A method for characterizing transition concertedness from polymer dynamics computer simulations
A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD...
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E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
1995 |
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| Umfang: |
9 Ill. ; 3 Tab. 16 |
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| Reproduktion: |
Wiley InterScience Backfile Collection 1832-2000 |
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| Übergeordnetes Werk: |
in: Biopolymers - New York : John Wiley & Sons, Inc., 35(1995) vom: Jan., Seite 31-46 |
| Übergeordnetes Werk: |
volume:35 ; year:1995 ; month:01 ; pages:31-46 ; extent:16 |
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| 520 | |a A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. | ||
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(DE-627)NLEJ159591120 DE-627 ger DE-627 rakwb eng A method for characterizing transition concertedness from polymer dynamics computer simulations 1995 9 Ill. 3 Tab. 16 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. Wiley InterScience Backfile Collection 1832-2000 Brown, Michael L. oth Venable, Richard M. oth Pastor, Richard W. oth in Biopolymers New York : John Wiley & Sons, Inc. 35(1995) vom: Jan., Seite 31-46 (DE-627)NLEJ15907066X (DE-600)1480801-8 0006-3525 nnns volume:35 year:1995 month:01 pages:31-46 extent:16 http://dx.doi.org/10.1002/bip.360350105 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 35 1995 1 31-46 16 |
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(DE-627)NLEJ159591120 DE-627 ger DE-627 rakwb eng A method for characterizing transition concertedness from polymer dynamics computer simulations 1995 9 Ill. 3 Tab. 16 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. Wiley InterScience Backfile Collection 1832-2000 Brown, Michael L. oth Venable, Richard M. oth Pastor, Richard W. oth in Biopolymers New York : John Wiley & Sons, Inc. 35(1995) vom: Jan., Seite 31-46 (DE-627)NLEJ15907066X (DE-600)1480801-8 0006-3525 nnns volume:35 year:1995 month:01 pages:31-46 extent:16 http://dx.doi.org/10.1002/bip.360350105 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 35 1995 1 31-46 16 |
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(DE-627)NLEJ159591120 DE-627 ger DE-627 rakwb eng A method for characterizing transition concertedness from polymer dynamics computer simulations 1995 9 Ill. 3 Tab. 16 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. Wiley InterScience Backfile Collection 1832-2000 Brown, Michael L. oth Venable, Richard M. oth Pastor, Richard W. oth in Biopolymers New York : John Wiley & Sons, Inc. 35(1995) vom: Jan., Seite 31-46 (DE-627)NLEJ15907066X (DE-600)1480801-8 0006-3525 nnns volume:35 year:1995 month:01 pages:31-46 extent:16 http://dx.doi.org/10.1002/bip.360350105 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 35 1995 1 31-46 16 |
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(DE-627)NLEJ159591120 DE-627 ger DE-627 rakwb eng A method for characterizing transition concertedness from polymer dynamics computer simulations 1995 9 Ill. 3 Tab. 16 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. Wiley InterScience Backfile Collection 1832-2000 Brown, Michael L. oth Venable, Richard M. oth Pastor, Richard W. oth in Biopolymers New York : John Wiley & Sons, Inc. 35(1995) vom: Jan., Seite 31-46 (DE-627)NLEJ15907066X (DE-600)1480801-8 0006-3525 nnns volume:35 year:1995 month:01 pages:31-46 extent:16 http://dx.doi.org/10.1002/bip.360350105 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 35 1995 1 31-46 16 |
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A method for characterizing transition concertedness from polymer dynamics computer simulations |
| abstract |
A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. |
| abstractGer |
A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. |
| abstract_unstemmed |
A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc. |
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A method for characterizing transition concertedness from polymer dynamics computer simulations |
| url |
http://dx.doi.org/10.1002/bip.360350105 |
| remote_bool |
true |
| author2 |
Brown, Michael L. Venable, Richard M. Pastor, Richard W. |
| author2Str |
Brown, Michael L. Venable, Richard M. Pastor, Richard W. |
| ppnlink |
NLEJ15907066X |
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z |
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false |
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false |
| author2_role |
oth oth oth |
| up_date |
2024-07-05T22:03:30.635Z |
| _version_ |
1803778272147800064 |
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It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc.</subfield></datafield><datafield tag="533" ind1=" " ind2=" "><subfield code="f">Wiley InterScience Backfile Collection 1832-2000</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Brown, Michael L.</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Venable, Richard M.</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Pastor, Richard W.</subfield><subfield code="4">oth</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">in</subfield><subfield code="t">Biopolymers</subfield><subfield code="d">New York : John Wiley & Sons, Inc.</subfield><subfield code="g">35(1995) vom: Jan., Seite 31-46</subfield><subfield code="w">(DE-627)NLEJ15907066X</subfield><subfield code="w">(DE-600)1480801-8</subfield><subfield code="x">0006-3525</subfield><subfield code="7">nnns</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:35</subfield><subfield code="g">year:1995</subfield><subfield code="g">month:01</subfield><subfield code="g">pages:31-46</subfield><subfield code="g">extent:16</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">http://dx.doi.org/10.1002/bip.360350105</subfield><subfield code="q">text/html</subfield><subfield code="z">Deutschlandweit zugänglich</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_U</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">ZDB-1-WIS</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_NL_ARTICLE</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">35</subfield><subfield code="j">1995</subfield><subfield code="c">1</subfield><subfield code="h">31-46</subfield><subfield code="g">16</subfield></datafield></record></collection>
|
| score |
7.4030848 |