Hasan al Rasyid
3 years ago
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title: "Paperlighter Template Implementation Example" |
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author: | |
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- number: 1 |
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name: "Author One" |
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correspond: true |
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affiliation: "My City University" |
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address: "Orenomachi, Orenoshi, Orenoken, Japan" |
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- number: 2 |
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name: "Author Two" |
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affiliation: "My Other City University" |
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address: "Hokanomachi, Orenoshi, Orenoken, Japan" |
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email: "xxx@myuni.ac.jp" |
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titleSmall: "Paperlighter Example" |
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authorSmall: "Author One et.al." |
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abstract: | |
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Using \LaTeX\{\} to write papers is concise and convenient. However, for |
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writing in life, complicated \LaTeX\{\} style-files (e.g., elegantpaper) |
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are difficult to access, or submission style-files (e.g., journal or |
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conference) are not free indeed. To tackle these problems and satisfy an |
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elegant and straightforward scientific writing, |
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\textbf{paperlighter.sty}, a one-column style-file, is designed. This |
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document is edited from icml2022.sty and provides a basic paper |
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template. Compared to icml2022.sty, paperlighter.sty contain fewer |
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operations, reducing adjustment while keep graceful. |
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\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.}} |
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--- |
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%\input{content/abstract} |
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%\input{content/format} |
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%\input{content/others} |
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\hypertarget{format-of-the-paperlighter}{% |
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\section{Format of the Paperlighter}\label{format-of-the-paperlighter}} |
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Format of paperlighter is defined in this section. |
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\hypertarget{dimensions}{% |
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\subsection{Dimensions}\label{dimensions}} |
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The text of the paper has an overall width of |
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6.75\textasciitilde{}inches, and height of 9.0\textasciitilde{}inches. |
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The left margin should be 0.75\textasciitilde{}inches and the top margin |
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1.0\textasciitilde{}inch (2.54\textasciitilde{}cm). The right and bottom |
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margins will depend on whether you print on US letter or A4 paper, but |
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all final versions must be produced for US letter size. |
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The paper body should be set in 10\textasciitilde{}point type with a |
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vertical spacing of 11\textasciitilde{}points. Please use Times typeface |
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throughout the text. |
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\hypertarget{title}{% |
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\subsection{Title}\label{title}} |
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The paper title should be set in 14\textasciitilde{}point bold type and |
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centered between two horizontal rules that are 1\textasciitilde{}point |
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thick, with 1.0\textasciitilde{}inch between the top rule and the top |
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edge of the page. Capitalize the first letter of content words and put |
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the rest of the title in lower case. |
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\hypertarget{author-information-for-submission}{% |
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\subsection{Author Information for |
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Submission}\label{author-information-for-submission}} |
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\label{author info} |
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Use \verb+\lighterauthor{...}+ to specify authors and |
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\verb+\lighteraddress{...}+ to specify affiliations. (Read the TeX code |
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used to produce this document for an example usage.) The author |
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information will not be printed unless \texttt{accepted} is passed as an |
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argument to the style file. |
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\hypertarget{abstract}{% |
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\subsection{Abstract}\label{abstract}} |
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The paper abstract should begin in the left column, |
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0.4\textasciitilde{}inches below the final address. The heading |
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`Abstract’ should be centered, bold, and in 11\textasciitilde{}point |
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type. The abstract body should use 10\textasciitilde{}point type, with a |
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vertical spacing of 11\textasciitilde{}points, and should be indented |
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0.25\textasciitilde{}inches more than normal on left-hand and right-hand |
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margins. Insert 0.4\textasciitilde{}inches of blank space after the |
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body. Keep your abstract brief and self-contained, limiting it to one |
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paragraph and roughly 4–6 sentences. Gross violations will require |
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correction at the camera-ready phase. |
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\hypertarget{partitioning-the-text}{% |
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\subsection{Partitioning the Text}\label{partitioning-the-text}} |
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You should organize your paper into sections and paragraphs to help |
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readers place a structure on the material and understand its |
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contributions. |
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\hypertarget{sections-and-subsections}{% |
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\subsubsection{Sections and |
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Subsections}\label{sections-and-subsections}} |
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Section headings should be numbered, flush left, and set in |
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11\textasciitilde{}pt bold type with the content words capitalized. |
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Leave 0.25\textasciitilde{}inches of space before the heading and |
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0.15\textasciitilde{}inches after the heading. |
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Similarly, subsection headings should be numbered, flush left, and set |
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in 10\textasciitilde{}pt bold type with the content words capitalized. |
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Leave 0.2\textasciitilde{}inches of space before the heading and |
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0.13\textasciitilde{}inches afterward. |
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Finally, subsubsection headings should be numbered, flush left, and set |
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in 10\textasciitilde{}pt small caps with the content words capitalized. |
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Leave 0.18\textasciitilde{}inches of space before the heading and |
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0.1\textasciitilde{}inches after the heading. |
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Please use no more than three levels of headings. |
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\hypertarget{paragraphs-and-footnotes}{% |
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\subsubsection{Paragraphs and |
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Footnotes}\label{paragraphs-and-footnotes}} |
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Within each section or subsection, you should further partition the |
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paper into paragraphs. Do not indent the first line of a given |
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paragraph, but insert a blank line between succeeding ones. |
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You can use footnotes\footnote{Footnotes |
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should be complete sentences.} to provide readers with additional |
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information about a topic without interrupting the flow of the paper. |
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Indicate footnotes with a number in the text where the point is most |
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relevant. Place the footnote in 9\textasciitilde{}point type at the |
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bottom of the column in which it appears. Precede the first footnote in |
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a column with a horizontal rule of |
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0.8\textasciitilde{}inches.\footnote{Multiple footnotes can |
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appear in each column, in the same order as they appear in the text, |
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but spread them across columns and pages if possible.} |
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\begin{figure}[ht] |
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\vskip 0.2in |
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\begin{center} |
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\centerline{\includegraphics[width=\columnwidth]{Figure/icml_numpapers.eps}} |
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\caption{Historical locations and number of accepted papers for International |
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Machine Learning Conferences (ICML 1993 -- ICML 2008) and International |
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Workshops on Machine Learning (ML 1988 -- ML 1992). At the time this figure was |
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produced, the number of accepted papers for ICML 2008 was unknown and instead |
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estimated.} |
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\label{icml-historical} |
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\end{center} |
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\vskip -0.2in |
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\end{figure} |
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\hypertarget{figures}{% |
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\subsection{Figures}\label{figures}} |
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You may want to include figures in the paper to illustrate your approach |
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and results. Such artwork should be centered, legible, and separated |
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from the text. Lines should be dark and at least |
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0.5\textasciitilde{}points thick for purposes of reproduction, and text |
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should not appear on a gray background. |
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Label all distinct components of each figure. If the figure takes the |
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form of a graph, then give a name for each axis and include a legend |
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that briefly describes each curve. Do not include a title inside the |
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figure; instead, the caption should serve this function. |
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Number figures sequentially, placing the figure number and caption |
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\emph{after} the graphics, with at least 0.1\textasciitilde{}inches of |
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space before the caption and 0.1\textasciitilde{}inches after it, as in |
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\cref{icml-historical}. The figure caption should be set in |
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9\textasciitilde{}point type and centered unless it runs two or more |
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lines, in which case it should be flush left. You may float figures to |
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the top or bottom of a column, and you may set wide figures across both |
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columns (use the environment \texttt{figure*} in \LaTeX). Always place |
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two-column figures at the top or bottom of the page. |
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\hypertarget{algorithms}{% |
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\subsection{Algorithms}\label{algorithms}} |
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If you are using \LaTeX, please use the |
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\texttt{algorithm\textquotesingle{}\textquotesingle{}\ and}algorithmic’’ |
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environments to format pseudocode. These require the corresponding |
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stylefiles, algorithm.sty and algorithmic.sty, which are supplied with |
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this package. \cref{alg:example} shows an example. |
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\begin{algorithm}[tb] |
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\caption{Bubble Sort} |
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\label{alg:example} |
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\begin{algorithmic} |
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\STATE {\bfseries Input:} data $x_i$, size $m$ |
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\REPEAT |
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\STATE Initialize $noChange = true$. |
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\FOR{$i=1$ {\bfseries to} $m-1$} |
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\IF{$x_i > x_{i+1}$} |
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\STATE Swap $x_i$ and $x_{i+1}$ |
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\STATE $noChange = false$ |
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\ENDIF |
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\ENDFOR |
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\UNTIL{$noChange$ is $true$} |
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\end{algorithmic} |
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\end{algorithm} |
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\hypertarget{tables}{% |
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\subsection{Tables}\label{tables}} |
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You may also want to include tables that summarize material. Like |
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figures, these should be centered, legible, and numbered consecutively. |
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However, place the title \emph{above} the table with at least |
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0.1\textasciitilde{}inches of space before the title and the same after |
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it, as in \cref{sample-table}. The table title should be set in |
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9\textasciitilde{}point type and centered unless it runs two or more |
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lines, in which case it should be flush left. |
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\begin{table}[t] |
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\caption{Classification accuracies for naive Bayes and flexible |
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Bayes on various data sets.} |
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\label{sample-table} |
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\vskip 0.15in |
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\begin{center} |
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\begin{small} |
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\begin{sc} |
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\begin{tabular}{lcccr} |
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\toprule |
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Data set & Naive & Flexible & Better? \\ |
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\midrule |
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Breast & 95.9$\pm$ 0.2& 96.7$\pm$ 0.2& $\surd$ \\ |
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Cleveland & 83.3$\pm$ 0.6& 80.0$\pm$ 0.6& $\times$\\ |
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Glass2 & 61.9$\pm$ 1.4& 83.8$\pm$ 0.7& $\surd$ \\ |
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Credit & 74.8$\pm$ 0.5& 78.3$\pm$ 0.6& \\ |
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Horse & 73.3$\pm$ 0.9& 69.7$\pm$ 1.0& $\times$\\ |
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Meta & 67.1$\pm$ 0.6& 76.5$\pm$ 0.5& $\surd$ \\ |
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Pima & 75.1$\pm$ 0.6& 73.9$\pm$ 0.5& \\ |
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Vehicle & 44.9$\pm$ 0.6& 61.5$\pm$ 0.4& $\surd$ \\ |
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\bottomrule |
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\end{tabular} |
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\end{sc} |
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\end{small} |
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\end{center} |
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\vskip -0.1in |
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\end{table} |
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Tables contain textual material, whereas figures contain graphical |
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material. Specify the contents of each row and column in the table’s |
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topmost row. Again, you may float tables to a column’s top or bottom, |
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and set wide tables across both columns. Place two-column tables at the |
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top or bottom of the page. |
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\hypertarget{theorems-and-such}{% |
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\subsection{Theorems and such}\label{theorems-and-such}} |
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The preferred way is to number definitions, propositions, lemmas, etc. |
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consecutively, within sections, as shown below. |
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\begin{definition} |
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\label{def:inj} |
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A function $f:X \to Y$ is injective if for any $x,y\in X$ different, $f(x)\ne f(y)$. |
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\end{definition} |
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Using \cref{def:inj} we immediate get the following result: |
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\begin{proposition} |
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If $f$ is injective mapping a set $X$ to another set $Y$, |
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the cardinality of $Y$ is at least as large as that of $X$ |
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\end{proposition} |
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\begin{proof} |
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Left as an exercise to the reader. |
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\end{proof} |
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\cref{lem:usefullemma} stated next will prove to be useful. |
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\begin{lemma} |
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\label{lem:usefullemma} |
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For any $f:X \to Y$ and $g:Y\to Z$ injective functions, $f \circ g$ is injective. |
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\end{lemma} |
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\begin{theorem} |
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\label{thm:bigtheorem} |
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If $f:X\to Y$ is bijective, the cardinality of $X$ and $Y$ are the same. |
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\end{theorem} |
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An easy corollary of \cref{thm:bigtheorem} is the following: |
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\begin{corollary} |
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If $f:X\to Y$ is bijective, |
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the cardinality of $X$ is at least as large as that of $Y$. |
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\end{corollary} |
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\begin{assumption} |
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The set $X$ is finite. |
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\label{ass:xfinite} |
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\end{assumption} |
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\begin{remark} |
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According to some, it is only the finite case (cf. \cref{ass:xfinite}) that is interesting. |
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\end{remark} |
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\hypertarget{citations-and-references}{% |
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\subsection{Citations and References}\label{citations-and-references}} |
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If you rely on the \LaTeX\{\} bibliographic facility, use |
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\texttt{natbib.sty} included in the style-file package to obtain |
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reference. |
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Citations within the text should include the authors’ last names and |
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year. If the authors’ names are included in the sentence, place only the |
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year in parentheses, for example when referencing Arthur Samuel’s |
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pioneering work \yrcite{Samuel59}. Otherwise place the entire reference |
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in parentheses with the authors and year separated by a comma |
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\cite{Samuel59}. List multiple references separated by semicolons |
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\cite{kearns89,Samuel59,mitchell80}. Use the `et\textasciitilde{}al.’ |
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construct only for citations with three or more authors or after listing |
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all authors to a publication in an earlier reference |
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\cite{MachineLearningI}. |
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Use an unnumbered first-level section heading for the references, and |
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use a hanging indent style, with the first line of the reference flush |
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against the left margin and subsequent lines indented by 10 points. The |
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references at the end of this document give examples for journal |
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articles \cite{Samuel59}, conference publications \cite{langley00}, book |
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chapters \cite{Newell81}, books \cite{DudaHart2nd}, edited volumes |
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\cite{MachineLearningI}, technical reports \cite{mitchell80}, and |
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dissertations \cite{kearns89}. |
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Alphabetize references by the surnames of the first authors, with single |
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author entries preceding multiple author entries. Order references for |
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the same authors by year of publication, with the earliest first. Make |
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sure that each reference includes all relevant information (e.g., page |
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numbers). |
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Please put some effort into making references complete, presentable, and |
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consistent, e.g.~use the actual current name of authors. If using |
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bibtex, please protect capital letters of names and abbreviations in |
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titles, for example, use \{B\}ayesian or \{L\}ipschitz in your .bib |
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file. |
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\hypertarget{acknowledgements}{% |
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\section{Acknowledgements}\label{acknowledgements}} |
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Acknowledgements is an unnumbered section at the end of the paper. |
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Typically, this will include thanks to colleagues who contributed to the |
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ideas, and to funding agencies and corporate sponsors that provided |
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financial support. |
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%\bibliographystyle{plainnat} |
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%\bibliography{ref} |
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\bibliographystyle{plainnat}% |
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\bibliography{manuscript}% |
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%\newpage |
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%\appendix |
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%\input{content/appendix} |
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\end{document} |
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# Basic properties of protein and nucleic acids |
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## Basic principle of protein |
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### Unit structure of protein |
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There are 4 levels of protein organization: |
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* Primary structure \ |
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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. |
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* Secondary structure \ |
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This is the region within the long protein chains organized into regular structures known as alpha-helices ($\alpha$-helices) and beta sheet. |
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* Tertiary structure \ |
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Tertiary structure is a description of the way that whole chain from one or several units folds and forms 3-dimensional shape, called domain. |
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* Fourth order structure \ |
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This structure is formed from several tertiary structure proteins or domains with more complex shape. |
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<!-- |
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\begin{figure}[h!] |
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\centering |
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\includegraphics[width=0.7\linewidth]{Figure1} |
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\caption{Structure of protein} |
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\label{fig:figure1} |
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\end{figure} |
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--> |
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### Basic motif of protein |
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There are two types of secondary structure for hydrophobic type: |
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* $\alpha$-helix\ |
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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. |
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* $\beta$ sheet\ |
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Beta sheet is also one of common motif in protein, consist of $\beta$ strands connected hydrogen bonds, forming a generally twisted and pleated sheet. |
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 |
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<!-- |
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\begin{figure}[h!] |
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\centering |
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\includegraphics[width=0.7\linewidth]{Alpha_beta_structure_(full)} |
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\caption{Secondary alpha-helix and beta sheet structures} |
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\label{fig:alphabetastructurefull} |
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\end{figure} |
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--> |
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## Structure of nucleic acid, DNA and protein |
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### 3 structures of DNA: |
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DNA has 3 conformation that include A-DNA, B-DNA, and Z-DNA forms |
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* A-DNA, has same periodic double helical structure\ |
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* B-DNA, slightly similar to A-DNA, but with longer and less compact than A-DNA\ |
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* Z-DNA, has double helical structure which the helix winds to the left in a zigzag pattern. |
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 |
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<!-- |
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\begin{figure}[h!] |
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\centering |
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\includegraphics[width=0.4\linewidth]{Dnaconformations} |
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\caption{3 types of DNA conformations: A-DNA, B-DNA, and Z-DNA} |
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\label{fig:dnaconformations} |
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\end{figure} |
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--> |
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# Lipid and membrane protein |
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Membrane is a function of protein that divides the biological cell into inside and outside part. |
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Functions of lipid bilayer are formation of boundary, permeability, and domain formation. |
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Lipids are divided into 2 types, hydrophobic and amphiphilic molecule. \ |
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## Phospholipid |
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This is one kind of lipid which is a major component in all cell membranes. |
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Phospholipids can form lipid bilayers because of their amphiphilic characteristic. |
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There are 3 kinds of self-assemble and conformation of phospholipid: |
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|
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* Spherical liposome\ |
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* Bilayer\ |
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* Micelle\ |
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Micelles and bilayers form in the polar medium by a process of hydrophobic effect. |
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 |
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|
<!-- |
||||||
|
\begin{figure}[h!] |
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|
\centering |
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|
\includegraphics[width=0.5\linewidth]{phospholipid} |
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|
\caption{Self-organization of phospholipids: a spherical liposome, a micelle, and a lipid bilayer.} |
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|
\label{fig:phospholipid} |
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|
\end{figure} |
||||||
|
--> |
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|
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|
|
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|
# Molecular dynamics simulation |
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|
## Simulation (Computational science) |
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|
Simulation is the one that connect the theory and experiment in science. |
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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. |
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|
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. |
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|
|
||||||
|
## Supercomputer\ |
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|
Supercomputer is a computer with high level of performance. |
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|
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). |
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|
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. |
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|
|
||||||
|
## 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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Loading…
Reference in new issue