysates in VPM3 medium. Nearly 300 runs (including replicates) were conducted with great efficiency by using 50 mL TubeSpin® bioreactors to propagate insect cell suspension cultures. Fractional factorial experiments were first used to determine the most important of the five default protein hydrolysates, and to screen for seven potential substitutes for the default meat peptone, Primatone RL. Validation studies informed by the screening tests showed that promising alternative media could be formulated based on just two protein hydrolysates, in particular the YST-AMP (Yeast Extract and Amyl Meat Peptone) and YST-POT (Yeast Extract and Lucratone Potato Peptone) combinations. The YST-AMP (meat-based) and YST-POT (meat-free) variants of VPM3 were optimized using response surface methodology, and were shown to be just as good as the default VPM3 and the commercial Sf-900 II media in supporting baculovirus yields, hence providing a means toward a more reproducible and scalable production process for HaSNPV biopesticides.

Applied Microbiology and Biotechnology, 2013

The cell density effect is a well-established constraint in the baculovirus-insect cell expressio... more The cell density effect is a well-established constraint in the baculovirus-insect cell expression platform, in which cell-specific productivity declines with increasing cell density, hence limiting the maximum achievable volumetric yield of protein product. A deeper elucidation of this phenomenon is sought in this study, by tracking the peak production of viral DNA (vDNA), recombinant LacZ mRNA, and β-galactosidase (β-gal) protein, over a wide range of cell densities. Sf9 suspension cell cultures were propagated in Sf-900 III serum-free medium and synchronously infected with rAcMNPV at multiple infection cell densities (ICDs) of between 0.5 and 8×10 6 cells/mL. There was a strong negative linear correlation between the specific β-gal yield and the peak cell density (PCD) post-infection, but contrary to previous reports, the yield decline started at a lower PCD of around 1×10 6 cells/mL. Most interestingly, there also was a corresponding strong negative linear correlation between the specific vDNA or LacZ mRNA yield, and the PCD. Comparing the infections at the highest and lowest PCDs tested, the yield decline was most dramatic for β-gal protein (95 %) and LacZ mRNA (90 %), while it was more moderate for vDNA (50 %). These declines were significantly reduced but not completely arrested, when spent medium was replaced with fresh at the ICD. These findings suggest that protein yield deterioration with increasing cell density originated from limitations during upstream events such as virus gene replication or transcription, rather than during the translational phase. Such limitations may be largely nutritional, but a more complex mechanism may be implicated.

Animal Feed Science and Technology, 2011

A trial was conducted using 275 growing Cherry Valley ducks to determine the apparent (AMEn) and ... more A trial was conducted using 275 growing Cherry Valley ducks to determine the apparent (AMEn) and true (TMEn) metabolizable energy corrected for nitrogen of maize, broken rice, rice bran, wheat bran, cassava meal, soybean meal and two fish meals with 550 g (low protein) and 600 g (high protein) crude protein (CP)/kg. The design was completely randomized with 5 pens replicates of 5 birds each per ingredient. Five extra pens were used to measure endogenous energy loss. Trial was conducted within 14 days with the last 4 days for feeding and excreta collection to measure the AMEn and TMEn. The AMEn were 14.65, 14.63, 12.33, 12.15, 13.38, 11.25, 11.85, and 11.92 MJ/kg dry matter for maize, broken rice, rice bran, wheat bran, cassava meal, soybean meal and low and high CP fish meals, respectively. The TMEn values were 0.76-1.47% higher than the AMEn values.