Abstract: In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.
Abstract: The quantitative study of cell mechanics is of
paramount interest, since it regulates the behaviour of the living cells
in response to the myriad of extracellular and intracellular
mechanical stimuli. The novel experimental techniques together with
robust computational approaches have given rise to new theories and
models, which describe cell mechanics as combination of
biomechanical and biochemical processes. This review paper
encapsulates the existing continuum-based computational approaches
that have been developed for interpreting the mechanical responses of
living cells under different loading and boundary conditions. The
salient features and drawbacks of each model are discussed from both
structural and biological points of view. This discussion can
contribute to the development of even more precise and realistic
computational models of cell mechanics based on continuum
approaches or on their combination with microstructural approaches,
which in turn may provide a better understanding of
mechanotransduction in living cells.
Abstract: Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular / nanoscale models is demonstrated.
Abstract: Wireless sensor networks (WSN) consists of many
sensor nodes that are placed on unattended environments such as
military sites in order to collect important information.
Implementing a secure protocol that can prevent forwarding forged
data and modifying content of aggregated data and has low delay
and overhead of communication, computing and storage is very
important. This paper presents a new protocol for concealed data
aggregation (CDA). In this protocol, the network is divided to
virtual cells, nodes within each cell produce a shared key to send
and receive of concealed data with each other. Considering to data
aggregation in each cell is locally and implementing a secure
authentication mechanism, data aggregation delay is very low and
producing false data in the network by malicious nodes is not
possible. To evaluate the performance of our proposed protocol, we
have presented computational models that show the performance
and low overhead in our protocol.
Abstract: One problem in evaluating recent computational models of human category learning is that there is no standardized method for systematically comparing the models' assumptions or hypotheses. In the present study, a flexible general model (called GECLE) is introduced that can be used as a framework to systematically manipulate and compare the effects and descriptive validities of a limited number of assumptions at a time. Two example simulation studies are presented to show how the GECLE framework can be useful in the field of human high-order cognition research.
Abstract: In order to give high expertise the computer aided
design of mechanical systems involves specific activities focused on
processing two type of information: knowledge and data. Expert rule
based knowledge is generally processing qualitative information and
involves searching for proper solutions and their combination into
synthetic variant. Data processing is based on computational models
and it is supposed to be inter-related with reasoning in the knowledge
processing. In this paper an Intelligent Integrated System is proposed,
for the objective of choosing the adequate material. The software is
developed in Prolog – Flex software and takes into account various
constraints that appear in the accurate operation of gears.
Abstract: A novel methodology has been used to design an
evaporator coil of a refrigerant. The methodology used is through a
complete Computer Aided Design /Computer Aided Engineering
approach, by means of a Computational Fluid Dynamic/Finite
Element Analysis model which is executed many times for the
thermal-fluid exploration of several designs' configuration by an
commercial optimizer. Hence the design is carried out automatically
by parallel computations, with an optimization package taking the
decisions rather than the design engineer. The engineer instead takes
decision regarding the physical settings and initializing of the
computational models to employ, the number and the extension of the
geometrical parameters of the coil fins and the optimization tools to
be employed. The final design of the coil geometry found to be better
than the initial design.
Abstract: The dynamics of Min proteins plays a center role in
accurate cell division. Although the nucleoids may presumably play
an important role in prokaryotic cell division, there is a lack of
models to account for its participation. In this work, we apply the
lattice Boltzmann method to investigate protein oscillation based on a
mesoscopic model that takes into account the nucleoid-s role. We
found that our numerical results are in reasonably good agreement
with the previous experimental results On comparing with the other
computational models without the presence of nucleoids, the
highlight of our finding is that the local densities of MinD and MinE
on the cytoplasmic membrane increases, especially along the cell
width, when the size of the obstacle increases, leading to a more
distinct cap-like structure at the poles. This feature indicated the
realistic pattern and reflected the combination of Min protein
dynamics and nucleoid-s role.
Abstract: Wireless sensor networks (WSN) consists of many sensor nodes that are placed on unattended environments such as military sites in order to collect important information. Implementing a secure protocol that can prevent forwarding forged data and modifying content of aggregated data and has low delay and overhead of communication, computing and storage is very important. This paper presents a new protocol for concealed data aggregation (CDA). In this protocol, the network is divided to virtual cells, nodes within each cell produce a shared key to send and receive of concealed data with each other. Considering to data aggregation in each cell is locally and implementing a secure authentication mechanism, data aggregation delay is very low and producing false data in the network by malicious nodes is not possible. To evaluate the performance of our proposed protocol, we have presented computational models that show the performance and low overhead in our protocol.
Abstract: DNA shuffling is a powerful method used for in vitro
evolute molecules with specific functions and has application in areas
such as, for example, pharmaceutical, medical and agricultural
research. The success of such experiments is dependent on a variety
of parameters and conditions that, sometimes, can not be properly
pre-established. Here, two computational models predicting DNA
shuffling results is presented and their use and results are evaluated
against an empirical experiment. The in silico and in vitro results
show agreement indicating the importance of these two models and
motivating the study and development of new models.