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It is also easier to learn compared to C programming language. Instead, it requires the program to
exit kernel in order to complete the data transfer. Model for coupled tr Page 166 and 167: 152
Chapter 7. The impact factor is one of the many elements that determine the quality of a journal.
Since the energy calculation can be done on arbitrary atom independently, the 31 data structure does
not require specific array formation as long as the coordinate (x, y, z) can be fetched in one burst.
Fullscreen Sharing Deliver a distraction-free reading experience with a simple link. Similar to the
Atom Coordinate data structure, Maps data structure is also used to calculate energy. Decision made
is to reduce complexity when implementing it on different parallel accelerators. Therefore, one way
to optimise memory access is by combining map information for each atom coordinate so they can
be fetched together. 3.3 Execution Procedures Table 3-1 shows all files that are required to run
hppNeuroDock. Map (.map) files inside Maps directory are automatically generated by AutoGrid.
Molecule (.pdbqt) files inside Inputs directory and parameter (.gpd,.dpf and.fld) files in the
Parameters directory are generated using AutoDockTools. The result is RMSD of the two ligands in
angstroms (). Numerical simulations have also been investigated on the PCF directional coupler
structure to validate experimental result and on the microfluidic optical fiber device to rapidly find
optimal fabrication-sensitivity design. Add Links Send readers directly to specific items or pages
with shopping and web links. AutoDock 4 is shown in magenta and hppNeuroDock is in cyan. For
translational genes, they are bounded within the lowest and highest grid coordinate. Adobe Express
Go from Adobe Express creation to Issuu publication. These can be formally solicited, informally
solicited or unsolicited. AutoDock is the main focus of this dissertation but AutoGrid is still
important. LFSR stands for Linear Feedback Shift Register is an efficient pseudo-random numbers
generator commonly used in FPGA (Alfke, 1996). The two classes are inherited from Dock and
GeneticAlgorithm classes respectively. Video Say more by seamlessly including video within your
publication. Furthermore, in common scenario, initialisation time is still far below the runtime that
can last for hours. The data is rearranged so the device can fetch as much data as possible in one
DRAM burst. HIDiC experiments: B Page 216 and 217: 202 Chapter 9. Hardware Processor
Graphics Memory Specifications 2.3GHz Intel Core i7 (i7-3615QM) NVIDIA GeForce GT 650M
1GB 8GB 1600MHz DDR3 Table 5-2: Software used for benchmark on Apple OS X version 10.8.4
Mountain Lion. Software Python NumPy PyOpenCL Version 2.7.3 1.7.1 2013.1 40 Table 5-3, Table
5-4 and Table 5-5 present the hardware specifications in more detail. After acquiring lowest free
energy from the population over number of generations, both energy and the conformation of the
molecule are then analysed. HIDiC experiments: B Page 204 and 205: 190 Chapter 9. You may
achieve amazing heights in business by making use of a proposal. Model for coupled tr Page 146 and
147: 132 Chapter 7. One of them can be seen on the figure as coloured in purple and located slightly
below the ligand. You need to assess all these factors before you make your final call.
Whereas, internal energy is calculated using semiempirical free energy function and information
taken from Bond and NonBond classes. Positive values indicate the improvement made by having
settler population.. 20. Thermodynamic prope Page 292 and 293: 278 Appendix A. Figure 3-4 shows
the entire execution flow except the rightmost column should be all in Python. Introduction 1.6.1
Jou Page 23 and 24: Chapter 2 Second law analysis 1 Cla Page 25 and 26: 2.3 Improving the Second
law effici Page 27: 2.3 Improving the Second law effici Page 30 and 31: 16 Chapter 3. Embed Host
your publication on your website or blog with just a few clicks. Meaning, the support for portable
computer with short runtime while providing desirable result is important. You need to keep in mind
all the points necessary for your company. With complete dock object that generates molecular pose
and calculates energy, the control is handed over to optimisation object. The method is also known as
nomadsettler genetic algorithm. It includes both nomad and settler populations iterated through
predefined number of generations. The difference could occur because of mutation happening during
the process of inheritance. R OrdLogit Interactive visualization of ordered logistic regression. A
routine has been developed that calculates the thermal and molar fluxes through the interface region,
based on input values for the boundary conditions, or driving forces. At times when feeling burned
out, I’d go hiking or travel to a distant town. Figure 3-2: DockOpenCL class diagram inherited from
Dock class. 28 Figure 3-3: GeneticAlgorithmOpenCL class diagram inherited from GeneticAlgorithm
class. Benchmarking is performed on sequential Python using CPU, parallel PythonOpenCL using
GPU and parallel Python-OpenCL using CPU. It has also been demonstrated as a potential reusable
and label-less PCF biosensor platform. Electrical heaters with a maximum duty of 25 kW will be
used as reboilers. Model for coupled tr Page 154 and 155: 140 Chapter 7. Model for coupled tr Page
150 and 151: 136 Chapter 7. This awesome gallery listed under Proposal Templates category.
Thermodynamic prope Page 278 and 279: 264 Appendix A. Statistics Make data-driven decisions to
drive reader engagement, subscriptions, and campaigns. Computer Physics Communications, 79,
pp.111-14. Khronos Group, 2012. The idea is similar to epigenetics (Weinhold, 2006) that takes other
factors outside DNA sequence to interfere gene function. However, why use a template when you
can write your entire manuscript on SciSpace, auto format it as per NTU Thesis's guidelines and
download the same in Word, PDF and LaTeX formats. Having the opportunity to present and obtain
feedback from individuals from different fields helped me realise how certain ideas can be made
simpler to reach a larger audience.”. In Parallel and Distributed Systems (ICPADS), 2012 IEEE 18th
International Conference on. It is integrated with Python Molecular Viewer (PMV) to visualise the
molecules in three-dimensional form.
The grid segmentation of rigid protein is used by AutoDock to calculate intermolecular energy.
Furthermore, data that is shared among work items within a same workgroup can be accessed
efficiently by avoiding traffic congestion to global memory. After signing up, you would need to
import your existing references from Word or Bib file to SciSpace. To get the closest estimation
value for an atom inside a grid box, AutoDock uses three-dimensional linear or trilinear interpolation
(Morris et al., 1998). Following are the formulas used to get approximated energy of an atom at
coordinate,, inside a grid box from 0, 0, 0 to 1, 1, 1 shown in Figure 2-3 (Steve, 1994). Python-
OpenCL GPU and Python-OpenCL CPU runtimes collect the data using parallel Python-OpenCL
implementation and run on GPU and CPU respectively. The theoretical work concerns the further
development of a model for the simultaneous transfer of mass and thermal energy, based on the
theory of irreversible thermodynamics. The highest speedup achieved within each table is highlighted
in cyan. The result is RMSD of the two ligands in angstroms (). Computational Chemistry, 16,
pp.2785-91. Tsai, C.S., 2002. An Introduction to Computational Biochemistry. Molecular docking is
a subset of molecular modelling that produces, alters, computes and estimates molecular formation
together with estimating related parameters in silico. LFSR method for random number generator is
used by sequential Python implementation only. Calcula Page 249 and 250: 10.4 Instrumentation 235
Figure 10. Using following example, the real time is 3.193 seconds and runtime is 1.39 seconds. So
the initialisation time is 1.803 seconds. Running. To find a good proposal, you do not need to shell
big money. The method is also known as nomadsettler genetic algorithm. Instead of using kernel
code, PyOpenCL provides parallel algorithms that can be executed from device side; some of them
are elementwise expression evaluation (map), sums and counts (reduce), prefix sums (scan) and
sorting (radix sort) (Klckner, 2013b). This dissertation introduces additional parameters to enable or
disable accelerator, to select different target device and to set genetic algorithm properties like
community size, population size and number of generations. Manual: User is prompted with the list
of available devices. AutoGrid prepares all ligand and protein information. I enjoy. It started as a
place for sharing programming-related knowledge and. Of course, the simulation can only provide
suggestion to scientists for further evaluation. 38 The. Video Say more by seamlessly including video
within your publication. The methods have been used and proven since AutoDock 3 (Morris et al.,
1998). Figure 1-2 shows the entire process when using AutoDock suite. Help Center Here you'll find
an answer to your question. Tool like Open Babel ( ) (O'Boyle et al., 2011) is useful to convert the
files from one format to another. Most addition is implemented in OpenCL files located inside
OpenCL directory and written in C, they are Dock.cl and GeneticAlgorithm.cl. The functions inside
the files are computationally intensive. At the population size 32, Python-OpenCL CPU performs
significantly better than the projected linear trend. 43 500. As Python and C have a same way of
allocating array in main memory, which in row-major order, arranging required data one to another in
a row manner can speed up data transfer. Conformations with negative free energy attract each other
to form a firm complex. Then SciSpace would allow you to download your references in NTU Thesis
Endnote style according to Elsevier guidelines.
HIDiC experiments: B Page 198 and 199: 184 Chapter 9. PyMOL is used to visualise the three-
dimensional structure of both HIV-1 and Indinavir. With population size higher than 256, the both
devices perform quite similarly. Below that, it performs slower because the GPU cores are not fully
utilised. Looking from the perspective of the whole protein size, the deviation of hppNeuroDock
from the AutoDock 4 result is quite minor. GPU performs slower in small population size (lower than
384) because of the cores are not fully utilised. Model for coupled tr Page 154 and 155: 140 Chapter
7. Statistics Make data-driven decisions to drive reader engagement, subscriptions, and campaigns.
The two OpenCL classes have extra fields for OpenCL handlers (like context, queue and program)
plus device buffers. Improving the effici Page 130 and 131: 116 Chapter 6. Following time
command returns overall execution time taken by python. Furthermore, data that is shared among
work items within a same workgroup can be accessed efficiently by avoiding traffic congestion to
global memory. So, for hppNeuroDock, only some parameters need to be updated on top of existing
dpf file, they are OpenCL for accelerator to use, CPU for device type, 10000 for community size,
150 for population size and 200 for number of generations. Each individual in a population has
capability to inherit its traits to the next generation. Heterogeneous parallel program using OpenCL
wrapper, PyOpenCL, has been successfully tested as well. HIDiC experiments: B Page 230 and 231:
216 Chapter 9. Another important model parameter is the number of control volumes that is used to
represent the films. The effect of the interface resistances on the calculation results was relatively
small. The impact factor is one of the many elements that determine the quality of a journal. Lou Pei-
Jen receives 2023 National Excellent Teacher Award more Current Spotlights Inauguration of the
Office of Future NTU Initiatives at National Taiwan University Nobel Laureate Hiroshi Amano's
Lecture Marks the Beginning of NTU Royal Palm Lecture Series Opening Ceremony for the 112th
Academic Year - Welcoming New Students to Become Part of the NTU Family Vice President Shan-
Chwen Chang was awarded the Third Class Order of Brilliant Star Congratulations! Prof. Therefore,
both NumPy and PyOpenCL modules are required for the implementation. Table 2-1: Comparison
between nomad and settler parameters showing that nomad population has more vibrant individuals
compared to settler population. Initialisation time can be broken down into Python setup time,
docking object instantiation, and for parallel execution, it includes both OpenCL compilation and
sending computational data from host to device global memory. It also provides design
considerations, implementation limitation and link to acquire the source code. HIDiC experiments: B
Page 226 and 227: 212 Chapter 9. The parameters are stored inside docking parameter file (.dpf).
Among them there are settings to tell which map files to use, where is the centre of ligand, which
are the flexible portions of the protein, what method of genetic algorithm to use and how many
iterations to run. Topics Quantum Electron., vol. 18, no. 4, pp. 1293-1297, 2012. It includes both
nomad and settler populations iterated through predefined number of generations. Table 5-9:
Sequential Python runtime (in seconds) using CPU based on different population sizes and numbers
of generations. Energy coefficient (.dat) file is provided by AutoDock. Add Links Send readers
directly to specific items or pages with shopping and web links.
With opposite or random order, the final molecule conformation are not the same. Following
AutoDock 4, this dissertation implements only non-covalent interaction. In order to obtain more
insight into these phenomena, two research directions have been pursued: a theoretical one and an
experimental one. The implementation of Python-OpenCL on top of hppNeuroDock has been tested
successfully. Model for coupled tr Page 160 and 161: 146 Chapter 7. Firstly, original molecule
coordinates need to be transformed into new coordinates as candidate binding mode or pose using
individual genes. There are two components, the random number as an array of binaries and a
custom logic. Lamarckian genetic algorithm integrates local search optimisation method to the
traditional Darwinian genetic algorithm (Morris et al., 1998). Instead of using either of them, this
dissertation introduces new model of genetic algorithm called historical genetic algorithm or nomad-
settler genetic algorithm. Using HIV-1 protease for the protein and Indinavir as the ligand,
hppNeuroDock produces ligand conformation with RMSD 1.53 deviated from AutoDock 4. The file
format downloaded from the sites can be different. This implementation has 24 dpf files in each
directory. Page 251 and 252: 10.4 Instrumentation 237 They have Page 253 and 254: 10.5
Experiments 239 Electrical dut Page 255 and 256: 10.5 Experiments 241 involve energy Page 257
and 258: 10.6 Conclusions 243 presented. Since the energy calculation can be done on arbitrary atom
independently, the 31 data structure does not require specific array formation as long as the
coordinate (x, y, z) can be fetched in one burst. SPIE 4904, Optical Fiber and Planar Waveguide
Technology II, China, 2002. Using following example, the real time is 3.193 seconds and runtime is
1.39 seconds. So the initialisation time is 1.803 seconds. Running. Thermodynamic prope Page 274
and 275: 260 Appendix A. For example, when you write your paper and hit autoformat, our system
will automatically update your article as per the NTU Thesis citation style. At the end of settler
iteration, the minimum free energy from both nomad and settler populations are reported together
with total runtime. 27 3.2 Python-OpenCL Implementation Python-OpenCL is implemented using
PyOpenCL wrapper that requires all buffers for device to be in NumPy data type. This benchmark is
performed using Apple MacBook Pro Retina (Mid 2012) laptop with following hardware
specifications (Table 5-1) and software versions (Table 5-2). Python Xaringan Chocolate CSS theme
created for the slide-making R package xaringan. R. So in total, the number of generations run is
double of what stated in dpf file. Furthermore, data that is shared among work items within a same
workgroup can be accessed efficiently by avoiding traffic congestion to global memory. Model for
coupled tr Page 156 and 157: 142 Chapter 7. Model for coupled tr Page 158 and 159: 144 Chapter 7.
Add Links Send readers directly to specific items or pages with shopping and web links. As Python
and C have a same way of allocating array in main memory, which in row-major order, arranging
required data one to another in a row manner can speed up data transfer. Computational unit is
focused on arithmetic calculations that require GPU or FPGA with massive arrays of computing
power. Improving the effici Page 136 and 137: 122 Chapter 6. Positive values indicate the
improvement made by having settler population.. 20. In reproduction phase, crossing over is
performed based on the genes from two selected parents.