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Register a new userProtein viscoelastic dynamics: a model system
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A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the model is a strongly over-damped oscillator described by a harmonic restoring force for small displacements that reversibly yields to stress under sufficiently large displacement. This simple dynamical system also reveals unexpectedly rich behavior, exhibiting a series of dynamical transitions and analogies with equilibrium thermodynamic phase transitions. The effects of noise and of inertia are briefly considered and described.
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We investigate the hopping dynamics of a colloidal particle across a potential barrier and within a viscoelastic, i.e., non-Markovian bath, and report two clearly separated time scales in the corresponding waiting time distributions. While the longer time scale exponentially depends on the barrier height, the shorter one is similar to the relaxation time of the fluid. This short time scale is a signature of the storage and release of elastic energy inside the bath, that strongly increases the hopping rate. Our results are in excellent agreement with numerical simulations of a simple Maxwell model.
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctuation relation, the system free energy landscape is evaluated. Three different structural transitions are identified along the unfolding pathways. Furthermore, the reconstruction of the the free and potential energy profiles in terms of inherent structure formalism allows us to put in direct correspondence these transitions with the equilibrium thermal transitions relevant for protein folding/unfolding. Through the study of the fluctuations of the protein structure at different temperatures, we identify the dynamical transitions, related to configurational rearrangements of the protein, which are precursors of the thermal transitions.
We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM disagrees with the bimodal distribution obtained from an all-atom model; however, the bimodal distribution is recovered by strengthening interactions between atoms that are backbone neighbors. We use the backbone-enhanced model to analyze allosteric mechanisms of trypsinogen, and find relatively strong communication between the regulatory and active sites.
We study a granular gas of viscoelastic particles (kinetic energy loss upon collision is a function of the particles relative velocities at impact) subject to a stochastic thermostat. We show that the system displays anomalous cooling and heating rates during thermal relaxation processes, this causing the emergence of thermal memory. In particular, a significant textit{Mpemba effect} is present; i.e., an initially hotter/cooler granular gas can cool down/heat up faster than an in comparison cooler/hotter granular gas. Moreover, a textit{Kovacs effect} is also observed; i.e., a non-monotonic relaxation of the granular temperature --if the gas undergoes certain sudden temperature changes before fixing its value. Our results show that both memory effects have distinct features, very different and eventually opposed to those reported in theory for granular fluids under simpler collisional models. We study our system via three independent methods: approximate solution of the kinetic equation time evolution and computer simulations (both molecular dynamics simulations and Direct Simulation Monte Carlo method), finding good agreement between them.
The locomotion of microorganisms and spermatozoa in complex viscoelastic fluids is of critical importance in many biological processes such as fertilization, infection, and biofilm formation. Depending on their propulsion mechanisms, microswimmers display various responses to a complex fluid environment: increasing or decreasing their swimming speed and efficiency, modifying their propulsion kinematics and swimming gaits, and experiencing different hydrodynamic interactions with their surroundings. In this article, we review the fundamental physics of locomotion of biological and synthetic microswimmers in complex viscoelastic fluids. Starting from a continuum framework, we describe the main theoretical approaches developed to model microswimming in viscoelastic fluids, which typically rely on asymptotically small dimensionless parameters. We then summarise recent progress on the mobility of single cells propelled by cilia, waving flagella and rotating helical flagella in unbounded viscoelastic fluids. We next briefly discuss the impact of other physical factors, including the micro-scale heterogeneity of complex biological fluids, the role of Brownian fluctuations of the microswimmers, the effect of polymer entanglement and the influence of shear-thinning viscosity. In particular, for solutions of long polymer chains whose sizes are comparable to the radius of flagella, continuum models cannot be used and instead Brownian Dynamics for the polymers can predict the swimming dynamics. Finally, we discuss the effect of viscoelasticity on the dynamics of microswimmers in the presence of surfaces or external flows and its impact on collective cellular behavior.
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