On the Escape Transition of a Tethered Gaussian Chain; Exact Results in Two Conjugate Ensembles

Summary: Upon compression between two pistons an end-tethered polymer chain undergoes an abrupt transition from a confined coil state to an inhomogeneous flower-like conformation that is partially escaped from the gap. In the thermodynamic limit the system demonstrates a first-order phase transition. A rigorous analytical theory of this phenomenon for a Gaussian chain is presented in two ensembles: a) the H-ensemble, in which the distance H between pistons plays the role of the control parameter, and b) the conjugate f-ensemble in which the external compression force f is the independent parameter. A loop region for 〈f(H)〉 with negative compressibility exists in the H-ensemble, while in the f-ensemble 〈H(f)〉 is strictly monotonic. The average lateral forces taken as functions of H (or 〈H〉, respectively) have distinctly different behavior in the two ensembles. This result is a clear counterexample of the main principles of statistical mechanics stating that all ensembles are equivalent in the thermodynamic limit. Another theorem states that the thermodynamic potential as a function of volume must be concave everywhere. We demonstrated that the exact free energy in the H-ensemble contradicts this statement. Inapplicability of these fundamental theorems to a macromolecule undergoing the escape transition is clearly related to the fact that phase coexistence in the present system is strictly impossible. This is a direct consequence of the tethering and the absence of global translational degrees of freedom of the polymer chain.     

Stretching and compression of a macromolecule under different modes of mechanical manupulations

This review is concerned with the response of an isolated polymer chain subjected to the action of the two different modes of the mechanical impact on the chain ends. In one mode, the end-to-end distance is changed in a controlled fashion and the fluctuating response force is measured; in the second case, an external stress field is applied to the chain end, and the measured response of the system is the fluctuating end-to-end distance. The main attention is focused on the results of the computer-aided simulation experiments and theoretical results. Upon stretching of an ideal chain, a real chain in a good solvent, or a globule, the resultant strain-force and force-strain dependences are shown to be different for chains with finite length L; however, this difference diminishes with an increase in the length of a molecule. When the anchored Gaussian chain is separated from the adsorbing surface, this difference disappears in the limit of high L; however, in the neighborhood of the phase transition, some characteristics (fluctuations, distribution functions) appear to be critically different under different impact modes even in the thermodynamic limit. The example of an abnormal system is discussed: The behavior of a polymer chain compressed by a small piston is different in the conjugated ensembles, and, as the system increases in size, this difference becomes even more pronounced.     

Sampling of rare events using hidden restraints

A method to enhance sampling of rare events is presented. It makes use of distance or dihedral-angle restraints to overcome an energy barrier separating two metastable states or to stabilize a transition state between the two metastable states. In order not to perturb these metastable end states themselves, a prefactor is introduced into the restraining energy function, which smoothly increases the weight of this function from zero to one at the transition state or on top of the separating energy barrier and then decreases the weight again to zero at the final state. The method is combined with multi-configurational thermodynamic integration and applied to two biomolecular systems, which were difficult to treat using standard thermodynamic integration. As first example the free energy difference of a cyclic alpha-aminoxy-hexapeptide-ion complex upon changing the ion from Cl- to Na+ was calculated. A large conformational rearrangement of the peptide was necessary to accommodate this change. Stabilizing the transition state by (hidden) restraints facilitates that. As a second example, the free energy difference between the 4C1 and the 1C4 conformation of beta-D-glucopyranoside was calculated. In unrestrained simulations the change from the 4C1 into the 1C4 conformation was never observed because of the high energy barrier separating the two states. Using (hidden) restraints, the transition from the 4C1 into the 1C4 state and back could be enforced without perturbing the end states. As comparison, for the same transitions the potential of mean force as obtained by using dihedral-angle constraints is provided.     

拉力诱导下的紧密高分子链相变行为

采用相互作用自回避行走(interacting self-avoiding walks,ISAWS)模型研究了一端固定的紧密高分子链在拉伸过程中的低温相变行为,观察到在拉伸过程中当温度T<0.1时平均拉力会出现一个震荡,随着温度的升高这种震荡现象又渐渐消失,这是由于紧密高分子链在低温时类似于β折叠的"冻结构象"被拉开而引起的.比较吸附条件下和无吸附作用下平均拉力、自由能以及相变行为的差别,发现在吸附条件下在拉伸的初始阶段为了克服表面吸附的相互作用,拉力会出现一个峰.吸附作用也使得外界作用到高分子链上的实际有效拉力减小,造成崩塌相态(collapsed phase)区域面积减少.另外发现在吸附条件下平均拉力还受温度变化的影响.在拉伸的初期由于单体间存在体积排除效应,平均拉力是随着温度的升高而降低,随着拉伸的深入当末端距到达一定长度时平均拉力是随着温度的升高而增加.并同Kumar等人在不考虑吸附作用下拉伸紧密高分子链得到的结果进行了比较.这些研究对于进一步研究外力诱导下吸附紧密高分子的相变有一定的参考价值.     

Lindemann measures for the solid-liquid phase transition

A set of Lindemann measures, based on positional deviations or return distances, defined with respect to mechanically stable inherent structure configurations, is applied to understand the solid-liquid phase transition in a Lennard-Jones-type system. The key quantity is shown to be the single-particle return distance-squared distribution. The first moment of this distribution is related to the Lindemann parameter which is widely used to predict the melting temperature of a variety of solids. The correlation of the single-particle return distance and local bond orientational order parameter in the liquid phase provides insights into mechanisms for melting. These generalized Lindemann measures, especially the lower order moments of the single-particle return distance distribution, show clear signatures of the transition of the liquid from the stable to the metastable, supercooled regime and serve as landscape-based indicators of the thermodynamic freezing transition for the Lennard-Jones-type system investigated.     

三维吸附紧密高分子单链的力学性质研究

采用PERM(pruned-enriched Rosenbluth method)算法,研究了吸附在界面附近的紧密高分子链力学行为.发现当界面的吸附能比较大时,紧密高分子链从紧贴于吸附界面到逐渐远离的过程中,其外形会经历4种典型的变化.同时紧密高分子链的尺寸大小如/N、xy/N、z/N,形状参数<δ*>,热力学性质如每个键的平均自由能A/N,平均相互作用能/N等,甚至所受外力的大小都会同时做出相应的变化,其出现变化的位置也一致.特别是随着紧密高分子链离开吸附界面的过程中,作用于高分子链上的外力明显出现几个力学平台,这与实验得到的结果完全一致.同时还研究了弱吸附能的情况,在这种情况下实验是很难进行的.     

Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles

Stretching experiments on single molecules of arbitrary length opened the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions, corresponding to different statistical mechanics ensembles, yield different force-displacement curves. We formulate analytical expressions and develop Monte Carlo simulations to quantitatively evaluate the difference between the Helmholtz and the Gibbs ensembles for a wide range of polymer models of biological relevance. We consider generalizations of the freely jointed chain and of the worm-like chain models with extensible bonds. In all cases we show that the convergence to the thermodynamic limit upon increasing contour length is described by a suitable power law and a specific scaling exponent, characteristic of each model.     

Polymer chains in good solvent within attracting walls

It is known that a polymer chain in an ideal solvent confined within parallel attracting walls undergoes a second-order transition at the temperature T* satisfying the equation exp[-ε/(k_BT*)]=6/5; here the model consists of a chain placed on a cubic lattice, and ε (<0) is the attractive energy experienced by a chain segment contacting a wall. We then investigate the effect induced by a good solvent upon the chain behavior. A single chain is considered; within the Gaussian approximation, we assume that its partition function may be factorized in two terms, one across the wall planes and another parallel to them. For an interplanar distance L significantly smaller than the average radius of gyration the compressed chain is assumed to reach a uniform density, so that the free energy contribution due to the intrachain atomic contacts is a function of the density alone. It may be shown that the effective value of ε/(k_BT*)(=σ) is the difference between the value to be expected “in vacuo” and β/(z-2), where z is the degree of coordination of the lattice and β is the excluded-volume parameter. As a result, for large values of L we may have an attractive effect exerted by the chain on the walls whereas at small L's we invariably have a repulsion. For the cubic lattice we have a repulsion and an attraction for large L approximatively for σ < ln(6/5)+β/(z-2) and for σ > (ln(6/5)+β/(z-2), respectively, whereas we have inversion between the two regimes at some distance L for intermediate values of σ. In the limit of an infinite molecular weight the inversion translates into a thermodynamic transition. We believe the present model may explain some important features seen in polymer adhesion.     

Measurement of nonequilibrium entropy from space-time thermodynamic integration

The entropy of a system transiently driven out of equilibrium by a time-inhomogeneous stochastic dynamics is first expressed as a transient response function generalizing the nonlinear Kawasaki-Crooks response. This function is then reformulated into three statistical averages defined over ensembles of nonequilibrium trajectories. The first average corresponds to a space-time thermodynamic perturbation relation, while the two following ones correspond to space-time thermodynamic integration relations. Provided that trajectories are initiated starting from a distribution of states that is analytically known, the ensemble averages are computationally amenable to Markov chain Monte Carlo methods. The relevance of importance sampling in path ensembles is confirmed in practice by computing the nonequilibrium entropy of a driven toy system. We finally study a situation where the dynamics produces entropy. In this case, we observe that space-time thermodynamic integration still yields converged estimates, while space-time thermodynamic perturbation turns out to converge very slowly.     

Analytic density-functional self-consistent-field theory of diblock copolymers near patterned surfaces

Analytical solutions are derived for the density profiles and the free energies of compressible diblock copolymer melts (or incompressible copolymer solutions) near patterned surfaces. The density-functional self-consistent-field theory is employed along with a Gaussian chain model for bonding constraints and a random mixing approximation for nonbonded interactions. An analytical solution is rendered possible by expanding the chain distribution function around an inhomogeneous reference state with a nontrivial analytical solution, by retaining the linear terms, and by requiring consistency with the homopolymer limit. The density profiles are determined by both real and complex roots of a sixth-degree polynomial that may easily be obtained by solving a generalized eigenvalue problem. This analytical formulation enables one to efficiently explore the large nine-dimensional parameter space and can serve as a first approximation to computationally intensive studies with more detailed models. Illustrative computations are provided for uniform and patterned surfaces above the order-disorder transition. The results are consistent with the previous self-consistent-field calculations in that lamellar ordering appears near the surface above the order-disorder transition and the lamella order perpendicular or parallel to the surface depending on the commensurability between the periods of the surface pattern and the density oscillations.     

Intramolecularly ordered globules and the collapse of short chains

We investigate the poor-solvent collapse of short chains having different stiffness through self-consistent minimization of the intramolecular free energy under the constraint of fixed segment lengths between adjacent beads. At first the chains form the Random Gaussian Globule, where the beads are distributed at random at the same average distance from the centre of mass, while the segments show very little correlation. At a larger attractive potential, this collapsed globule undergoes a transition to one or more ordered compact states, depending on the chain stiffness. Under very strong contraction, all chains are described as a Compact Ordered Globule: the beads are again at a constant average distance from the centre of mass, while the segments jump back and forth at the globule's wall with a very large correlation. At intermediate contraction, the thinner and stiffer chains form the Oscillating Ordered Globule wherein the beads are alternatively distributed on two concentric on two concentric shells. In this case, we also find metastable states with nonsymmetrical conformations of the chain with respect to its ends. We also briefly discuss the thermodynamics of the coil-globule and globule-globule transitions, showing that in long polymer chains these ordered conformations cannot involve the whole chain. However, we suggest that they might still be found as local globules that form for kinetic reasons.     

A novel method for evaluating the critical nucleus and the surface tension in systems with first order phase transition

We introduce a novel method for calculating the size of the critical nucleus and the value of the surface tension in systems with first order phase transition. The method is based on classical nucleation theory, and it consists in studying the thermodynamics of a sphere of given radius embedded in a frozen metastable surrounding. The frozen configuration creates a pinning field on the surface of the free sphere. The pinning field forces the sphere to stay in the metastable phase as long as its size is smaller than the critical nucleus. We test our method in two first order systems, both on a two-dimensional lattice: a system where the parameter tuning the transition is the magnetic field, and a second system where the tuning parameter is the temperature. In both cases the results are satisfying. Unlike previous techniques, our method does not require an infinite volume limit to compute the surface tension, and it therefore gives reliable estimates even by using relatively small systems. However, our method cannot be used at, or close to, the critical point, i.e., at coexistence, where the critical nucleus becomes infinitely large.     

Controlling activated processes of nonadiabatically, periodically driven dynamical systems: a multiple scale perturbation approach

We arrive at the escape rate from a metastable state for a system of Brownian particles driven periodically by a space dependent, rapidly oscillating external perturbation (with frequency ω) in one dimension (one of the most important class of nonequilibrium system). Though the problem may seem to be time-dependent, and is poised on the extreme opposite side of adiabaticity, there exists a multiple scale perturbation theory ("Kapitza window") by means of which the dynamics can be treated in terms of an effective time-independent potential that is derived as an expansion in orders of 1/ω to the order ω(-3). The resulting time-independent equation is then used to calculate the escape rate of physical systems from a metastable state induced by external monochromatic field in the moderate-to-large damping limit and to investigate the effect of ω on the resulting rate in conjunction with the thermal energy. With large value of ω, we find that the environment with moderate-to-large damping impedes the escape process of the particle while high amplitude of the periodic driving force allows the particle to cross the barrier with a large escape rate. A comparison of our theoretical expression with numerical simulation gives a satisfactory agreement.     

Model study for large deformation of physical polymeric gels

A model for large deformation of polymer gels with physical cross-linking is developed and shown to be in good agreement with experimental stress-strain curves which show strain hardening in intermediate strains followed by strain softening in large deformations near the yield strain. The model takes into account the coil-helix transition equilibrium and allows for the distribution of the end-to-end distance. The gel is considered to be formed by long flexible chains and crystalline zones acting as junctions of the chains. The number of segments contained in a flexible chain is variable due to the equilibrium between the two regions. As the end-to-end distance increases due to the deformation, more and more segments are reeled out from the junction zone. Finally, one end of the chain is librated from the junction and the chain becomes dangling. The appearance of dangling chains causes the strain softening because they cease to contribute to the elasticity. From the parameter dependence of the stress-strain relations, it was found that the yield behavior depends strongly on the distribution of end-to-end distance. The yield strain is approximately given by the ratio of the upper limit of the number of segments and the average end-to-end distance. The standard deviation of the end-to-end distance affects significantly the width of the peak in the stress-strain curve, thus determining the degree of strain softening.     

Self-assembly of patchy particles into polymer chains: a parameter-free comparison between Wertheim theory and Monte Carlo simulation

The authors numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear chains. The simplicity of the model allows for a close comparison, with no fitting parameters, between simulations and theoretical predictions based on the Wertheim perturbation theory. This comparison offers a unique framework for the analytic prediction of the properties of self-assembling particle systems in terms of molecular parameters and liquid state correlation functions. The Wertheim theory has not been previously subjected to stringent tests against simulation data for ordering across the polymerization transition. The authors numerically determine many of the thermodynamic properties governing this basic form of self-assembly (energy per particle, order parameter or average fraction of particles in the associated state, average chain length, chain length distribution, average end-to-end distance of the chains, and the static structure factor) and find that predictions of the Wertheim theory accord remarkably well with the simulation results.     

A limit of stability in supercooled liquid clusters

We examine the metastable liquid phase of a supercooled gold nanocluster by studying the free energy landscape using the largest solidlike embryo as an order parameter. Just below freezing, the free energy exhibits a local minimum at small embryo sizes and a maximum at a larger critical embryo size. At T=660 K the free energy becomes a monotonically decreasing function of the order parameter as the liquid phase becomes unstable, indicating that we have reached a limit of stability. In contrast to the mean-field theory predictions for a spinodal, the size of the critical embryo remains finite as the limit of stability is approached. We also calculate the rate of nucleation, independently from our free energy calculations, and observe a rapid increase in its temperature dependence when the free energy barrier is on the order of kT. We suggest that this supports the idea that freezing becomes a barrierless process at low temperatures.     

Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: a case study of polymer cyclization

Motivated by recent experimental efforts to measure the duration of individual folding∕unfolding transitions in proteins and RNA, here we use simulations to study the duration of a simple transition mimicking an elementary step in biopolymer folding: the closure of a loop in a long polymer chain. While the rate of such a transition is well approximated by a one-dimensional Smoluchowski model that views the end-to-end distance dynamics of a polymer chain as diffusion governed by the one-dimensional potential of mean force, the same model fails rather dramatically to describe the duration of such transitions. Instead, the latter timescale is well described by a model where the chain ends diffuse freely, uninfluenced by the average entropic force imposed by the polymer chain. The effective diffusion coefficient then depends on the length scale of the loop closure transition. Our findings suggest that simple one-dimensional models, when applied to estimate the duration of reactive events in complex molecular systems, should be used with caution.     

Ab initio molecular dynamics simulation of the aqueous Ru2+/Ru3+ redox reaction: the Marcus perspective

A well-behaved (low spin) transition metal aqua ion, Ru(aq)(2+), is used as a model system in an ab initio molecular dynamics study of a redox half reaction to which the Marcus theory of electron transfer is assumed to apply. Using constraint methods, we show that aqueous Ru(2+) can be reversibly transformed to Ru(3+) under the control of the classical solvent electrostatic potential as order parameter. The mean force is found to vary linearly with the order parameter in accordance with the Marcus theory. As can be expected for a half reaction, the slope in the oxidized and reduced states are asymmetric differing by approximately a factor of two. As a further test, we verify that the corresponding quadratic potential of mean force is in excellent agreement with the free energy profile obtained from the Gaussian distribution of potential fluctuations sampled from free (unconstrained) runs of the reduced and oxidized system. Similar to experimental electrochemical methods, our simulation scheme enables us to manipulate the effective thermodynamic driving force and align the free energy minima of product and reactant state. The activation energy and reaction entropy computed under these conditions are discussed and analyzed from the Marcus perspective.