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Hasan al Rasyid 3 years ago
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      manuscript.md

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manuscript.md
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@ -11,17 +11,17 @@ author:
affiliation: "My Other City University" affiliation: "My Other City University"
address: "Hokanomachi, Orenoshi, Orenoken, Japan" address: "Hokanomachi, Orenoshi, Orenoken, Japan"
email: "xxx@myuni.ac.jp" email: "xxx@myuni.ac.jp"
titleSmall: "Paperlighter Example" titleshort: "Paperlighter Example"
authorSmall: "Author One et.al." authorshort: "Author One et.al."
linkDir: | linkDir:
- Figure - Figure
- Output - Output
appendix: | appendix:
- appendix/1 - appendix/1
- appendix/2 - appendix/2
abstract: abstract:
Using \LaTeX\{\} to write papers is concise and convenient. However, for Using \LaTeX{} to write papers is concise and convenient. However, for
writing in life, complicated \LaTeX\{\} style-files (e.g., elegantpaper) writing in life, complicated \LaTeX{} style-files (e.g., elegantpaper)
are difficult to access, or submission style-files (e.g., journal or are difficult to access, or submission style-files (e.g., journal or
conference) are not free indeed. To tackle these problems and satisfy an conference) are not free indeed. To tackle these problems and satisfy an
elegant and straightforward scientific writing, elegant and straightforward scientific writing,
@ -34,11 +34,11 @@ abstract:
--- ---
# Format of the Paperlighter} # Format of the Paperlighter
Format of paperlighter is defined in this section. Format of paperlighter is defined in this section.
## Dimensions}\label{dimensions}} ## Dimensions
The text of the paper has an overall width of The text of the paper has an overall width of
6.75\textasciitilde{}inches, and height of 9.0\textasciitilde{}inches. 6.75\textasciitilde{}inches, and height of 9.0\textasciitilde{}inches.
@ -51,7 +51,7 @@ The paper body should be set in 10\textasciitilde{}point type with a
vertical spacing of 11\textasciitilde{}points. Please use Times typeface vertical spacing of 11\textasciitilde{}points. Please use Times typeface
throughout the text. throughout the text.
## Title}\label{title}} ## Title
The paper title should be set in 14\textasciitilde{}point bold type and The paper title should be set in 14\textasciitilde{}point bold type and
centered between two horizontal rules that are 1\textasciitilde{}point centered between two horizontal rules that are 1\textasciitilde{}point
@ -67,7 +67,7 @@ used to produce this document for an example usage.) The author
information will not be printed unless \texttt{accepted} is passed as an information will not be printed unless \texttt{accepted} is passed as an
argument to the style file. argument to the style file.
## Abstract}\label{abstract}} ## Abstract
The paper abstract should begin in the left column, The paper abstract should begin in the left column,
0.4\textasciitilde{}inches below the final address. The heading 0.4\textasciitilde{}inches below the final address. The heading
@ -318,139 +318,3 @@ Typically, this will include thanks to colleagues who contributed to the
ideas, and to funding agencies and corporate sponsors that provided ideas, and to funding agencies and corporate sponsors that provided
financial support. financial support.
<!--
# Basic properties of protein and nucleic acids
## Basic principle of protein
### Unit structure of protein
There are 4 levels of protein organization:
* Primary structure \
It consists of a chain arrangement/sequence of amino acids that are joined together to make protein. It usually uses abbreviations for the amino and residues. The example in figure (1) is Polypeptide amino.
* Secondary structure \
This is the region within the long protein chains organized into regular structures known as alpha-helices ($\alpha$-helices) and beta sheet.
* Tertiary structure \
Tertiary structure is a description of the way that whole chain from one or several units folds and forms 3-dimensional shape, called domain.
* Fourth order structure \
This structure is formed from several tertiary structure proteins or domains with more complex shape.
![Structure of protein](./Figures/Figure1)
-->
<!--
\begin{figure}[h!]
\centering
\includegraphics[width=0.7\linewidth]{Figure1}
\caption{Structure of protein}
\label{fig:figure1}
\end{figure}
-->
<!--
### Basic motif of protein
There are two types of secondary structure for hydrophobic type:
* $\alpha$-helix\
This is one of common motif in secondary structure of protein. It consists of hydrogen bond with conformation of N-H group donates a hydrogen bond to the C=O group of amino acid. This structure has small Coulomb interaction in hydrogen bond and has dipole moment.
* $\beta$ sheet\
Beta sheet is also one of common motif in protein, consist of $\beta$ strands connected hydrogen bonds, forming a generally twisted and pleated sheet.
![Secondary alpha-helix and beta sheet structures](./Figures/Alpha_beta_structure_full)
-->
<!--
\begin{figure}[h!]
\centering
\includegraphics[width=0.7\linewidth]{Alpha_beta_structure_(full)}
\caption{Secondary alpha-helix and beta sheet structures}
\label{fig:alphabetastructurefull}
\end{figure}
-->
<!--
## Structure of nucleic acid, DNA and protein
### 3 structures of DNA:
DNA has 3 conformation that include A-DNA, B-DNA, and Z-DNA forms
* A-DNA, has same periodic double helical structure\
* B-DNA, slightly similar to A-DNA, but with longer and less compact than A-DNA\
* Z-DNA, has double helical structure which the helix winds to the left in a zigzag pattern.
![3 types of DNA conformations: A-DNA, B-DNA, and Z-DNA](./Figures/Dnaconformations)
-->
<!--
\begin{figure}[h!]
\centering
\includegraphics[width=0.4\linewidth]{Dnaconformations}
\caption{3 types of DNA conformations: A-DNA, B-DNA, and Z-DNA}
\label{fig:dnaconformations}
\end{figure}
-->
<!--
# Lipid and membrane protein
Membrane is a function of protein that divides the biological cell into inside and outside part.
Functions of lipid bilayer are formation of boundary, permeability, and domain formation.
Lipids are divided into 2 types, hydrophobic and amphiphilic molecule. \
## Phospholipid
This is one kind of lipid which is a major component in all cell membranes.
Phospholipids can form lipid bilayers because of their amphiphilic characteristic.
There are 3 kinds of self-assemble and conformation of phospholipid:
* Spherical liposome\
* Bilayer\
* Micelle\
Micelles and bilayers form in the polar medium by a process of hydrophobic effect.
![Self-organization of phospholipids: a spherical liposome, a micelle, and a lipid bilayer.](./Figures/phospholipid)
-->
<!--
\begin{figure}[h!]
\centering
\includegraphics[width=0.5\linewidth]{phospholipid}
\caption{Self-organization of phospholipids: a spherical liposome, a micelle, and a lipid bilayer.}
\label{fig:phospholipid}
\end{figure}
-->
<!--
# Molecular dynamics simulation
## Simulation (Computational science)
Simulation is the one that connect the theory and experiment in science.
When the theory contributes in analysis and prediction, and experiments are contributing in confirming the theory and developing, simulation takes part in calculation in advanced theoretical and virtual simulation experiment.
Simulation is using the computer to do things, such as reproduce, understand, and predict the theory and also the experiment.
Simulation is applied in many fields, such as science, pharmacy, climate, earthquake, finance and social, and many other things.
## Supercomputer\
Supercomputer is a computer with high level of performance.
One of the biggest supercomputer in Japan is K Computer, located in Kobe, is having 705,024 cores and 10.510 PFlops (floating-point operations per second).
Supercomputer is practically used in computational science, such as biological, material, earth, and fundamental physical sciences.
Also, supercomputer is used in simulation of next-generation technology.
## Computational science in biology\
Computational science is usually used in exploring phenomena in biological system; substances, structure and functions of proteins, membranes, and enzymes, energy and chemical reaction, and signal transduction.
These can be modeled using molecular dynamics (MD) simulation.
The fundamental parts in MD are analytical mechanics (Newton's equation), Schrodinger's equation in quantum mechanics, statistical mechanics, and electromagnetization principle.
### _Brownian Dynamics_
Brownian dynamics describes the physical phenomena of zig-zag motion of particle. The motion is arising from collision between the particles. This motion resulted diffusion equation that obeys the law of mass conservation, formulated in the equation:
\begin{equation}
\frac{\partial \rho (x,t)}{\partial t} = -\frac{\partial J(x,t)}{\partial x}
\end{equation}
where $\rho (x,t)$ is density of material and $J (x,t)$ is flux, the rate of flow.
### _Langevin Equation_
This equation describes the \textit{Brownian motion} that uses Newton's equation of motion and degree of freedom. $\varrho$ is denoted as the friction coefficient.
\begin{equation}
m\frac{d^2 x}{d t^2} = F - \varrho \frac{dx}{dt} + \xi (t)
\end{equation}
### Einstein's relational expression:
\begin{equation}
D=\frac{k_BT}{\varrho}
\end{equation}
-->

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