From c6b5bdf8b807f4896017f9141170cce901d9af6e Mon Sep 17 00:00:00 2001 From: Hasan al Rasyid Date: Sat, 12 Mar 2022 17:52:20 +0900 Subject: [PATCH] pending --- manuscript.md | 478 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 477 insertions(+), 1 deletion(-) diff --git a/manuscript.md b/manuscript.md index 1eae4cf..a54d223 100644 --- a/manuscript.md +++ b/manuscript.md @@ -1 +1,477 @@ -HIT ME +--- +title: "Paperlighter Template Implementation Example" +author: | + - number: 1 + name: "Author One" + correspond: true + affiliation: "My City University" + address: "Orenomachi, Orenoshi, Orenoken, Japan" + - number: 2 + name: "Author Two" + affiliation: "My Other City University" + address: "Hokanomachi, Orenoshi, Orenoken, Japan" +email: "xxx@myuni.ac.jp" +titleSmall: "Paperlighter Example" +authorSmall: "Author One et.al." +abstract: | + Using \LaTeX\{\} to write papers is concise and convenient. However, for + writing in life, complicated \LaTeX\{\} style-files (e.g., elegantpaper) + are difficult to access, or submission style-files (e.g., journal or + conference) are not free indeed. To tackle these problems and satisfy an + elegant and straightforward scientific writing, + \textbf{paperlighter.sty}, a one-column style-file, is designed. This + document is edited from icml2022.sty and provides a basic paper + template. Compared to icml2022.sty, paperlighter.sty contain fewer + operations, reducing adjustment while keep graceful. + \textbf{\textit{Notably, the paper's main content only describes the format of icml2022.sty. We place the content to show the actual effect of paperlighter.sty.}} +--- + + +%\input{content/abstract} + + +%\input{content/format} +%\input{content/others} +\hypertarget{format-of-the-paperlighter}{% +\section{Format of the Paperlighter}\label{format-of-the-paperlighter}} + +Format of paperlighter is defined in this section. + +\hypertarget{dimensions}{% +\subsection{Dimensions}\label{dimensions}} + +The text of the paper has an overall width of +6.75\textasciitilde{}inches, and height of 9.0\textasciitilde{}inches. +The left margin should be 0.75\textasciitilde{}inches and the top margin +1.0\textasciitilde{}inch (2.54\textasciitilde{}cm). The right and bottom +margins will depend on whether you print on US letter or A4 paper, but +all final versions must be produced for US letter size. + +The paper body should be set in 10\textasciitilde{}point type with a +vertical spacing of 11\textasciitilde{}points. Please use Times typeface +throughout the text. + +\hypertarget{title}{% +\subsection{Title}\label{title}} + +The paper title should be set in 14\textasciitilde{}point bold type and +centered between two horizontal rules that are 1\textasciitilde{}point +thick, with 1.0\textasciitilde{}inch between the top rule and the top +edge of the page. Capitalize the first letter of content words and put +the rest of the title in lower case. + +\hypertarget{author-information-for-submission}{% +\subsection{Author Information for +Submission}\label{author-information-for-submission}} + +\label{author info} + +Use \verb+\lighterauthor{...}+ to specify authors and +\verb+\lighteraddress{...}+ to specify affiliations. (Read the TeX code +used to produce this document for an example usage.) The author +information will not be printed unless \texttt{accepted} is passed as an +argument to the style file. + +\hypertarget{abstract}{% +\subsection{Abstract}\label{abstract}} + +The paper abstract should begin in the left column, +0.4\textasciitilde{}inches below the final address. The heading +`Abstract’ should be centered, bold, and in 11\textasciitilde{}point +type. The abstract body should use 10\textasciitilde{}point type, with a +vertical spacing of 11\textasciitilde{}points, and should be indented +0.25\textasciitilde{}inches more than normal on left-hand and right-hand +margins. Insert 0.4\textasciitilde{}inches of blank space after the +body. Keep your abstract brief and self-contained, limiting it to one +paragraph and roughly 4–6 sentences. Gross violations will require +correction at the camera-ready phase. + +\hypertarget{partitioning-the-text}{% +\subsection{Partitioning the Text}\label{partitioning-the-text}} + +You should organize your paper into sections and paragraphs to help +readers place a structure on the material and understand its +contributions. + +\hypertarget{sections-and-subsections}{% +\subsubsection{Sections and +Subsections}\label{sections-and-subsections}} + +Section headings should be numbered, flush left, and set in +11\textasciitilde{}pt bold type with the content words capitalized. +Leave 0.25\textasciitilde{}inches of space before the heading and +0.15\textasciitilde{}inches after the heading. + +Similarly, subsection headings should be numbered, flush left, and set +in 10\textasciitilde{}pt bold type with the content words capitalized. +Leave 0.2\textasciitilde{}inches of space before the heading and +0.13\textasciitilde{}inches afterward. + +Finally, subsubsection headings should be numbered, flush left, and set +in 10\textasciitilde{}pt small caps with the content words capitalized. +Leave 0.18\textasciitilde{}inches of space before the heading and +0.1\textasciitilde{}inches after the heading. + +Please use no more than three levels of headings. + +\hypertarget{paragraphs-and-footnotes}{% +\subsubsection{Paragraphs and +Footnotes}\label{paragraphs-and-footnotes}} + +Within each section or subsection, you should further partition the +paper into paragraphs. Do not indent the first line of a given +paragraph, but insert a blank line between succeeding ones. + +You can use footnotes\footnote{Footnotes +should be complete sentences.} to provide readers with additional +information about a topic without interrupting the flow of the paper. +Indicate footnotes with a number in the text where the point is most +relevant. Place the footnote in 9\textasciitilde{}point type at the +bottom of the column in which it appears. Precede the first footnote in +a column with a horizontal rule of +0.8\textasciitilde{}inches.\footnote{Multiple footnotes can +appear in each column, in the same order as they appear in the text, +but spread them across columns and pages if possible.} + +\begin{figure}[ht] +\vskip 0.2in +\begin{center} +\centerline{\includegraphics[width=\columnwidth]{Figure/icml_numpapers.eps}} +\caption{Historical locations and number of accepted papers for International +Machine Learning Conferences (ICML 1993 -- ICML 2008) and International +Workshops on Machine Learning (ML 1988 -- ML 1992). At the time this figure was +produced, the number of accepted papers for ICML 2008 was unknown and instead +estimated.} +\label{icml-historical} +\end{center} +\vskip -0.2in +\end{figure} + +\hypertarget{figures}{% +\subsection{Figures}\label{figures}} + +You may want to include figures in the paper to illustrate your approach +and results. Such artwork should be centered, legible, and separated +from the text. Lines should be dark and at least +0.5\textasciitilde{}points thick for purposes of reproduction, and text +should not appear on a gray background. + +Label all distinct components of each figure. If the figure takes the +form of a graph, then give a name for each axis and include a legend +that briefly describes each curve. Do not include a title inside the +figure; instead, the caption should serve this function. + +Number figures sequentially, placing the figure number and caption +\emph{after} the graphics, with at least 0.1\textasciitilde{}inches of +space before the caption and 0.1\textasciitilde{}inches after it, as in +\cref{icml-historical}. The figure caption should be set in +9\textasciitilde{}point type and centered unless it runs two or more +lines, in which case it should be flush left. You may float figures to +the top or bottom of a column, and you may set wide figures across both +columns (use the environment \texttt{figure*} in \LaTeX). Always place +two-column figures at the top or bottom of the page. + +\hypertarget{algorithms}{% +\subsection{Algorithms}\label{algorithms}} + +If you are using \LaTeX, please use the +\texttt{algorithm\textquotesingle{}\textquotesingle{}\ and}algorithmic’’ +environments to format pseudocode. These require the corresponding +stylefiles, algorithm.sty and algorithmic.sty, which are supplied with +this package. \cref{alg:example} shows an example. + +\begin{algorithm}[tb] + \caption{Bubble Sort} + \label{alg:example} +\begin{algorithmic} + \STATE {\bfseries Input:} data $x_i$, size $m$ + \REPEAT + \STATE Initialize $noChange = true$. + \FOR{$i=1$ {\bfseries to} $m-1$} + \IF{$x_i > x_{i+1}$} + \STATE Swap $x_i$ and $x_{i+1}$ + \STATE $noChange = false$ + \ENDIF + \ENDFOR + \UNTIL{$noChange$ is $true$} +\end{algorithmic} +\end{algorithm} + +\hypertarget{tables}{% +\subsection{Tables}\label{tables}} + +You may also want to include tables that summarize material. Like +figures, these should be centered, legible, and numbered consecutively. +However, place the title \emph{above} the table with at least +0.1\textasciitilde{}inches of space before the title and the same after +it, as in \cref{sample-table}. The table title should be set in +9\textasciitilde{}point type and centered unless it runs two or more +lines, in which case it should be flush left. + +\begin{table}[t] +\caption{Classification accuracies for naive Bayes and flexible +Bayes on various data sets.} +\label{sample-table} +\vskip 0.15in +\begin{center} +\begin{small} +\begin{sc} +\begin{tabular}{lcccr} +\toprule +Data set & Naive & Flexible & Better? \\ +\midrule +Breast & 95.9$\pm$ 0.2& 96.7$\pm$ 0.2& $\surd$ \\ +Cleveland & 83.3$\pm$ 0.6& 80.0$\pm$ 0.6& $\times$\\ +Glass2 & 61.9$\pm$ 1.4& 83.8$\pm$ 0.7& $\surd$ \\ +Credit & 74.8$\pm$ 0.5& 78.3$\pm$ 0.6& \\ +Horse & 73.3$\pm$ 0.9& 69.7$\pm$ 1.0& $\times$\\ +Meta & 67.1$\pm$ 0.6& 76.5$\pm$ 0.5& $\surd$ \\ +Pima & 75.1$\pm$ 0.6& 73.9$\pm$ 0.5& \\ +Vehicle & 44.9$\pm$ 0.6& 61.5$\pm$ 0.4& $\surd$ \\ +\bottomrule +\end{tabular} +\end{sc} +\end{small} +\end{center} +\vskip -0.1in +\end{table} + +Tables contain textual material, whereas figures contain graphical +material. Specify the contents of each row and column in the table’s +topmost row. Again, you may float tables to a column’s top or bottom, +and set wide tables across both columns. Place two-column tables at the +top or bottom of the page. + +\hypertarget{theorems-and-such}{% +\subsection{Theorems and such}\label{theorems-and-such}} + +The preferred way is to number definitions, propositions, lemmas, etc. +consecutively, within sections, as shown below. + +\begin{definition} +\label{def:inj} +A function $f:X \to Y$ is injective if for any $x,y\in X$ different, $f(x)\ne f(y)$. +\end{definition} + +Using \cref{def:inj} we immediate get the following result: + +\begin{proposition} +If $f$ is injective mapping a set $X$ to another set $Y$, +the cardinality of $Y$ is at least as large as that of $X$ +\end{proposition} +\begin{proof} +Left as an exercise to the reader. +\end{proof} + +\cref{lem:usefullemma} stated next will prove to be useful. + +\begin{lemma} +\label{lem:usefullemma} +For any $f:X \to Y$ and $g:Y\to Z$ injective functions, $f \circ g$ is injective. +\end{lemma} +\begin{theorem} +\label{thm:bigtheorem} +If $f:X\to Y$ is bijective, the cardinality of $X$ and $Y$ are the same. +\end{theorem} + +An easy corollary of \cref{thm:bigtheorem} is the following: + +\begin{corollary} +If $f:X\to Y$ is bijective, +the cardinality of $X$ is at least as large as that of $Y$. +\end{corollary} +\begin{assumption} +The set $X$ is finite. +\label{ass:xfinite} +\end{assumption} +\begin{remark} +According to some, it is only the finite case (cf. \cref{ass:xfinite}) that is interesting. +\end{remark} + +\hypertarget{citations-and-references}{% +\subsection{Citations and References}\label{citations-and-references}} + +If you rely on the \LaTeX\{\} bibliographic facility, use +\texttt{natbib.sty} included in the style-file package to obtain +reference. + +Citations within the text should include the authors’ last names and +year. If the authors’ names are included in the sentence, place only the +year in parentheses, for example when referencing Arthur Samuel’s +pioneering work \yrcite{Samuel59}. Otherwise place the entire reference +in parentheses with the authors and year separated by a comma +\cite{Samuel59}. List multiple references separated by semicolons +\cite{kearns89,Samuel59,mitchell80}. Use the `et\textasciitilde{}al.’ +construct only for citations with three or more authors or after listing +all authors to a publication in an earlier reference +\cite{MachineLearningI}. + +Use an unnumbered first-level section heading for the references, and +use a hanging indent style, with the first line of the reference flush +against the left margin and subsequent lines indented by 10 points. The +references at the end of this document give examples for journal +articles \cite{Samuel59}, conference publications \cite{langley00}, book +chapters \cite{Newell81}, books \cite{DudaHart2nd}, edited volumes +\cite{MachineLearningI}, technical reports \cite{mitchell80}, and +dissertations \cite{kearns89}. + +Alphabetize references by the surnames of the first authors, with single +author entries preceding multiple author entries. Order references for +the same authors by year of publication, with the earliest first. Make +sure that each reference includes all relevant information (e.g., page +numbers). + +Please put some effort into making references complete, presentable, and +consistent, e.g.~use the actual current name of authors. If using +bibtex, please protect capital letters of names and abbreviations in +titles, for example, use \{B\}ayesian or \{L\}ipschitz in your .bib +file. + +\hypertarget{acknowledgements}{% +\section{Acknowledgements}\label{acknowledgements}} + +Acknowledgements is an unnumbered section at the end of the paper. +Typically, this will include thanks to colleagues who contributed to the +ideas, and to funding agencies and corporate sponsors that provided +financial support. + +%\bibliographystyle{plainnat} +%\bibliography{ref} +\bibliographystyle{plainnat}% +\bibliography{manuscript}% + +%\newpage +%\appendix +%\input{content/appendix} + +\end{document} + +# 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) + + + +### 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) + + +## 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) + + +# 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) + + + +# 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} +