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Monte Carlo Simulations of the Equilibrium Properties of Semi-stiff Polymer Chains: Efficient Sampling from Compact to Extended Structures
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Polymers is a class of molecules which can have many different structures due to a large number of degrees of freedom. Many biopolymers, e.g. DNA, but also synthetic macromolecules have special structural features due to their backbone stiffness. Since such structural properties are important for e.g. the biological function, a lot of effort has been put into the investigation of the configurational properties of semi-stiff molecules.

A theoretical treatment of these systems is often accompanied by computer simulations. The main idea is to compare theoretically derived models with experimental results for real polymers. Using Monte Carlo simulations, I have investigated how this computational technique can build a bridge between theoretical models and experimentally observed phenomena. The effort was mainly directed to develop sampling techniques, for efficiently exploring the configurational space of semi-stiff chains in a wide range of structures. The work was concentrated on compact conformations, since they, as is well known from previous studies, are difficult to sample using conventional methods.

In my studies I have shown that the simple and, at a first glance, time consuming method of bead-by-bead regrow as a way of changing the configuration of a semi-stiff chain gave very promising and encouraging results when combined with modern simulation techniques, like Entropic Sampling with the Wang-Landau algorithm. The resulting simulation package was also suitable for parallelization which resulted in a further speed-up of the calculations.

In addition to the more elaborate sampling methods, I also investigated external conditions to induce compaction of a semi-stiff polymer. In the case of a polyampholyte the condensing agent could be a multivalent salt, creating effective attraction between the loops of the chain, while for neutral polymers, an external field and the geometry of the confining volume can induce a compaction.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2011. , 64 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 831
Keyword [en]
polymers, equilibrium properties, statistical mechanics, computer simulation, Monte Carlo, Wang-Landau, compact structures, parallel computations
National Category
Physical Chemistry
Research subject
Chemistry with specialization in Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-151618ISBN: 978-91-554-8088-2OAI: oai:DiVA.org:uu-151618DiVA: diva2:411549
Public defence
2011-05-31, A2001, Ångström Laboratory, Lägerhyddsvägen 1, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2011-05-10 Created: 2011-04-14 Last updated: 2011-07-01Bibliographically approved
List of papers
1. Number fluctuations of the condensing agent affects the coil-toroid coexistence for semi-stiff polyelectrolytes
Open this publication in new window or tab >>Number fluctuations of the condensing agent affects the coil-toroid coexistence for semi-stiff polyelectrolytes
2010 (English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 22, no 41, 414103Article in journal (Refereed) Published
Abstract [en]

A semi-stiff charged polymer with counterions and salt was investigated using a Monte Carlo method with the Wang–Landau sampling scheme. Simulations show the coexistence of thermodynamically stable structures—prolonged and compact (toroidal-like). The transition between the two states is accompanied by concentration fluctuations for the condensing agent. Compact structures are accompanied by more multivalent counterions than prolonged ones.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-122556 (URN)10.1088/0953-8984/22/41/414103 (DOI)000291926300005 ()21386586 (PubMedID)
Available from: 2010-04-14 Created: 2010-04-14 Last updated: 2015-09-11Bibliographically approved
2. Free Energy Monte Carlo Simulations on a Distributed Network
Open this publication in new window or tab >>Free Energy Monte Carlo Simulations on a Distributed Network
2012 (English)In: Applied Parallel and Scientific Computing: 10th International Conference, PARA 2010, Reykjavík, Iceland, June 6-9, 2010, Revised Selected Papers, Part II, 2012, Vol. 7134, 1-2 p.Conference paper (Refereed)
Abstract [en]

While the use of enhanced sampling techniques and parallel computing to determine potentials of mean force is in widespread use in modern Molecular Dynamics and Monte Carlo simulation studies, there have been few methods that efficiently combine heterogeneous computer resources of varying quality and speeds in realizing a single simulation result on a distributed network. Here, we apply an algorithm based on the Monte Carlo method of Wang and Landau within a client-server framework, in which individual computing nodes report a histogram of regions of phase space visited and corresponding updates to a centralized server at regular intervals entirely asynchronously. The server combines the data and reports the sum to all nodes so that the overall free energy determination scales linearly with the total amount of resources allocated. We discuss our development of this technique and present results for molecular simulations of DNA.

Series
, Lecture Notes in Computer Science, 7134
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-151617 (URN)10.1007/978-3-642-28145-7_1 (DOI)000309716000001 ()978-3-642-28144-0 (ISBN)
Conference
10th Nordic International Conference on Applied Parallel Computing - State of the Art in Scientific and Parallel Computing (PARA) Location: Univ Iceland, Sch Engn & Nat Sci, jun 6-9, 2020, Reykjavik, ICELAND
Available from: 2011-04-14 Created: 2011-04-14 Last updated: 2012-11-26Bibliographically approved
3. Method for sampling compact configurations for semistiff  polymers
Open this publication in new window or tab >>Method for sampling compact configurations for semistiff  polymers
2011 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, Vol. 84, no 1, 016702- p.Article in journal (Refereed) Published
Abstract [en]

The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-151616 (URN)10.1103/PhysRevE.84.016702 (DOI)000293399500004 ()
Available from: 2011-04-14 Created: 2011-04-14 Last updated: 2013-06-13Bibliographically approved
4. Determination of the equilibrium charge distribution for polyampholytes of different compactness in a single computer experiment
Open this publication in new window or tab >>Determination of the equilibrium charge distribution for polyampholytes of different compactness in a single computer experiment
2011 (English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 23, no 37, 375102- p.Article in journal (Refereed) Published
Abstract [en]

The conformational properties of charge-balanced polyampholytes described by the end-to-end distance or radius of gyration depend on parameters such as the temperature and pH as well as on the detailed charge distribution along the backbone. In this work we present a method to determine the charge distribution along a semi-stiff polyampholyte backbone which will result in a thermodynamically stable structure for the compactness of interest, from several loops to an uncoiled structure, performed in a single computer experiment.

Keyword
polyampholytes, semi-stiff polymers, Monte Carlo, Wang-Landau, compact structures, shape transitions
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-151611 (URN)10.1088/0953-8984/23/37/375102 (DOI)000294785400010 ()
Available from: 2011-04-14 Created: 2011-04-14 Last updated: 2011-09-27Bibliographically approved
5. Polymer shape transition by nonuniform confinement
Open this publication in new window or tab >>Polymer shape transition by nonuniform confinement
(English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648XArticle in journal (Refereed) Submitted
Keyword
semi-stiff polymers, Monte Carlo, Wang-Landau, Extended Ensemble, compact structures, shape transitions
Identifiers
urn:nbn:se:uu:diva-151607 (URN)
Available from: 2011-04-14 Created: 2011-04-14 Last updated: 2011-07-08Bibliographically approved

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