Self-generated disorder and structural glass formation in homopolymer globules

Theory of molecular crowding in Brownian hard-sphere liquids

We derive an analytical pair potential of mean force for Brownian molecules in the liquid state. Our approach accounts for many-particle correlations of crowding particles of the liquid and for diffusive transport across the spatially modulated local density of crowders in the dense environment. Focusing on the limit of equal-size particles, we show that this diffusive transport leads to additional density- and structure-dependent terms in the interaction potential and to a much stronger attraction (by a factor of ≈4 at average volume fraction of crowders φ{0}=0.25) than in the standard depletion interaction where the diffusive effects are neglected. As an illustration of the theory, we use it to study the size of a polymer chain in a solution of inert crowders. Even in the case of an athermal background solvent, when a classical chain should be fully swollen, we find a sharp coil-globule transition of the ideal chain collapsing at a critical value of the crowder volume fraction φ{c}≈0.145.

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N (G) is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε < ε(s) with fast internal dynamics and a solid-like regime (for ε > ε(s) with slow internal dynamics. The cohesion strength ε(s) of this freezing transition depends on N (G) . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N (G) . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.

Probing structural and dynamical transitions in polymer globules by force

The dynamics of proteins and biopolymers play a crucial role in their function. By using Brownian dynamics we show that polymer globules, which serve as a model system for proteins, undergo a size-dependent dynamical transition from a liquid-like state at high T to a frozen state at low T with a relaxation time that diverges at the transition point. Furthermore, a stretch-induced melting transition is shown to be readily controlled by external forces that exploit the polymer connectivity to modify the size of the globule. This pathway could be a general route to enhance the rate of conformational changes in naturally occurring biopolymers.

Compact phases of polymers with hydrogen bonding

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen-bond formation, respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strengths of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen-bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling beta sheets appearing in the native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.

Interacting growth walk: a model for hyperquenched homopolymer glass?

We show that the compact self-avoiding walk configurations, kinetically generated by the recently introduced interacting growth walk (IGW) model, can be considered as members of a canonical ensemble if they are assigned random values of energy. Such a mapping is necessary for studying the thermodynamic behavior of this system. We have presented the specific heat data for the IGW, obtained from extensive simulations on a square lattice; we observe a broad hump in the specific heat above the theta point, contrary to expectation.

Slow relaxation and solvent effects in the collapse of a polymer

Using molecular dynamic simulations we study the quench of a homopolymer chain into a poor solvent at finite temperature. We show that, depending on the quench depth, there are different relaxation pathways to the collapsed state. Solvent effects are introduced through an effective Lennard-Jones potential depending on the local monomer density. The various relaxation regimes are characterized by the contact correlation function. As the quench depth increases, the system evolves towards a glassy state, and the relaxation dynamics continuously changes from an exponential to a stretched exponential law. The characteristic relaxation time diverges at low temperature following an Arrhenius law, like in the case of strong glasses. We found that the stretching exponent depends on aging in a nonuniversal way. The solvent modifies the globular state by diminishing the effects of frustration and glassy behavior.