Understanding biological glasses via large-scale molecular dynamics simulations

Lead Research Organisation: University of Bristol
Department Name: Mathematics


(no more than 4,000 characters inc spaces) The glassy phase is a state of matter between a liquid and a solid. Glasses are like a liquid in the way that they are statistically isotropic, and they are like solids in that the atomic motion is largely suppressed. Considering the large plethora of glassy materials and the broad spectrum of routes that can lead to their formation, understanding the physical properties of glassy materials is one of the most difficult and, at the same time, fascinating "grand challenge problem" of our time [1].
Remarkably, Nature has found its way to preserve life during environmental stresses by taking advantage of glassy states. Anhydrobiosis (from the Greek "life without water") is an astounding strategy that allows certain spores, seeds, insects, crustaceans, nematodes, rotifers and tardigrades to survive environmental extremes such as, e.g., extreme drought, lack of nutrients, intense radiations, etc. During anhydrobiosis, these organisms increase the production of sugars (namely, threalose in invertebrates and sucrose in plants) up to a point in which sugars permeate inside and outside the cells replacing water molecules and creating a glassy matrix known as biological glass. The biological glass prevents otherwise lethal damages caused by the absence of water (like proteins and DNA unfolding, membranes rupture, etc.), and induces an almost completely desiccated state known as "tun" state, in which the metabolism of the organism either stops completely or decreases to a level that cannot be measured. On the other hand, when environmental circumstances eventually stabilize and water become available again, the biological glass melts and the metabolism increases, restoring all vital signs.
This research will investigate the formation and the effects of biological glasses in a typical biophysical membrane via molecular dynamics simulations in order to understand (i) how biological glasses are formed in terms of dehydration rate, (ii) what are their properties depending on the adopted protocol, and (iii) how biological membranes recover functionality after rehydration. In order to achieve this goal, we will perform large-scale molecular dynamics simulations with the code GROMACS that can run on GPUs, as standard CPU simulations cannot tackle the complexity of this problem and the required long simulation times. We will simulate mixtures of water and sugar (trehalose or sucrose) confined in DMPC lipids. We will simultaneously model the behavior of the water+sugar+DMPC mixture at different concentrations of sugars (to mimic the sugar production in anhydrobiotes) and at different temperatures (to mimic desiccation conditions). For each system, we will perform dehydration-rehydration cycles. During the desiccation cycles, we will observe (as in experiments) the disruption of the DMPC membrane in the runs far from the ideal protocol adopted by anhydrobiotes, allowing us to identify and to characterize the mechanisms leading to and governing anhydrobiosis.
From this project we will comprehensively draw a general picture of the thermodynamic conditions at which biological glasses are produced as well as the molecular mechanisms that lead to their formation, allowing us to understand how anhydrobiotes survive extreme conditions.
[1] K. Binder and W. Kob. Glassy Materials and Disor- dered Solids. World Scientific, 2011.
[2] S. Yashina, S. Gubin, S. Maksimovich, A. Yashina, E. Gakhova, and D. Gilichinskyb. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in siberian permafrost. Proc. Natl. Ac. Sci. USA, 109:4008-4013, 2012.
[3] D. Sloan, R. Alves Batista, and A. Loeb. The resilience of life to astrophysical events. Sci. Rep., 7:5419, 2017.
[4] F. Martelli, H.-Y. Ko, E. C. Og uz, and R. Car. Local- order metric for condensed phase environments. Phys. Rev. B, 97:064105, 2016.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
EP/T51763X/1 01/10/2019 30/09/2024
2388766 Studentship EP/T51763X/1 01/04/2020 31/03/2024 Alberto Toffano