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Method for sampling compact configurations for semistiff  polymers
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
Saint-Petersburg State University, Physical Faculty.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
2011 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, 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.

Place, publisher, year, edition, pages
2011. Vol. 84, no 1, 016702- p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-151616DOI: 10.1103/PhysRevE.84.016702ISI: 000293399500004OAI: oai:DiVA.org:uu-151616DiVA: diva2:410697
Available from: 2011-04-14 Created: 2011-04-14 Last updated: 2017-12-11Bibliographically approved
In thesis
1. Monte Carlo Simulations of the Equilibrium Properties of Semi-stiff Polymer Chains: Efficient Sampling from Compact to Extended Structures
Open this publication in new window or tab >>Monte Carlo Simulations of the Equilibrium Properties of Semi-stiff Polymer Chains: Efficient Sampling from Compact to Extended Structures
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
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:nbn:se:uu:diva-151618 (URN)978-91-554-8088-2 (ISBN)
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

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Siretskiy, AlexeyElvingson, Christer

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