Short-time dynamics of polypeptides

Pulling on grafted flexible polymers can cause twisted bundles

Bundles of semiflexible polymers can twist at low temperatures to balance energy gain from attraction and energy cost from bending. This raises the question whether twisting can be also observed for bundles of rather flexible grafted polymers stretched out by pulling force. Here, we address this question using Monte Carlo computer simulations of small bundles. Our data show that for weak forces F < Fl, intertwined globular conformations are favored, whereas for strong forces F > Fu, rod-like bundles emerge. In the intermediate force window Fl < F < Fu, bundles with a helical twist can be clearly identified. Applying a field to all monomers yields qualitatively the same effect. This suggests the conclusion that rather flexible polymers under pulling force or field behave effectively like semiflexible polymers without external pull.

Numerical evidence of Janssen-Oerding's prediction in a three-dimensional spin model far from equilibrium

In 1994, Jansen and Oerding predicted an interesting anomalous tricritical dynamic behavior in three-dimensional models via renormalization group theory. However, we highlight the lack of literature about the computational verification of this universal behavior. Here, we use some tricks to capture the log corrections and the parameters predicted by these authors using the three-dimensional Blume-Capel model. We quantify the crossover phenomena by computing the critical exponents near the tricritical point. In addition, we also perform a more detailed study of the dynamic localization of the phase diagram via power-law optimization.

Pearl-Necklace-Like Local Ordering Drives Polypeptide Collapse

The collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between hydration effects and intrapeptide interactions. Once intrapeptide van der Waal interactions dominate, the chain collapses along a nonequilibrium pathway characterized by formation of pearl-necklace-like local clusters as intermediates that eventually coagulate into a single globule. By describing this coarsening through the contact probability as a function of distance along the chain, we extract a time-dependent length scale that grows in a linear fashion. The collapse dynamics is characterized by a dynamical critical exponent z ≈ 0.5 that is much smaller than the values of z = 1–2 reported for nonbiological polymers. This difference in the exponents is explained by the instantaneous formation of intrachain hydrogen bonds and local ordering that may be correlated with the observed fast folding times of proteins.

Nonequilibrium critical dynamics of the two-dimensional Ashkin-Teller model at the Baxter line

We investigate the short-time universal behavior of the two-dimensional Ashkin-Teller model at the Baxter line by performing time-dependent Monte Carlo simulations. First, as preparatory results, we obtain the critical parameters by searching the optimal power-law decay of the magnetization. Thus, the dynamic critical exponents θ_{m} and θ_{p}, related to the magnetic and electric order parameters, as well as the persistence exponent θ_{g}, are estimated using heat-bath Monte Carlo simulations. In addition, we estimate the dynamic exponent z and the static critical exponents β and ν for both order parameters. We propose a refined method to estimate the static exponents that considers two different averages: one that combines an internal average using several seeds with another, which is taken over temporal variations in the power laws. Moreover, we also performed the bootstrapping method for a complementary analysis. Our results show that the ratio β/ν exhibits universal behavior along the critical line corroborating the conjecture for both magnetization and polarization.

'Dynamic Distance' Reaction Coordinate for Competing Bonds: Applications in Classical and Ab Initio Simulations

A versatile reaction coordinate, the "dynamic distance", is introduced for the study of reactions involving the rupture and formation of a series of chemical bonds or contacts. The dynamic distance is a mass-weighted mean of selected distances. When implemented as a generalized constraint, the dynamic distance is particularly suited for driving activated processes by controlled increase during a simulation. As a single constraint acting upon multiple degrees of freedom, the sequence of events along the resulting reaction pathway is determined unambiguously by the underlying energy landscape. Free energy profiles can be readily obtained from the mean constraint force. In this paper both theoretical aspects and numerical implementation are discussed, and the unique and diverse properties of this reaction coordinate are demonstrated using three examples:  In the framework of Car-Parrinello molecular dynamics, we present results for the prototypical double proton-transfer reaction in formic acid dimer and the photocycle of the guanine-cytosine DNA base pair. As a classical mechanical example, the opening of the binding pocket of the enzyme rubisco is analyzed.

Time-dependent Monte Carlo simulations of critical and Lifshitz points of the axial-next-nearest-neighbor Ising model

In this work, we study the critical behavior of second-order points, specifically the Lifshitz point (LP) of a three-dimensional Ising model with axial competing interactions [the axial-next-nearest-neighbor Ising (ANNNI) model], using time-dependent Monte Carlo simulations. We use a recently developed technique that helps us localize the critical temperature corresponding to the best power law for magnetization decay over time: <M>(m(0)=1)~t(-β/νz), which is expected of simulations starting from initially ordered states. We obtain original results for the dynamic critical exponent z, evaluated from the behavior of the ratio F(2)(t)=<M(2)>(m(0)=0)/<M>(2)(m(0)=1)~t(3/z), along the critical line up to the LP. We explore all the critical exponents of the LP in detail, including the dynamic critical exponent θ that characterizes the initial slip of magnetization and the global persistence exponent θ(g) associated with the probability P(t) that magnetization keeps its signal up to time t. Our estimates for the dynamic critical exponents at the Lifshitz point are z=2.34(2) and θ(g)=0.336(4), values that are very different from those of the three-dimensional Ising model (the ANNNI model without the next-nearest-neighbor interactions at the z axis, i.e., J(2)=0), i.e., z≈2.07 and θ(g)≈0.38. We also present estimates for the static critical exponents β and ν, obtained from extended time-dependent scaling relations. Our results for static exponents are in good agreement with previous works.

Generalized Metropolis dynamics with a generalized master equation: an approach for time-independent and time-dependent Monte Carlo simulations of generalized spin systems

The extension of Boltzmann-Gibbs thermostatistics, proposed by Tsallis, introduces an additional parameter q to the inverse temperature β. Here, we show that a previously introduced generalized Metropolis dynamics to evolve spin models is not local and does not obey the detailed energy balance. In this dynamics, locality is only retrieved for q=1, which corresponds to the standard Metropolis algorithm. Nonlocality implies very time-consuming computer calculations, since the energy of the whole system must be reevaluated when a single spin is flipped. To circumvent this costly calculation, we propose a generalized master equation, which gives rise to a local generalized Metropolis dynamics that obeys the detailed energy balance. To compare the different critical values obtained with other generalized dynamics, we perform Monte Carlo simulations in equilibrium for the Ising model. By using short-time nonequilibrium numerical simulations, we also calculate for this model the critical temperature and the static and dynamical critical exponents as functions of q. Even for q≠1, we show that suitable time-evolving power laws can be found for each initial condition. Our numerical experiments corroborate the literature results when we use nonlocal dynamics, showing that short-time parameter determination works also in this case. However, the dynamics governed by the new master equation leads to different results for critical temperatures and also the critical exponents affecting universality classes. We further propose a simple algorithm to optimize modeling the time evolution with a power law, considering in a log-log plot two successive refinements.

Residue length and solvation model dependency of elastinlike polypeptides

We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n, where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

Critical domain-wall dynamics of model B

With Monte Carlo methods, we simulate the critical domain-wall dynamics of model B, taking the two-dimensional Ising model as an example. In the macroscopic short-time regime, a dynamic scaling form is revealed. Due to the existence of the quasirandom walkers, the magnetization shows intrinsic dependence on the lattice size L . An exponent which governs the L dependence of the magnetization is measured to be sigma=0.243(8) .