Hairpin formation - Revision history

Rovigattil at 08:24, 18 June 2015

2015-06-18T08:24:39Z

← Older revision		Revision as of 08:24, 18 June 2015
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	== Introduction ==		== Introduction ==
	In this example, you will simulate a single strand of length 18 and sequence <tt>GCGTTGCTTCTCCAACGC</tt> at 334 K (~61 °C) in three different ways:		In this example, you will simulate a single strand of length 18 and sequence <tt>GCGTTGCTTCTCCAACGC</tt> at 334 K (~61 °C) in three different ways:
	* with a ~~molecular dynamics~~ (MD) simulation of the sequence-averaged (SA) model. The input file is <tt>~~inputMD~~</tt>.		* with a virtual move Monte Carlo (VMMC) simulation of the sequence-averaged (SA) model. The input file is <tt>input</tt>.
	* with ~~an MD~~ simulation of the sequence-dependent (SD) model. The input file is <code>~~inputMD_seq_dep~~</code>.		* with a VMMC simulation of the sequence-dependent (SD) model. The input file is <code>input_seq_dep</code>.
	* with a ~~Monte Carlo (MC)~~ simulation of the SA model in which two base pairs are connected by mutual traps (i.e. additional attractive interactions between two nucleotides). The input file is <tt>~~inputTRAP~~</tt>.		* with a VMMC simulation of the SA model in which two base pairs are connected by mutual traps (i.e. additional attractive interactions between two nucleotides). The input file is <tt>input_trap</tt>.
	The traps act between the pairs depicted in blue and red in the sequence G<span style="color:red">C</span><span style="color:blue">G</span>TTGCTTCTCCAA<span style="color:blue">C</span><span style="color:red">G</span>C. The details of the interaction associated to the traps can be changed in the file <tt>hairpin_forces.dat</tt>.		The traps act between the pairs depicted in blue and red in the sequence G<span style="color:red">C</span><span style="color:blue">G</span>TTGCTTCTCCAA<span style="color:blue">C</span><span style="color:red">G</span>C. The details of the interaction associated to the traps can be changed in the file <tt>hairpin_forces.dat</tt>.

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	\|-		\|-
	\|SA model		\|SA model
	\|~~inputMD~~		\|input
	\|energy.dat		\|energy.dat
	\|hb_energy.dat		\|hb_energy.dat
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	\|-		\|-
	\|SD model		\|SD model
	\|~~inputMD_seq_dep~~		\|input_seq_dep
	\|energy_seq_dep.dat		\|energy_seq_dep.dat
	\|hb_energy_seq_dep.dat		\|hb_energy_seq_dep.dat
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	\|-		\|-
	\|SA model with traps		\|SA model with traps
	\|~~inputTRAP~~		\|input_trap
	\|energy_trap.dat		\|energy_trap.dat
	\|hb_energy_trap.dat		\|hb_energy_trap.dat
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	== Results ==		== Results ==
	As mentioned in the [[#Introduction\|introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units). <math>U_{HB}</math> is stored in the second column of the HB energy file as a function of MD steps. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always ~~formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are~~ formed.		As mentioned in the [[#Introduction\|introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units). <math>U_{HB}</math> is stored in the second column of the HB energy file as a function of MD steps. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed.

	<div style="text-align:center">		<div style="text-align:center">

Rovigattil at 09:28, 16 June 2015

2015-06-16T09:28:20Z

← Older revision		Revision as of 09:28, 16 June 2015
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	== Preparation ==		== Preparation ==
	The script <tt>run.sh</tt> generates the input files and runs all the three simulations, one after the other. With the default input files, each simulation, lasting <math>10^8</math> steps by default, takes approximately one hour on a modern CPU. The default <tt>run.sh</tt> expects <tt>$EXEC</tt> to be in the <tt>../..</tt> directory. If this is not the case, open <tt>run.sh</tt> and change the ~~variable~~ <tt>CODEDIR</tt> accordingly.		The script <tt>run.sh</tt> generates the input files and runs all the three simulations, one after the other. With the default input files, each simulation, lasting <math>10^8</math> steps by default, takes approximately one hour on a modern CPU. The default <tt>run.sh</tt> expects <tt>$EXEC</tt> to be in the <tt>../../bin</tt> directory . If this is not the case, open <tt>run.sh</tt> and change the variables <tt>CODEDIR</tt> and <tt>$OXDNA_BIN</tt> accordingly.

	If you only want to generate the initial configuration, you can issue <tt>./run.sh --generate-only</tt>. Then you can run the simulations by yourself. The generated initial configuration files are <tt>initial.top</tt> (which contains the topology) and <tt>initial.conf</tt> (which contains positions and orientations of the nucleotides).		If you only want to generate the initial configuration, you can issue <tt>./run.sh --generate-only</tt>. Then you can run the simulations by yourself. The generated initial configuration files are <tt>initial.top</tt> (which contains the topology) and <tt>initial.conf</tt> (which contains positions and orientations of the nucleotides).
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	! Input		! Input
	! energy file		! energy file
			! HB energy file
	! trajectory file		! trajectory file
	! last configuration file		! last configuration file
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	\|inputMD		\|inputMD
	\|energy.dat		\|energy.dat
			\|hb_energy.dat
	\|trajectory.dat		\|trajectory.dat
	\|last_conf.dat		\|last_conf.dat
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	\|inputMD_seq_dep		\|inputMD_seq_dep
	\|energy_seq_dep.dat		\|energy_seq_dep.dat
			\|hb_energy_seq_dep.dat
	\|trajectory_seq_dep.dat		\|trajectory_seq_dep.dat
	\|last_conf_seq_dep.dat		\|last_conf_seq_dep.dat
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	\|inputTRAP		\|inputTRAP
	\|energy_trap.dat		\|energy_trap.dat
			\|hb_energy_trap.dat
	\|trajectory_trap.dat		\|trajectory_trap.dat
	\|last_conf_trap.dat		\|last_conf_trap.dat
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	== Results ==		== Results ==
	As mentioned in the [[#Introduction\|introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units). <math>U_{HB}</math> is stored in the ~~fifth~~ column of the energy file as a function of MD steps. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.		As mentioned in the [[#Introduction\|introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units). <math>U_{HB}</math> is stored in the second column of the HB energy file as a function of MD steps. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.

	<div style="text-align:center">		<div style="text-align:center">

Rovigattil: /* Results */

2014-12-03T10:40:52Z

Results

← Older revision		Revision as of 10:40, 3 December 2014
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	<div style="text-align:center">		<div style="text-align:center">
	~~http~~:~~//kratos.phys.uniroma1.it/~~histo_MD.png		[[Image:histo_MD.png]]

	<h5>Figure 1: Probability of having a hydrogen-bonding interaction energy <math>U_{HB}</math> for the SA model. Inset: time series of the hydrogen-bonding energy.</h5>		<h5>Figure 1: Probability of having a hydrogen-bonding interaction energy <math>U_{HB}</math> for the SA model. Inset: time series of the hydrogen-bonding energy.</h5>
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	<div style="text-align:center">		<div style="text-align:center">
	~~http~~:~~//kratos.phys.uniroma1.it/~~histo_MD_seq_dep.png		[[Image:histo_MD_seq_dep.png]]

	<h5>Figure 2: Same as Figure 1, but for the SD model.</h5>		<h5>Figure 2: Same as Figure 1, but for the SD model.</h5>
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	<div style="text-align:center">		<div style="text-align:center">
	~~http~~:~~//kratos.phys.uniroma1.it/~~histo_TRAP.png		[[Image:histo_TRAP.png]]

	<h5>Figure 3: Same as Figure 1, but for the system with mutual traps. Time is expressed in Monte Carlo sweeps.</h5>		<h5>Figure 3: Same as Figure 1, but for the system with mutual traps. Time is expressed in Monte Carlo sweeps.</h5>
	</div>		</div>

Rovigatti: /* Results */

2012-04-21T17:14:39Z

Results

← Older revision		Revision as of 17:14, 21 April 2012
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	== Results ==		== Results ==
	As mentioned in the [[#Introduction\|~~Introduction~~]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units). <math>U_{HB}</math> is stored in the fifth column of the energy file as a function of MD steps. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.		As mentioned in the [[#Introduction\|introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units). <math>U_{HB}</math> is stored in the fifth column of the energy file as a function of MD steps. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.

	<div style="text-align:center">		<div style="text-align:center">

Rovigatti: /* Results */

2012-04-21T17:14:15Z

Results

← Older revision		Revision as of 17:14, 21 April 2012
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	== Results ==		== Results ==
	As mentioned in the [[#Introduction\|Introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.		As mentioned in the [[#Introduction\|Introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units). <math>U_{HB}</math> is stored in the fifth column of the energy file as a function of MD steps. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.

	<div style="text-align:center">		<div style="text-align:center">

Rovigatti at 17:13, 21 April 2012

2012-04-21T17:13:43Z

← Older revision		Revision as of 17:13, 21 April 2012
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	http://kratos.phys.uniroma1.it/histo_MD.png		http://kratos.phys.uniroma1.it/histo_MD.png

	<h5>Figure 1: Probability of having a hydrogen-bonding interaction energy <math>U_{HB}</math> for the SA model. Inset: time series of the hydrogen-bonding energy ~~(stored in the fifth column of the energy file as a function of MD steps~~.</h5>		<h5>Figure 1: Probability of having a hydrogen-bonding interaction energy <math>U_{HB}</math> for the SA model. Inset: time series of the hydrogen-bonding energy.</h5>
	</div>		</div>

Rovigatti at 15:23, 19 April 2012

2012-04-19T15:23:07Z

← Older revision		Revision as of 15:23, 19 April 2012
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			<!--<div style="text-align:center">
			http://kratos.phys.uniroma1.it/hairpin.png
			</div>-->

	[[Category:Examples]]		[[Category:Examples]]
	== Introduction ==		== Introduction ==

Rovigatti: /* Results */

2012-04-19T15:21:49Z

Results

← Older revision		Revision as of 15:21, 19 April 2012
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	== Results ==		== Results ==
	As mentioned in the [[#Introduction\|Introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed~~~\cite{ouldridge_jcp}~~. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.		As mentioned in the [[#Introduction\|Introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.

	<div style="text-align:center">		<div style="text-align:center">

Rovigatti: /* Running */

2012-04-19T15:21:39Z

Running

← Older revision		Revision as of 15:21, 19 April 2012
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	== Running ==		== Running ==
	In order to run the whole example, it is sufficient to issue the command <tt>./run.sh</tt> (or <tt>bash run.sh</tt>). As described in [[#Preparation\|Preparation]], you can generate the initial configuration and then run the simulations by hand. The three simulations, described in [[#Introduction\|Introduction]], can be performed issuing <tt>$EXEC input</tt>, where <tt>input</tt> is a text file that specifies the simulation configuration. For this example, three files have been prepared: <tt>inputMD</tt>, <tt>inputMD_seq_dep</tt> and <tt>inputTRAP</tt>. ~~Table~\ref{tbl:sim} report~~ all the files associated to each simulations.		In order to run the whole example, it is sufficient to issue the command <tt>./run.sh</tt> (or <tt>bash run.sh</tt>). As described in [[#Preparation\|Preparation]], you can generate the initial configuration and then run the simulations by hand. The three simulations, described in [[#Introduction\|Introduction]], can be performed issuing <tt>$EXEC input</tt>, where <tt>input</tt> is a text file that specifies the simulation configuration. For this example, three files have been prepared: <tt>inputMD</tt>, <tt>inputMD_seq_dep</tt> and <tt>inputTRAP</tt>. The table below reports all the files associated to each simulations.

	{\|		{\|

Rovigatti at 15:21, 19 April 2012

2012-04-19T15:21:10Z

← Older revision		Revision as of 15:21, 19 April 2012
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	== Results ==		== Results ==
	As mentioned in the [[#Introduction\|Introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram $P(U_{HB})$ for the hydrogen-bonding (HB) energy $U_{HB}$ of the system (in simulation units~~~\cite{ouldridge_jcp})~~. Both the minimum in $P(U_{HB})$ and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since $U_{HB}$ oscillates between $0$ (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed~\cite{ouldridge_jcp}. This is clearly visible in the snapshot at the beginning of this document, in which $4$ base-pairs are formed.		As mentioned in the [[#Introduction\|Introduction]], temperature has been chosen so that the hairpin is near its melting temperature when simulated via SA model. Figure 1 shows the probability distribution histogram <math>P(U_{HB})</math> for the hydrogen-bonding (HB) energy <math>U_{HB}</math> of the system (in simulation units. Both the minimum in <math>P(U_{HB})</math> and a direct inspection of the time series (inset) show that the hairpin is indeed near the melting temperature, since <math>U_{HB}</math> oscillates between 0 (no HBs) and ~ -3.5, which corresponds to 4-5 hydrogen-bonded nucleotides. At this temperature the fraying effect is relevant, and therefore the last base-pair is not always formed~\cite{ouldridge_jcp}. This is clearly visible in the snapshot at the beginning of this document, in which 4 base-pairs are formed.

	<div style="text-align:center">		<div style="text-align:center">
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	Figure 2 shows $P(U_{HB})$ and $U_{HB}$ for the SD hairpin. In this case, one expects a different melting temperature. Indeed, at this temperature the hairpin is nearly always in its folded conformation and the average value of $U_{HB}$ is lower than in the SA case. Although stacking interactions play a role, the major contribution to this effect is due to the presence of four <tt>GC</tt> only two <tt>AT</tt> base-pairs in the stem.		Figure 2 shows <math>P(U_{HB})</math> and <math>U_{HB}</math> for the SD hairpin. In this case, one expects a different melting temperature. Indeed, at this temperature the hairpin is nearly always in its folded conformation and the average value of <math>U_{HB}</math> is lower than in the SA case. Although stacking interactions play a role, the major contribution to this effect is due to the presence of four <tt>GC</tt> only two <tt>AT</tt> base-pairs in the stem.

	<div style="text-align:center">		<div style="text-align:center">