The modelling of splicing systems is simulated by the process of cleaving and recombining DNA molecules with the presence of a ligase and restriction enzymes which are biologically called as endodeoxyribonucleases. The molecules resulting from DNA splicing systems are known as splicing languages. Palindrome is a sequence of strings that reads the same forward and backward. In this research, the splicing languages resulting from DNA splicing systems with one non-palindromic restriction enzyme are determined using the notation from Head splicing system. The generalisations of splicing languages for DNA splicing systems involving a cutting site and two non-overlapping cutting sites of one non-palindromic restriction enzyme are presented in the first and second theorems, respectively, which are proved using direct and induction methods. The result from the first theorem shows a trivial string which is the initial DNA molecule; while the second theorem determines a splicing language consisting of a set of resulting DNA molecules from the respective DNA splicing system.
Abstract In DNA splicing system, DNA molecules are cut and recombined with the presence of restriction enzymes and a ligase. The splicing system is analyzed via formal language theory where the molecules resulting from the splicing system generate a language which is called a splicing language. In nature, DNA molecules can be read in two ways; forward and backward. A sequence of string that reads the same forward and backward is known as a palindrome. Palindromic and non-palindromic sequences can also be recognized in restriction enzymes. Research on splicing languages from DNA splicing systems with palindromic and non-palindromic restriction enzymes have been done previously. This research is motivated by the problem of DNA assembly to read millions of long DNA sequences where the concepts of automata and grammars are applied in DNA splicing systems to simplify the assembly in short-read sequences. The splicing languages generated from DNA splicing systems with palindromic and non- palindromic restriction enzymes are deduced from the grammars which are visualised as automata diagrams, and presented by transition graphs where transition labels represent the language of DNA molecules resulting from the respective DNA splicing systems.
Symmetric methods such as the implicit midpoint rule (IMR), implicit trapezoidal
rule (ITR) and 2-stage Gauss method are beneficial in solving Hamiltonian problems
since they are also symplectic. Symplectic methods have advantages over non-symplectic
methods in the long term integration of Hamiltonian problems. The study is to show
the efficiency of IMR, ITR and the 2-stage Gauss method in solving simple harmonic
oscillators (SHO). This study is done theoretically and numerically on the simple harmonic
oscillator problem. The theoretical analysis and numerical results on SHO problem
showed that the magnitude of the global error for a symmetric or symplectic method
with stepsize h is linearly dependent on time t. This gives the linear error growth when
a symmetric or symplectic method is applied to the simple harmonic oscillator problem.
Passive and active extrapolations have been implemented to improve the accuracy of the
numerical solutions. Passive extrapolation is observed to show quadratic error growth
after a very short period of time. On the other hand, active extrapolation is observed to
show linear error growth for a much longer period of time.
In numerical methods, boundary element method has been widely used to solve
acoustic problems. However, it suffers from certain drawbacks in terms of computational
efficiency. This prevents the boundary element method from being applied to large-scale
problems. This paper presents proposal of a new multiscale technique, coupled with
boundary element method to speed up numerical calculations. Numerical example is
given to illustrate the efficiency of the proposed method. The solution of the proposed
method has been validated with conventional boundary element method and the proposed
method is indeed faster in computation.
Monthly data about oil production at several drilling wells is an example of
spatio-temporal data. The aim of this research is to propose nonlinear spatio-temporal
model, i.e. Feedforward Neural Network - VectorAutoregressive (FFNN-VAR) and FFNN
- Generalized Space-Time Autoregressive (FFNN-GSTAR), and compare their forecast
accuracy to linearspatio-temporal model, i.e. VAR and GSTAR. These spatio-temporal
models are proposed and applied for forecasting monthly oil production data at three
drilling wells in East Java, Indonesia. There are 60 observations that be divided to two
parts, i.e. the first 50 observations for training data and the last 10 observations for
testing data. The results show that FFNN-GSTAR(11) and FFNN-VAR(1) as nonlinear
spatio-temporal models tend to give more accurate forecast than VAR(1) and GSTAR(11)
as linear spatio-temporal models. Moreover, further research about nonlinear spatiotemporal
models based on neural networks and GSTAR is needed for developing new
hybrid models that could improve the forecast accuracy.
In irradiation process, instead of traverse on the targeted cells, there is side
effect happens to non-targeted cells. The targeted cells that had been irradiated with
ionizing radiation emits damaging signal molecules to the surrounding and then, dam-
age the bystander cells. The type of damage considered in this work is the number of
double-strand breaks (DSBs) of deoxyribonucleic acid (DNA) in cell’s nucleus. By us-
ing mathematical approach, a mechanistic model that can describe this phenomenon is
developed based on a structured population approach. Then, the accuracy of the model
is validated by its ability to match the experimental data. The Particle Swarm (PS)
optimization is employed for the data fitting procedure. PS optimization searches the
parameter value that minimize the errors between the model simulation data and exper-
imental data. It is obtained that the mathematical modelling proposed in this paper is
strongly in line with the experimental data.
Subsea cable laying is a risky and challenging operation faced by engineers, due to many uncertainties arise during the operation. In order to ensure that subsea cables are laid out diligently, the analysis of subsea cable tension during the laying operation is crucial. This study focuses on the fatigue failure of cables that will cause large hang-off loads based on catenary configuration after laying operation. The presented problem was addressed using mathematical modelling with consideration for a number of defining parameters, which include external forces such as current velocity and design parameters such as cable diameter. There were two types of subsea cable tension analyses studied: tensional analysis of catenary configurations and tensional analysis of lazy wave configurations. The latter involved a buoyancy module that was incorporated in the current catenary configuration that reduced subsea cable tension and enhanced subsea cable lifespan. Both analyses were solved using minimization through the gradient- based approach concerning on the tensional analysis of the subsea cable in different configurations. Lazy wave configurations were shown to successfully reduce cable tension, especially at the hang-off section.
Riverbank filtration (RBF) system is a surface water technology that is based
on the natural treatment of filtration instead of the use of chemicals, to pre-treat sur-
face water and provides public water supplies. Hydraulic conductivity value is one of the
significant factors affecting the water quality in RBF systems. In this article, an analyti-
cal modelling is developed to investigate the effect of this parameter on one dimensional
contaminant transport in RBF system. The model is solved by using Green’s function
approach. The model is applied for the first RBF system conducted in Malaysia. Gener-
ally, the results show that increasing the hydraulic conductivity value lead to an increase
in contaminant concentration in pumping well area.
1Malaysia
2 (UKM)43600 Bangi, Selangor, Malaysia
∗Corresponding author:
Numerous studies have linked biodiversity with zoonotic disease control. However, researchers have warned against simply believing that the increase in biodiversity can reduce the infection disease in the community. They proposed that amplification effect (increase in biodiversity accompanied by an increase in disease prevalence) might sometimes occur. Thus, we formulated a deterministic model to consider the impact of an amplification or dilution agent on the SNV transmission in the deer mouse population. Bifurcation analysis was carried out to examine the combined influences of the environmental carrying capacity, the interspecific competition strength and the impact of amplification or dilution agent on the deer mouse population. Our results showed that the system with amplification agent required a higher carrying capacity or stronger interspecific strength to compensate for its amplification effect in suppressing the SNV prevalence; this situation explains the lack of reduction in SNV prevalence despite the presence of high biodiversity in some empirical studies. In this study, we highlight the importance of investigating the roles of the additional species in an assemblage to better understand their relationship with the SNV prevalence in deer mouse population.
The constraint of two ordered extreme minima random variables when one
variable is consider to be stochastically smaller than the other one has been carried
out in this article. The quantile functions of the probability distribution have been
used to establish partial ordering between the two variables. Some extensions and
generalizations are given for the stochastic ordering using the important of sign of the
shape parameter.
Invadopodia are finger-like protrusions located at subcellular membrane which can lead to cancer cell invasion. The formation of invadopodia involves several steps such as actin polymerizations, degradation of extracellular matrix which produce ligand and signal stimulation that is occurred from the binding of ligand with epidermal growth factor receptor. In this paper, a mathematical model of signal transduction is investigated. Both signal and ligand are represented by Laplace equation with Dirichlet boundary condition for each region. The cell membrane is treated as free boundary surface to separate any activity that occurred in intracellular and extracellular regions. The motion of the interface is taken as gradient of interior signal and the cell membrane is set as zero level set function. The problem is solved numerically using finite difference scheme of upwind, interpolation and extrapolation methods. The results showed that the formation of invadopodia is formed when protrusions exist on the cell membrane.
The hydromagnetic mixed convection flow of Cassonnano fluid under the influence of chemical reaction,thermal radiation and heat generation or absorption is investigated. The flow is induced due to unsteady nonlinearly stretching sheet saturated in a porous medium. The governing nonlinear coupled partial differential equations are converted into the system of coupled ordinary differential equations using similarity transformations and then solved numerically via Keller box method. The effects of pertinent parameters on velocity, temperature and nanoparticles concentration as well as wall shear stress, heat and mass transfer rate are analyzed and displayed graphically. The results for skin friction coefficient and local Nusselt number are compared with previously published work and found to be in good agreement. Findings demonstrate that increase in Casson parameter enhanced the friction factor and heat transfer rate. It is noticed that the heat transfer rate is declined with increment in Brownian motion and thermophoresis parameters. The nanoparticles concentration is seen to be higher in generative chemical reaction and opposite effect is observed in destructive chemical reaction. Increase in unsteadiness parameter decreased the fluid velocity, temperature and nanoparticles concentration. The magnitude of wall shear stress is also reduced with increase in unsteadiness and porous medium parameters.
The well-known geostatistics method (variance-reduction method) is commonly used to determine the optimal rain gauge network. The main problem in geostatistics method to determine the best semivariogram model in order to be used in estimating the variance. An optimal choice of the semivariogram model is an important point for a good data evaluation process. Three different semivariogram models which are Spherical, Gaussian and Exponential are used and their performances are compared in this study. Cross validation technique is applied to compute the errors of the semivariograms. Rain-fall data for the period of 1975 – 2008 from the existing 84 rain gauge stations covering the state of Johor are used in this study. The result shows that the exponential model is the best semivariogram model and chosen to determine the optimal number and location of rain gauge station.
Logging activity is one of the most important activities for tropical countries
including Malaysia, as it produces quality trees for papers. One of the important tree
species is the Acacia Mangium which it produces a soft tree for papermaking enterprises.
The papers are exported to Europe and countries which have high demand for paper
due to the rapid development of the printing industry. Thus we analyzed the height for
individual trees. We investigate the maximum height of the trees from 1990 to 2006
and we fit the data using extreme value model. Some of the data are missing and three
imputation methods we used to solve this problem.
It has come to attention that Malaysia have been aiming to build its own
nuclear power plant (NPP) for electricity generation in 2030 to diversify the national
energy supply and resources. As part of the regulation to build a NPP, environmental
risk assessment analysis which includes the atmospheric dispersion assessment has to
be performed as required by the Malaysian Atomic Energy Licensing Board (AELB)
prior to the commissioning process. The assessment is to investigate the dispersion of
radioactive effluent from the NPP in the event of nuclear accident. This article will focus
on current development of locally developed atmospheric dispersion modeling code
based on Gaussian Plume model. The code is written in Fortran computer language
and has been benchmarked to a readily available HotSpot software. The radionuclide
release rate entering the Gaussian equation is approximated to the value found in the
Fukushima NPP accident in 2011. Meteorological data of Mersing District, Johor of
year 2013 is utilized for the calculations. The results show that the dispersion of radionuclide
effluent can potentially affect areas around Johor Bahru district, Singapore
and some parts of Riau when the wind direction blows from the North-northeast direction.
The results from our code was found to be in good agreement with the one
obtained from HotSpot, with less than 1% discrepancy between the two.
In this paper we consider a harvesting model of predator-prey fishery in which
the prey is directly infected by some external toxic substances. The toxic infection is
indirectly transmitted to the predator during the feeding process. The model is a modified
version from the classic Lotka-Volterra predator-prey model. The stability and bifurcation
analyses are addressed. Numerical simulations of the model are performed and bifurcation
diagrams are studied to investigate the dynamical behaviours between the predator and
the prey. The effects of toxicity and harvesting on the stability of steady states found in
the model are discussed.
The box plot has been used for a very long time since 70s in checking the existence
of outliers and the asymmetrical shape of data. The existing box plot is constructed
using five values of statistics calculated from either the discrete or continous data. Many
improvement of box plots have deviated from the elegant and simplier approach of exploratory
data analysis by incorporating many other statistic values resulting the turning
back of the noble philosophy behind the creation of box plot. The modification using
range value with the minimum and maximum values are being incorporated to suit the
need of selected discrete distribution when outliers is not an important criteria anymore.
The new modification of box plot is not based on the asymmetrical shape of distribution
but more on the spreading and partitioning data into range measure. The new propose
name for the box plot with only three values of statistics is called range-box plot.
Simulation is used to measure the robustness and the efficiency of the forecasting
techniques performance over complex systems. A method for simulating multivariate
time series was presented in this study using vector autoregressive base-process. By
applying the methodology to the multivariable meteorological time series, a simulation
study was carried out to check for the model performance. MAPE and MAE performance
measurements were used and the results show that the proposed method that consider
persistency in volatility gives better performance and the accuracy error is six time smaller
than the normal hybrid model.
Subsea cable laying process is a difficult task for an engineer due to many
uncertain situations which occur during the operation. It is very often that the cable being
laid out is not perfectly fit on the route being planned, which results in the formation of
slack. In order to control wastages during installation, the slack needs to be minimized
and the movement of a ship/vessel needs to be synchronized with the cable being laid out.
The current problem was addressed using a mathematical model by considering a number
of defining parameters such as the external forces, the cable properties and geometry. Due
to the complexity, the model is developed for a steady-state problem assuming velocity
of the vessel is constant, seabed is flat and the effect of wind and wave is insignificant.
Non-dimensional system is used to scale the engineering parameters and grouped them
into only two main parameters which are the hydrodynamic drag of the fluid and the
bending stiffness of the cable. There are two solutions generated in this article; numerical
and asymptotic solutions. The result of these solutions suggests that the percentage of
slack can be reduced by the increase of the prescribed cable tension, and also the increase
in either the drag coefficient of the sea water or the bending stiffness of the cable, similarly
will result in lower slack percentage
Dengue is a mosquito-borne disease caused by virus and found mostly in urban and semi-urban areas, in many regions of the world. Female Aedes mosquitoes, which usually bite during daytime, spread the disease. This flu-like disease may progress to severe dengue and cause fatality. A generic reaction-diffusion model for transmission of mosquito-borne diseases was proposed and formulated. The motivation is to explore the ability of the generic model to reproduce observed dengue cases in Borneo, Malaysia. Dengue prevalence in four districts in Borneo namely Kuching, Sibu, Bintulu and Miri are compared with simulations results obtained from the temporal and spatio-temporal generic model respectively. Random diffusion of human and mosquito populations are taken into account in the spatio-temporal model. It is found that temporal simulations closely resemble the general behavior of actual prevalence in the three locations except for Bintulu. The recovery rate in Bintulu district is found to be the lowest among the districts, suggesting a different dengue serotype may be present. From observation, the temporal generic model underestimates the recovery rate in comparison to the spatio-temporal generic model.