Thermodynamic free energy methods to investigate shape transitions in bilayer membranes

DOI10.1007/S12572-015-0159-5MaRDI QIDQ336079zbMATH OpenOpenAlexWikidataFDO

Authors N. Ramakrishnan, Richard W. Tourdot, R. Radhakrishnan

Publication date 10 November 2016

Published in International Journal of Advances in Engineering Sciences and Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1510.02940, http://europepmc.org/articles/pmc5016036

zbMATH Keywords

thermodynamic integrationend-point-catastrophefree energy techniquesumbrella samplingWidom insertion

Mathematics Subject Classification ID

Cell biology (92C37) Irreversible thermodynamics, including Onsager-Machlup theory (82C35) Membranes (74K15)

Abstract: The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While computational methods to delineate the free energy landscape are routinely used to analyze the relative stability of conformational states, to determine phase boundaries, and to compute ligand-receptor binding energies its use in problems involving the cell membrane is limited. Here, we present an overview of four different free energy methods to study morphological transitions in bilayer membranes, induced either by the action of curvature remodeling proteins or due to the application of external forces. Using a triangulated surface as a model for the cell membrane and using the framework of dynamical triangulation Monte Carlo, we have focused on the methods of Widom insertion, thermodynamic integration, Bennett acceptance scheme, and umbrella sampling and weighted histogram analysis. We have demonstrated how these methods can be employed in a variety of problems involving the cell membrane. Specifically, we have shown that the chemical potential, computed using Widom insertion, and the relative free energies, computed using thermodynamic integration and Bennett acceptance method, are excellent measures to study the transition from curvature sensing to curvature inducing behavior of membrane associated proteins. The umbrella sampling and WHAM analysis has been used to study the thermodynamics of tether formation in cell membranes and the quantitative predictions of the computational model are in excellent agreement with experimental measurements. Furthermore, we also present a method based on WHAM and thermodynamic integration to handle problems related to end-point-catastrophe that are common in most free energy methods

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Cites work

• scientific article; zbMATH DE number 3511136 (Why is no real title available?)
• scientific article; zbMATH DE number 1082719 (Why is no real title available?)
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• Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations

Cited in

(1)

• Towards an understanding of the temperature/pressure configurational and free-energy landscape of biomolecules

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