Abstract: The subcellular organelles called oil bodies (OBs) are lipid-filled quasi-spherical droplets produced from the endoplasmic reticulum (ER) and then released into the cytoplasm during seed development. It is believed that an OB grows by coalescence with other OBs and that its stability depends on the composition of oleosins, major proteins inserted in the hemi membrane that covers OBs. In this study, we measured the OB-volume distribution from different genotypes of A. thaliana after 7, 8, 9, 10 and 11 days of seed development. In order to test the hypothesis of OBs dynamics, we developed a simple mathematical model using non-linear differential equations inspired from the theory of coagulation. The model describes the evolution of OB-volume distribution during the first steps of seed development by taking into consideration the production of OBs, the increase of triacylglycerol volume to be stored, and the growth by coalescence of OBs. Fitted parameters values show an increase in the OB production and coalescence rates in A. thaliana oleosin mutants compared to wild type.
Abstract: This paper employs a new approach to regulate the
blood glucose level of type I diabetic patient under an intensive
insulin treatment. The closed-loop control scheme incorporates
expert knowledge about treatment by using reinforcement learning
theory to maintain the normoglycemic average of 80 mg/dl and the
normal condition for free plasma insulin concentration in severe
initial state. The insulin delivery rate is obtained off-line by using Qlearning
algorithm, without requiring an explicit model of the
environment dynamics. The implementation of the insulin delivery
rate, therefore, requires simple function evaluation and minimal
online computations. Controller performance is assessed in terms of
its ability to reject the effect of meal disturbance and to overcome the
variability in the glucose-insulin dynamics from patient to patient.
Computer simulations are used to evaluate the effectiveness of the
proposed technique and to show its superiority in controlling
hyperglycemia over other existing algorithms
Abstract: Along with forward supply chain organization needs
to consider the impact of reverse logistics due to its economic
advantage, social awareness and strict legislations. In this paper, we
develop a system dynamics framework for a closed-loop supply
chain with fuzzy demand and fuzzy collection rate by incorporating
product exchange policy in forward channel and various recovery
options in reverse channel. The uncertainty issues associated with
acquisition and collection of used product have been quantified using
possibility measures. In the simulation study, we analyze order
variation at both retailer and distributor level and compare bullwhip
effects of different logistics participants over time between the
traditional forward supply chain and the closed-loop supply chain.
Our results suggest that the integration of reverse logistics can reduce
order variation and bullwhip effect of a closed-loop system. Finally,
sensitivity analysis is performed to examine the impact of various
parameters on recovery process and bullwhip effect.
Abstract: This is the second part of the paper. It, aside from the
core subroutine test reported previously, focuses on the simulation of
turbulence governed by the full STF Navier-Stokes equations on a
large scale. Law of the wall is found plausible in this study as a model
of the boundary layer dynamics. Model validations proceed to
include velocity profiles of a stationary turbulent Couette flow, pure
sloshing flow simulations, and the identification of water-surface
inclination due to fluid accelerations. Errors resulting from the
irrotational and hydrostatic assumptions are explored when studying
a wind-driven water circulation with no shakings. Illustrative
examples show that this numerical strategy works for the simulation
of sloshing-shear mixed flow in a 3-D rigid rectangular base tank.
Abstract: Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.
Abstract: Energetic and structural results for ethanol-water mixtures as a function of the mole fraction were calculated using Monte Carlo methodology. Energy partitioning results obtained for equimolar water-ethanol mixture and ether organic liquids are compared. It has been shown that at xet=0.22 the RDFs for waterethanol and ethanol-ethanol interactions indicated strong hydrophobic interactions between ethanol molecules and the local structure of solution is less structured at this concentration as at ether ones. Results obtained for ethanol-water mixture as a function of concentration are in good agreement with the experimental data.
Abstract: In this experimental work, we have shown that the
geometric shape of the grooves (furrows) plays an important role in
sediment dynamics. In addition, the rheological behaviour of solid
discharge does not depend only on the velocity discharge but also on
the geometric shape.
Abstract: We consider the topological entropy of maps that in
general, cannot be described by one-dimensional dynamics. In particular,
we show that for a multivalued map F generated by singlevalued
maps, the topological entropy of any of the single-value map bounds the topological entropy of F from below.
Abstract: Multi-loop (De-centralized) Proportional-Integral-
Derivative (PID) controllers have been used extensively in process
industries due to their simple structure for control of multivariable
processes. The objective of this work is to design multiple-model
adaptive multi-loop PID strategy (Multiple Model Adaptive-PID)
and neural network based multi-loop PID strategy (Neural Net
Adaptive-PID) for the control of multivariable system. The first
method combines the output of multiple linear PID controllers,
each describing process dynamics at a specific level of operation.
The global output is an interpolation of the individual multi-loop
PID controller outputs weighted based on the current value of the
measured process variable. In the second method, neural network
is used to calculate the PID controller parameters based on the
scheduling variable that corresponds to major shift in the process
dynamics. The proposed control schemes are simple in structure with
less computational complexity. The effectiveness of the proposed
control schemes have been demonstrated on the CSTR process,
which exhibits dynamic non-linearity.
Abstract: In this paper we study a system composed by carbon
nanotube (CNT) and bundle of carbon nanotube (BuCNT) interacting
with a specific fatty acid as molecular probe. Full system is
represented by open nanotube (or nanotubes) and the linoleic acid
(LA) relaxing due the interaction with CNT and BuCNT. The LA has
in his form an asymmetric shape with COOH termination provoking
a close BuCNT interaction mainly by van der Waals force field. The
simulations were performed by classical molecular dynamics with
standard parameterizations.
Our results show that these BuCNT and CNT are dynamically
stable and it shows a preferential interaction position with LA
resulting in three features: (i) when the LA is interacting with CNT
and BuCNT (including both termination, CH2 or COOH), the LA is
repelled; (ii) when the LA terminated with CH2 is closer to open
extremity of BuCNT, the LA is also repelled by the interaction
between them; and (iii) when the LA terminated with COOH is
closer to open extremity of BuCNT, the LA is encapsulated by the
BuCNT. These simulations are part of a more extensive work on
searching efficient selective molecular devices and could be useful to
reach this goal.
Abstract: As wireless sensor networks are energy constraint networks
so energy efficiency of sensor nodes is the main design issue.
Clustering of nodes is an energy efficient approach. It prolongs the
lifetime of wireless sensor networks by avoiding long distance communication.
Clustering algorithms operate in rounds. Performance of
clustering algorithm depends upon the round time. A large round
time consumes more energy of cluster heads while a small round
time causes frequent re-clustering. So existing clustering algorithms
apply a trade off to round time and calculate it from the initial
parameters of networks. But it is not appropriate to use initial
parameters based round time value throughout the network lifetime
because wireless sensor networks are dynamic in nature (nodes can be
added to the network or some nodes go out of energy). In this paper
a variable round time approach is proposed that calculates round
time depending upon the number of active nodes remaining in the
field. The proposed approach makes the clustering algorithm adaptive
to network dynamics. For simulation the approach is implemented
with LEACH in NS-2 and the results show that there is 6% increase
in network lifetime, 7% increase in 50% node death time and 5%
improvement over the data units gathered at the base station.
Abstract: In recent years, tuned mass damper (TMD) control systems for civil engineering structures have attracted considerable attention. This paper emphasizes on the application of particle swarm application (PSO) to design and optimize the parameters of the TMD control scheme for achieving the best results in the reduction of the building response under earthquake excitations. The Integral of the Time multiplied Absolute value of the Error (ITAE) based on relative displacement of all floors in the building is taken as a performance index of the optimization criterion. The problem of robustly TMD controller design is formatted as an optimization problem based on the ITAE performance index to be solved using the PSO technique which has a story ability to find the most optimistic results. An 11- story realistic building, located in the city of Rasht, Iran is considered as a test system to demonstrate effectiveness of the proposed method. The results analysis through the time-domain simulation and some performance indices reveals that the designed PSO based TMD controller has an excellent capability in reduction of the seismically excited example building.
Abstract: In this paper parametric analytical studies have been carried out to examine the intrinsic flow physics pertaining to the liftoff time of solid propellant rockets. Idealized inert simulators of solid rockets are selected for numerical studies to examining the preignition chamber dynamics. Detailed diagnostic investigations have been carried out using an unsteady two-dimensional k-omega turbulence model. We conjectured from the numerical results that the altered variations of the igniter jet impingement angle, turbulence level, time and location of the first ignition, flame spread characteristics, the overall chamber dynamics including the boundary layer growth history are having bearing on the time for nozzle flow chocking for establishing the required thrust for the rocket liftoff. We concluded that the altered flow choking time of strap-on motors with the pre-determined identical ignition time at the lift off phase will lead to the malfunctioning of the rocket. We also concluded that, in the light of the space debris, an error in predicting the liftoff time can lead to an unfavorable launch window amounts the satellite injection errors and/or the mission failures.
Abstract: Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.
Abstract: Simultaneous transient conduction and radiation heat
transfer with heat generation is investigated. Analysis is carried out
for both steady and unsteady situations. two-dimensional gray
cylindrical enclosure with an absorbing, emitting, and isotropically
scattering medium is considered. Enclosure boundaries are assumed
at specified temperatures. The heat generation rate is considered
uniform and constant throughout the medium. The lattice Boltzmann
method (LBM) was used to solve the energy equation of a transient
conduction-radiation heat transfer problem. The control volume finite
element method (CVFEM) was used to compute the radiative
information. To study the compatibility of the LBM for the energy
equation and the CVFEM for the radiative transfer equation, transient
conduction and radiation heat transfer problems in 2-D cylindrical
geometries were considered. In order to establish the suitability of the
LBM, the energy equation of the present problem was also solved
using the the finite difference method (FDM) of the computational
fluid dynamics. The CVFEM used in the radiative heat transfer was
employed to compute the radiative information required for the
solution of the energy equation using the LBM or the FDM (of the
CFD). To study the compatibility and suitability of the LBM for the
solution of energy equation and the CVFEM for the radiative
information, results were analyzed for the effects of various
parameters such as the boundary emissivity. The results of the LBMCVFEM
combination were found to be in excellent agreement with
the FDM-CVFEM combination. The number of iterations and the
steady state temperature in both of the combinations were found
comparable. Results are found for situations with and without heat
generation. Heat generation is found to have significant bearing on
temperature distribution.
Abstract: The analysis to detect arrhythmias and life-threatening
conditions are highly essential in today world and this analysis
can be accomplished by advanced non-linear processing methods
for accurate analysis of the complex signals of heartbeat dynamics.
In this perspective, recent developments in the field of multiscale
information content have lead to the Microcanonical Multiscale
Formalism (MMF). We show that such framework provides several
signal analysis techniques that are especially adapted to the
study of heartbeat dynamics. In this paper, we just show first hand
results of whether the considered heartbeat dynamics signals have
the multiscale properties by computing local preticability exponents
(LPEs) and the Unpredictable Points Manifold (UPM), and thereby
computing the singularity spectrum.
Abstract: The ubiquitous payment problems within construction
industry of China are notoriously hard to be resolved, thus lead to a
series of impacts to the industry chain. Among of them, the most direct
result is affecting the normal operation of contractors negatively. A
wealth of research has already discussed reasons of the payment
problems by introducing a number of possible improvement strategies.
But the causalities of these problems are still far from harsh reality. In
this paper, the authors propose a model for cash flow system of
construction projects by introducing System Dynamics techniques to
explore causal facets of the payment problem. The effects of payment
arrears on both cash flow and profitability of project are simulated into
four scenarios by using data from real projects. Simulating results
show visible clues to help contractors quantitatively determining the
consequences for the construction project that arise from payment
delay.
Abstract: Video sensor networks operate on stringent requirements
of latency. Packets have a deadline within which they have
to be delivered. Violation of the deadline causes a packet to be
treated as lost and the loss of packets ultimately affects the quality
of the application. Network latency is typically a function of many
interacting components. In this paper, we propose ways of reducing
the forwarding latency of a packet at intermediate nodes. The
forwarding latency is caused by a combination of processing delay
and queueing delay. The former is incurred in order to determine the
next hop in dynamic routing. We show that unless link failures in a
very specific and unlikely pattern, a vast majority of these lookups
are redundant. To counter this we propose source routing as the
routing strategy. However, source routing suffers from issues related
to scalability and being impervious to network dynamics. We propose
solutions to counter these and show that source routing is definitely
a viable option in practical sized video networks. We also propose a
fast and fair packet scheduling algorithm that reduces queueing delay
at the nodes. We support our claims through extensive simulation on
realistic topologies with practical traffic loads and failure patterns.
Abstract: The present models and simulation algorithms of intracellular stochastic kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even for small prokaryotic cells. In this work a mathematical treatment of diffusion that can be incorporated in a stochastic algorithm simulating the dynamics of a reaction-diffusion system is presented. The movement of a molecule A from a region i to a region j of the space is represented as a first order reaction Ai k- ! Aj , where the rate constant k depends on the diffusion coefficient. The diffusion coefficients are modeled as function of the local concentration of the solutes, their intrinsic viscosities, their frictional coefficients and the temperature of the system. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the intrinsic reaction kinetics and diffusion dynamics. To demonstrate the method the simulation results of the reaction-diffusion system of chaperoneassisted protein folding in cytoplasm are shown.