Simulation study on the translocation of a partially charged polymer through a nanopore

The translocation of a partially charged polymer through a neutral nanopore under external electrical field is studied by using dynamic Monte Carlo method on a simple cubic lattice. One monomer in the polymer is charged and it suffers a driving force when it locates inside the pore. Two time scales, mean first passage time τ(FP) with the first monomer restricted to never draw back into cis side and translocation time τ for polymer continuously threading through nanopore, are calculated. The first passage time τ(FP) decreases with the increase in the driving force f, and the dependence of τ(FP) on the position of charged monomer M is in agreement with the theoretical results using Fokker-Planck equation [A. Mohan, A. B. Kolomeisky, and M. Pasquali, J. Chem. Phys. 128, 125104 (2008)]. But the dependence of τ on M shows a different behavior: It increases with f for M < N/2 with N the polymer length. The novel behavior of τ is explained qualitatively from dynamics of polymer during the translocation process and from the free energy landscape.     

Validation of Markov state models using Shannon's entropy

Markov state models are kinetic models built from the dynamics of molecular simulation trajectories by grouping similar configurations into states and examining the transition probabilities between states. Here we present a procedure for validating the underlying Markov assumption in Markov state models based on information theory using Shannon's entropy. This entropy method is applied to a simple system and is compared with the previous eigenvalue method. The entropy method also provides a way to identify states that are least Markovian, which can then be divided into finer states to improve the model.     

Superparamagnetic blocking and superspin-glass freezing in ultra small δ-(Fe(0.67)Mn(0.33))OOH particles

The magnetic properties of ultra-small (~2 nm) δ-(Fe(0.67)Mn(0.33))OOH nanoparticles prepared by a microemulsion technique have been investigated by magnetization and ac susceptibility measurements at variable frequency. The results provide evidence of two different magnetic regimes whose onset is identified by two maxima in the zero-field-cooled susceptibility: a large one, centered at ~150 K (T(mh)), and a narrow one at ~30 K (T(ml)). The two temperatures exhibit a different frequency dependence: T(mh) follows a Vogel-Fulcher law τ = τ(0)exp[(E(a)/k(B))/(T-T(0))], indicating a blocking of weakly interacting nanoparticle moments, whereas T(ml) follows a power law τ = τ(0)(T(g)/T(mν)-T(g))(α), suggesting a collective freezing of nanoparticle moments (superspin-glass state). This picture is coherent with the field dependence of T(ml) and T(mh) and with the temperature dependence of the coercivity, strongly increasing below 30 K.     

Mesoscopic simulation of an ionomeric membrane based on sulfonated aromatic poly(ether ether ketone)

Mesoscopic simulation in the framework of the mesoscopic dynamics method (a version of the dynamic density functional method) was performed for a proton conducting membrane based on sulfonated aromatic poly(ether ether ketone) in a wide range of water content in the system. For the selected parametric field, the model demonstrates microphase separation of hydrophilic and hydrophobic segments of the polymer. In the bulk of the membrane, a spatial network of water channels forms, whose walls consist of polar (sulfonated) units of the macromolecule. Independent molecular dynamics simulation for one set of parameters gives close values of the structural characteristics of the membrane, which confirms the correctness of the mesoscopic model.     

Polymer-clay nanocomposites: a multiscale molecular modeling approach

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) simulations. The predicted structure of the nylon 6 PCN system considered is in excellent agreement with previous experimental and atomistic simulation results.     

Thermodynamic scaling of α-relaxation time and viscosity stems from the Johari-Goldstein β-relaxation or the primitive relaxation of the coupling model

By now it is well established that the structural α-relaxation time, τ(α), of non-associated small molecular and polymeric glass-formers obey thermodynamic scaling. In other words, τ(α) is a function Φ of the product variable, ρ(γ)/T, where ρ is the density and T the temperature. The constant γ as well as the function, τ(α) = Φ(ρ(γ)/T), is material dependent. Actually this dependence of τ(α) on ρ(γ)/T originates from the dependence on the same product variable of the Johari-Goldstein β-relaxation time, τ(β), or the primitive relaxation time, τ(0), of the coupling model. To support this assertion, we give evidences from various sources itemized as follows. (1) The invariance of the relation between τ(α) and τ(β) or τ(0) to widely different combinations of pressure and temperature. (2) Experimental dielectric and viscosity data of glass-forming van der Waals liquids and polymer. (3) Molecular dynamics simulations of binary Lennard-Jones (LJ) models, the Lewis-Wahnstr?m model of ortho-terphenyl, 1,4 polybutadiene, a room temperature ionic liquid, 1-ethyl-3-methylimidazolium nitrate, and a molten salt 2Ca(NO(3))(2)·3KNO(3) (CKN). (4) Both diffusivity and structural relaxation time, as well as the breakdown of Stokes-Einstein relation in CKN obey thermodynamic scaling by ρ(γ)/T with the same γ. (5) In polymers, the chain normal mode relaxation time, τ(N), is another function of ρ(γ)/T with the same γ as segmental relaxation time τ(α). (6) While the data of τ(α) from simulations for the full LJ binary mixture obey very well the thermodynamic scaling, it is strongly violated when the LJ interaction potential is truncated beyond typical inter-particle distance, although in both cases the repulsive pair potentials coincide for some distances.     

Mesoscopic description of solvent effects on polymer dynamics

Solvent effects on polymer dynamics and structure are investigated using a mesoscopic solvent model that accounts for hydrodynamic interactions among the polymer beads. The simulation method combines molecular dynamics of the polymer chain, interacting with the solvent molecules through intermolecular forces, with mesoscopic multiparticle collision dynamics for the solvent molecules. Changes in the intermolecular forces between the polymer beads and mesoscopic solvent molecules are used to vary the solvent conditions from those for good to poor solvents. Polymer collapse and expansion dynamics following changes in solvent conditions are studied for homopolymer and block copolymer solutions. The frictional properties of polymers are also investigated.     

Voltammetry at microcylinder electrodes: Part IV. Normal and differential pulse voltammetry

Expressions for reversible normal pulse (NP) and differential pulse(DP) voltammograms at microcylinder electrodes, which are powerful and convenient tools in in vivo measurements, were derived in connection with the effects of successive pulse electrolysis. These expressions were computed numerically, varying the pulse interval, τ, and the pulse width, δ. Consequently, it was found that the use of τ>10δ for NP and τ>5δ for DP did not distort the well-known shapes of the voltammograms. By choosing τ=10δ for NP voltammetry or τ=5δ for DP voltammetry, the analysis time was greatly reduced. Methods of analysing reversible NP and DP waves are presented. NP and DP measurements were carried out at platinum and carbon fiber microcylinder electrodes for various values of τ and δ. The minimum values of δ for undistorted voltammograms found experimentally were τ = 5δ for NP voltammetry and τ = 2δ for DP voltammetry.     

Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories

Simulating electron spin resonance (ESR) spectra directly from molecular dynamics simulations of a spin-labeled protein necessitates a large number (hundreds or thousands) of relatively long (hundreds of nanoseconds) trajectories. To meet this challenge, we explore the possibility of constructing accurate stochastic models of the spin label dynamics from atomistic trajectories. A systematic, two-step procedure, based on the probabilistic framework of hidden Markov models, is developed to build a discrete-time Markov chain process that faithfully captures the internal spin label dynamics on time scales longer than about 150 ps. The constructed Markov model is used both to gain insight into the long-lived conformations of the spin label and to generate the stochastic trajectories required for the simulation of ESR spectra. The methodology is illustrated with an application to the case of a spin-labeled poly alanine alpha helix in explicit solvent.     

Kinetics of polymer failure at moderate and low temperatures

The time of expectation for breakdown (life-time, τ) was measured as a function of temperature (T) and tensile stress (σ) for a variety of polymers, including nylon-6, polyethylene, poly(ethylene terephthalate) and poly(tetrafluoroethylene). At moderate temperatures (above ∼200 K), the τ(1/T)_σ dependences are exponential (of the Boltzmann-Frenkel type). The elementary acts of polymer fracture occur at these temperatures through the thermal-fluctuation above-barrier transitions. At low temperatures (below ∼200 K), τ is T-independent (an athermic plateau) and, therefore, the above-barrier mechanism is ruled out. It is concluded that the elementary acts of fracture proceed at low temperatures via the tunnel below-barrier mechanism. Possible types of tunnel processes (tunneling of atoms or electrons) are discussed.     

分数Maxwell模型应用于PTFE松弛模量的研究

用分数Maxwell模型对聚合物PTFE(Polytetrafluoethylene)的应力松弛过程进行了研究. 分数Maxwell模型的渐近行为是确定其参数的基本依据, 但根据实验数据确定的松弛时间与渐近解成立的条件并不自恰. 通过适当选定松弛时间, 利用起始时段的实验数据确定初始松弛指数和松弛模量, 并适当优化末端松弛指数, 分数Maxwell模型可以对粘弹性应力松弛过程给出非常好的描述.     

Monte Carlo simulations of charged dendrimer-linear polyelectrolyte complexes and explicit counterions

We study complexes composed of one dendrimer of generation G = 4 (G4 dendrimer) with N(t) = 32 charged terminal groups and an oppositely charged linear polyelectrolyte accompanied by neutralizing counterions in an athermal solvent using Monte Carlo simulations based on the bond fluctuation model. In our study both the full Coulomb potential and the excluded volume interactions are taken into account explicitly with the reduced temperature τ and the chain length N(ch) as the main simulation parameters. Our calculations indicate that there exist three temperature ranges that determine the behavior of such complexes. At τ(complex) stable charged dendrimer-linear polyelectrolyte complexes are formed first, which are subsequently accompanied by selective counterion localization within the complex interior at τ(loc) ≤ τ(complex), and counterion condensation as temperature is further decreased below τ(cond) < τ(loc). In particular, we observe that condensation takes place exclusively on the excess charges in the complex and thus no condensation is observed at the compensation point (N(ch) = N(t)), irrespective of τ. For N(ch) ≠ N(t) the complex is overally charged. Furthermore, we discuss the size and structure of the dendrimer and the linear polyelectrolyte within the complex, as well as spatial distributions of monomers and counterions. Conformations of the chain in the bound state are analysed in terms of loops, trains, and tails.     

Factors Affecting Polymer Translocation Through a Nanopore in a Membrane

The variation of the translocation time with respect to the solvent quality was also studied. It showed that there is a transition, as the solvent quality improves from \poor to \good: when ABc, τ increases with increasing AB. When the chain length was changed, it was found that when the absorbed energy u0 was greater than uc, τ was proportional to N1:602; for u0相似文献   

Diffusion models of protein folding

In theory and in the analysis of experiments, protein folding is often described as diffusion along a single coordinate. We explore here the application of a one-dimensional diffusion model to interpret simulations of protein folding, where the parameters of a model that "best" describes the simulation trajectories are determined using a Bayesian analysis. We discuss the requirements for such a model to be a good approximation to the global dynamics, and several methods for testing its accuracy. For example, one test considers the effect of an added bias potential on the fitted free energies and diffusion coefficients. Such a bias may also be used to extend our approach to determining parameters for the model to systems that would not normally explore the full coordinate range on accessible time scales. Alternatively, the propagators predicted from the model at different "lag" times may be compared with observations from simulation. We then present some applications of the model to protein folding, including Kramers-like turnover in folding rates of coarse-grained models, the effect of non-native interactions on folding, and the effect of the chosen coordinate on the observed position-dependence of the diffusion coefficients. Lastly, we consider how our results are useful for the interpretation of experiments, and how this type of Bayesian analysis may eventually be applied directly to analyse experimental data.     

Dissipative particle dynamic simulation study of lipid membrane

The lipid membrane plays crucial roles in countless biologic processes, ranging from cell motility, endo- and exocytosis, and cell division to protein aggregation and trafficking. To gain a molecular insight in these biologic processes, the recently developed mesoscale simulation technique, dissipative particle dynamics (DPD) simulation, has become an invaluable tool. By providing a brief survey of existing atomistic and popular coarse-grained models used today in studying the dynamics (including vesicle formation and (protein-mediated) vesicle fusion) and phase behavior of lipid bilayers, this review illustrates how mesoscopic DPD models can be used to obtain a better understanding of these biologic processes currently inaccessible to atomistic and most coarse-grained models.     

Translocation of α-helix chains through a nanopore

The translocation of α-helix chains through a nanopore is studied through Langevin dynamics simulations. The α-helix chains exhibit several different characteristics about their average translocation times and the α-helix structures when they transport through the nanopores under the driving forces. First, the relationship between average translocation times τ and the chain length N satisfies the scaling law, τ～N(α), and the scaling exponent α depends on the driving force f for the small forces while it is close to the Flory exponent (ν) in the other force regions. For the chains with given chain lengths, it is observed that the dependence of the average translocation times can be expressed as τ～f(-1/2) for the small forces while can be described as τ～f in the large force regions. Second, for the large driving force, the average number of α-helix structures N(h) decreases first and then increases in the translocation process. The average waiting time of each bead, especially of the first bead, is also dependent on the driving forces. Furthermore, an elasticity spring model is presented to reasonably explain the change of the α-helix number during the translocation and its elasticity can be locally damaged by the large driving forces. Our results demonstrate the unique behaviors of α-helix chains transporting through the pores, which can enrich our insights into and knowledge on biopolymers transporting through membranes.     

A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics

A new mesoscopic membrane model is developed in order to examine long-wavelength structural and dynamical membrane phenomena. Two different explicit mesoscopic solvent models are employed. The first mesoscopic solvent is denoted the big liquid oscillating blob system, which is parametrized to model water at a coarse-grained level and is motivated by a Langevin-like approach; the resulting membrane dynamics predict a solvent viscosity dependence consistent with the known viscosity of water. The second mesoscopic solvent is a Weeks-Chandler-Anderson model. Here, it is found that the correct mesoscopic hydrodynamic scaling of the membrane undulation dynamics is still preserved, although accelerated. When the behavior of the two membranes in close proximity to one another is examined, very little correlated motion is observed. However, the theoretically predicted scaling of the entropic undulation energy is confirmed, demonstrating that the entropic interaction between two membranes becomes increasingly repulsive with decreasing separation.