Model introduction - Revision history

Doye at 14:34, 13 May 2020

2020-05-13T14:34:45Z

← Older revision		Revision as of 14:34, 13 May 2020
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	This interactions are illustrated below. Orientational modulations of the stacking potential encourage the bases to form coplanar stacks, the twist arising from the different length scales of the backbone separation and the optimum stacking separation. The possibility of unstacking allows single strands to be very flexible. Hydrogen bonding can occur between complementary bases when they are anti-aligned, leading to the formation of double helical structures.		This interactions are illustrated below. Orientational modulations of the stacking potential encourage the bases to form coplanar stacks, the twist arising from the different length scales of the backbone separation and the optimum stacking separation. The possibility of unstacking allows single strands to be very flexible. Hydrogen bonding can occur between complementary bases when they are anti-aligned, leading to the formation of double helical structures.

	~~http~~:~~//www-thphys.physics.ox.ac.uk/people/ThomasOuldridge/Site/The_model~~.png		[[File:the_model_half.png\|500px]]

	(a) Model interaction sites with their interaction ranges (the typical range of an interaction is twice the radius of the sphere shown).		(a) Model interaction sites with their interaction ranges (the typical range of an interaction is twice the radius of the sphere shown).
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	(c) A duplex in this representation.		(c) A duplex in this representation.

			[[File:interactions.png\|600px]]

	~~http://www-thphys.physics.ox.ac.uk/people/ThomasOuldridge/Site/interactions.png~~		Indication of the interactions which hold together a typical duplex.

	Indication of the interactions which hold together a typical duplex~~. V(b.b.) indicates the phosphate-sugar backbone connectivity~~.

	In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release.		In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release.
	The melting temperatures of a set of short DNA oligomers in the sequence-dependent coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]		The melting temperatures of a set of short DNA oligomers in the sequence-dependent coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]

	The model ~~does not incorporate the differentiation between the major and minor grooves of DNA double helices, and~~ incorporates electrostatics only through the short-ranged excluded volume. For this reason, it is only appropriate for the study of systems at high salt concentration, when electrostatic interactions are strongly screened.		The original model incorporates electrostatics only through the short-ranged excluded volume. For this reason, it is only appropriate for the study of systems at high salt concentration, when electrostatic interactions are strongly screened. It also does not incorporate the differentiation between the major and minor grooves of DNA double helices.

			===oxDNA2===

			A new version of the oxDNA model, called oxDNA2, has been released in 2015 ([http://arxiv.org/abs/1504.00821],[http://scitation.aip.org/content/aip/journal/jcp/142/23/10.1063/1.4921957]). It introduces different widths for the major and minor DNA double helical grooves (an example double helix is shown below), a new electrostatic interaction which allows DNA to be studied at salt concentrations equivalent to 0.1M <nowiki>[NaCl]</nowiki> and above, improved large-scale structure prediction, and differentiation between AA and TT stacking strengths.

			https://dna.physics.ox.ac.uk/images/3/37/Perfect_yesmm_nopov.png

			The oxDNA2 model is included in the latest release of the oxDNA code. It can be used in a very similar way to the original oxDNA model. Only a couple of lines in the input file must be added. Firstly, the following line must be included:

			<pre>
			interaction_type = DNA2
			</pre>

			In addition, the salt concentration for the simulation must be specified. For example, to run a simulation with a salt concentration of 0.5M, one should write:

			<pre>
			salt_concentration = 0.5
			</pre>

			Everything else should work in the same way as it does for the original oxDNA model.

	===Simulation units===		===Simulation units===
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	\|-		\|-
	\| 1 unit of length		\| 1 unit of length
	\| 8.518x10<math>^{-10}</math> m		\| 8.518x10<math>^{-10}</math> m = 0.8518 nm
	\|-		\|-
	\| 1 unit of energy		\| 1 unit of energy
	\| 4.142x10<math>^{-20}</math> J		\| thermal energy at 3000K - approximately 4.142x10<math>^{-20}</math> J = 41.42 pN nm
	\|-		\|-
	\| 1 unit of temperature		\| 1 unit of temperature
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	\|-		\|-
	\| 1 unit of force		\| 1 unit of force
	\| 4.863x10<math>^{-11}</math> N		\| 4.863x10<math>^{-11}</math> N = 48.63 pN
	\|-		\|-
	\| 1 unit of mass		\| 1 unit of mass
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	\|-		\|-
	\| 1 unit of time		\| 1 unit of time
	\| 3.03x10<math>^{-12}</math> s		\| 3.03x10<math>^{-12}</math> s = 3.03 ps
			\|-
			\| 1 unit of force constant (1 unit force/1 unit length)
			\| 57.09 pN/nm
			\|-
			\| 1 unit of torque (1 unit force * 1 unit length)
			\| 41.423 pN * nM
			\|}

			===Useful conversions===

			{\|
	\|-		\|-
			\| Boltzmann's constant - in simulation units, we set Boltzmann's constant to 1 so that we can measure temperature and energy with the same unit. Therefore in simulation units energy/K Boltzmann's constant is 0.001/3.
	\|}		\|}

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	P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)		P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
	[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])		[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])

			B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, ''J. Chem. Phys.'' '''142''', 234901 (2015)
			[http://scitation.aip.org/content/aip/journal/jcp/142/23/10.1063/1.4921957 Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/1504.00821 arXiv])

Snodinb: /* Simulation units */

2014-03-11T17:39:09Z

Simulation units

← Older revision		Revision as of 17:39, 11 March 2014
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	===Simulation units===		===Simulation units===
	The code uses ~~dimensionless~~ units for energy, mass, length and time for ~~convenience~~. The relationship between simulation units (SU) and SI units is given below.		The code uses units for energy, mass, length and time that are convenient for a typical system. The relationship between simulation units (SU) and SI units is given below.

	{\|		{\|

Snodinb: /* Simulation units */

2014-03-11T17:37:21Z

Simulation units

← Older revision		Revision as of 17:37, 11 March 2014
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	===Simulation units===		===Simulation units===
	The code uses dimensionless energy, mass, length and ~~timescales~~ for convenience. The relationship between simulation units (SU) and SI units is given below.		The code uses dimensionless units for energy, mass, length and time for convenience. The relationship between simulation units (SU) and SI units is given below.

	{\|		{\|

Sulc: /* Simulation units */

2014-03-11T15:51:20Z

Simulation units

← Older revision		Revision as of 15:51, 11 March 2014
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	\|-		\|-
	\| 1 unit of mass		\| 1 unit of mass
	\| 1.~~66x10~~<math>^{-25}</math> kg		\| 5.24x10<math>^{-25}</math> kg
	\|-		\|-
	\| 1 unit of time		\| 1 unit of time

Sulc at 15:50, 11 March 2014

2014-03-11T15:50:21Z

← Older revision		Revision as of 15:50, 11 March 2014
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	\|-		\|-
	\| 1 unit of time		\| 1 unit of time
	\| 1.~~71x10~~<math>^{-12}</math> s		\| 3.03x10<math>^{-12}</math> s
	\|-		\|-
	\|}		\|}

Romano: /* Simulation units */

2012-12-12T11:35:55Z

Simulation units

← Older revision		Revision as of 11:35, 12 December 2012
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	\| 4.142x10<math>^{-20}</math> J		\| 4.142x10<math>^{-20}</math> J
	\|-		\|-
	\| 1 unit of ~~Temperature~~		\| 1 unit of temperature
	\| 3000 K		\| 3000 K
	\|-		\|-
	\| 1 unit of ~~Force~~		\| 1 unit of force
	\| 4.863x10<math>^{-11}</math> N		\| 4.863x10<math>^{-11}</math> N
	\|-		\|-
	\| 1 unit of ~~Mass~~		\| 1 unit of mass
	\| 1.66x10<math>^{-25}</math> kg		\| 1.66x10<math>^{-25}</math> kg
	\|-		\|-
	\| 1 unit of ~~Time~~		\| 1 unit of time
	\| 1.71x10<math>^{-12}</math> s		\| 1.71x10<math>^{-12}</math> s
	\|-		\|-

Romano: /* Simulation units */

2012-12-12T11:35:29Z

Simulation units

← Older revision		Revision as of 11:35, 12 December 2012
Line 39:		Line 39:
	\|-		\|-
	\| 1 unit of energy		\| 1 unit of energy
	\| 4.~~142~~<math>^{-20}</math> J		\| 4.142x10<math>^{-20}</math> J
	\|-		\|-
	\| 1 unit of Temperature		\| 1 unit of Temperature
Line 45:		Line 45:
	\|-		\|-
	\| 1 unit of Force		\| 1 unit of Force
	\| 4.~~863~~<math>^{-11}</math> N		\| 4.863x10<math>^{-11}</math> N
	\|-		\|-
	\| 1 unit of Mass		\| 1 unit of Mass
	\| 1.66<math>^{-25}</math> kg		\| 1.66x10<math>^{-25}</math> kg
	\|-		\|-
	\| 1 unit of Time		\| 1 unit of Time
	\| 1.71<math>^{-12}</math> s		\| 1.71x10<math>^{-12}</math> s
	\|-		\|-
	\|}		\|}

Sulc at 09:53, 2 October 2012

2012-10-02T09:53:51Z

← Older revision		Revision as of 09:53, 2 October 2012
Line 23:		Line 23:

	In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release.		In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release.
	The melting temperatures of a set of short DNA oligomers in the coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]		The melting temperatures of a set of short DNA oligomers in the sequence-dependent coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]

	The model does not incorporate the differentiation between the major and minor grooves of DNA double helices, and incorporates electrostatics only through the short-ranged excluded volume. For this reason, it is only appropriate for the study of systems at high salt concentration, when electrostatic interactions are strongly screened.		The model does not incorporate the differentiation between the major and minor grooves of DNA double helices, and incorporates electrostatics only through the short-ranged excluded volume. For this reason, it is only appropriate for the study of systems at high salt concentration, when electrostatic interactions are strongly screened.
Line 64:		Line 64:
	[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])		[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])

	P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ~~"arxiv"~~ (2012)		P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
	[http://~~arxiv~~.org/~~abs~~/~~1207.3391~~ Sequence-dependent thermodynamics of a coarse-grained DNA model]		[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])

Sulc at 09:52, 2 October 2012

2012-10-02T09:52:04Z

← Older revision		Revision as of 09:52, 2 October 2012
Line 22:		Line 22:
	Indication of the interactions which hold together a typical duplex. V(b.b.) indicates the phosphate-sugar backbone connectivity.		Indication of the interactions which hold together a typical duplex. V(b.b.) indicates the phosphate-sugar backbone connectivity.

	In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release~~: a paper discussing this parameterisation and its effects is currently in preparation~~.		In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release.
	The melting temperatures of a set of short DNA oligomers in the coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]		The melting temperatures of a set of short DNA oligomers in the coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]

Sulc at 17:35, 23 July 2012

2012-07-23T17:35:57Z

← Older revision		Revision as of 17:35, 23 July 2012
Line 63:		Line 63:
	T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)		T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
	[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])		[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])

			P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, "arxiv" (2012)
			[http://arxiv.org/abs/1207.3391 Sequence-dependent thermodynamics of a coarse-grained DNA model]