arXiv subjects

Dimitrios Vavylonis

Publications and source records attributed to Dimitrios Vavylonis.

13 recordsLinked to original sources

arXiv2005

Actin Polymerization Kinetics, Cap Structure and Fluctuations

Polymerization of actin proteins into dynamic structures is essential to eukaryotic cell life. This has motivated a large body of in vitro experiments measuring polymerization kinetics of individual filaments. Here we model these kinetics, accounting for all relevant steps revealed by experiment: polymerization, depolymerization, random ATP hydrolysis and release of phosphate (Pi). We relate filament growth rates to the dynamics of ATP-actin and ADP-Pi-actin caps which develop at filament ends. At the critical concentration of the barbed end, c_crit, we find a short ATP cap and a long fluctuation-stabilized ADP-Pi cap. We show that growth rates and the critical concentration at the barbed end are intimately related to cap structure and dynamics. Fluctuations in filament lengths are described by the length diffusion coefficient, D. Recently Fujiwara et al. [Nature Cell Biol. (2002) 4, 666] and Kuhn and Pollard [Biohys. J. (2005) 88, 1387] observed large length fluctuations slightly above c_crit, provoking speculation that growth may proceed by oligomeric rather than monomeric on-off events. For the single monomer growth process we find that $D$ exhibits a pronounced peak below c_crit}, due to filaments alternating between capped and uncapped states, a mild version of the dynamic instability of microtubules. Fluctuations just above c_crit are enhanced but much smaller than those reported experimentally. Future measurements of D as a function of concentration can help identify the origin of the observed fluctuations.

q-bio.BM↗

arXiv2004

Non-Equilibrium in Adsorbed Polymer Layers

High molecular weight polymer solutions have a powerful tendency to deposit adsorbed layers when exposed to even mildly attractive surfaces. The equilibrium properties of these dense interfacial layers have been extensively studied theoretically. A large body of experimental evidence, however, indicates that non-equilibrium effects are dominant whenever monomer-surface sticking energies are somewhat larger than kT, a common case. Polymer relaxation kinetics within the layer are then severely retarded, leading to non-equilibrium layers whose structure and dynamics depend on adsorption kinetics and layer ageing. Here we review experimental and theoretical work exploring these non-equilibrium effects, with emphasis on recent developments. The discussion addresses the structure and dynamics in non-equilibrium polymer layers adsorbed from dilute polymer solutions and from polymer melts and more concentrated solutions. Two distinct classes of behaviour arise, depending on whether physisorption or chemisorption is involved. A given adsorbed chain belonging to the layer has a certain fraction of its monomers bound to the surface, f, and the remainder belonging to loops making bulk excursions. A natural classification scheme for layers adsorbed from solution is the distribution of single chain f values, P(f), which may hold the key to quantifying the degree of irreversibility in adsorbed polymer layers. Here we calculate P(f) for equilibrium layers; we find its form is very different to the theoretical P(f) for non-equilibrium layers which are predicted to have infinitely many statistical classes of chain. Experimental measurements of P(f) are compared to these theoretical predictions.

cond-mat.soft↗

arXiv2003

Dynamics of Living Polymers

We study theoretically the dynamics of living polymers which can add and subtract monomer units at their live chain ends. The classic example is ionic living polymerization. In equilibrium, a delicate balance is maintained in which each initiated chain has a very small negative average growth rate (``velocity'') just sufficient to negate the effect of growth rate fluctuations. This leads to an exponential molecular weight distribution (MWD) with mean Nbar. After a small perturbation of relative amplitude epsilon, e.g. a small temperature jump, this balance is destroyed: the velocity acquires a boost greatly exceeding its tiny equilibrium value. For epsilon > epsilon_c = 1/Nbar^{1/2} the response has 3 stages: (1) Coherent chain growth or shrinkage, leaving a highly non-linear hole or peak in the MWD at small chain lengths. During this episode, lasting time taufast ~ Nbar, the MWD's first moment and monomer concentration m relax very close to equilibrium. (2) Hole-filling (or peak decay) after taufill ~ epsilon^2 Nbar^2. The absence or surfeit of small chains is erased. (3) Global MWD shape relaxation after tauslow ~ Nbar^2. By this time second and higher MWD moments have relaxed. During episodes (2) and (3) the fast variables (Nbar,m) are enslaved to the slowly varying number of free initiators (chains of zero length). Thus fast variables are quasi-statically fine-tuned to equilibrium. The outstanding feature of these dynamics is their ultrasensitivity: despite the perturbation's linearity, the response is non-linear until the late episode (3). For very small perturbations, epsilon < epsilon_c, response remains non-linear but with a less dramatic peak or hole during episode (1). Our predictions are in agreement with viscosity measurements on the most widely studied system, alpha-methylstyrene.

cond-mat.soft↗

arXiv2003

The Slowly Formed Guiselin Brush

We study polymer layers formed by irreversible adsorption from a polymer melt. Our theory describes an experiment which is a ``slow'' version of that proposed by Guiselin [Europhys. Lett., v. 17 (1992) p. 225] who considered instantaneously irreversibly adsorbing chains and predicted a universal density profile of the layer after swelling with solvent to produce the ``Guiselin brush.'' Here we ask what happens when adsorption is not instantaneous. The classic example is chemisorption. In this case the brush is formed slowly and the final structure depends on the experiment's duration, $t_{final}$. We find the swollen layer consists of an inner region of thickness $z^* \sim t_{final}^{-5/3}$ with approximately constant density and an outer region extending up to height $h \sim N^{5/6}$ which has the same density decay $\sim z^{-2/5}$ as for the Guiselin case.

cond-mat.soft↗

arXiv2003

Irreversible Adsorption from Dilute Polymer Solutions

We study irreversible polymer adsorption from dilute solutions theoretically. Universal features of the resultant non-equilibrium layers are predicted. Two cases are considered, distinguished by the value of the local monomer-surface sticking rate Q: chemisorption (very small Q) and physisorption (large Q). Early stages of layer formation entail single chain adsorption. While single chain physisorption times tau_ads are typically microsecs, for chemisorbing chains of N units we find experimentally accessible times tau_ads = Q^{-1} N^{3/5}, ranging from secs to hrs. We establish 3 chemisorption universality classes, determined by a critical contact exponent: zipping, accelerated zipping and homogeneous collapse. For dilute solutions, the mechanism is accelerated zipping: zipping propagates outwards from the first attachment, accelerated by occasional formation of large loops which nucleate further zipping. This leads to a transient distribution omega(s) \sim s^{-7/5} of loop lengths s up to a size s_max \approx (Q t)^{5/3} after time t. By tau_ads the entire chain is adsorbed. The outcome of the single chain adsorption episode is a monolayer of fully collapsed chains. Having only a few vacant sites to adsorb onto, late arriving chains form a diffuse outer layer. In a simple picture we find for both chemisorption and physisorption a final loop distribution Omega(s) \sim s^{-11/5} and density profile c(z) \sim z^{-4/3} whose forms are the same as for equilibrium layers. In contrast to equilibrium layers, however, the statistical properties of a given chain depend on its adsorption time; the outer layer contains many classes of chain, each characterized by different fraction of adsorbed monomers f. Consistent with strong physisorption experiments, we find the f values follow a distribution P(f) \sim f^{-4/5}.

cond-mat.soft↗

arXiv2003

Pulsed Laser Polymerization at Low Conversions: Broadening and Chain Transfer Effects

Pulsed laser polymerization (PLP) is widely employed to measure propagation rate coefficients k_p in free radical polymerization. Various properties of PLP have been established in previous works, mainly using numerical methods. The objective of this paper is to obtain analytical results. We obtain the most general analytical solution for the dead chain molecular weight distribution (MWD) under low conversion conditions which has been hitherto obtained. Simultaneous disproportionation and combination termination processes are treated. The hallmarks of PLP are the dead MWD discontinuities located at integer multiples of n_0 = k_p t_0 C_M, where t_0 is the laser period and C_M is the monomer concentration. We show that chain transfer reduces their amplitude by factors e^{-c_{tr} L n_0}, consistent with numerical results obtained by other workers. Here c_{tr} is the chain transfer coefficient and L is an integer. Additionally, transfer generates a small amplitude continuous contribution to the MWD. These results generalize earlier analytical results obtained for the case of disproportionation only. We also considered 2 classes of broadening: (i) Poisson broadening of growing living chains and (ii) intrinsic broadening by the MWD measuring equipment (typically gel permeation chromatography, GPC). Broadening smoothes the MWD discontinuities. Under typical PLP experimental conditions, the associated inflection points are very close to the discontinuities of the unbroadened MWD. Previous numerical works have indicated that the optimal procedure is to use the inflection point to infer k_p. We prove that this is a correct procedure provided the GPC resolution σis better than n_0^{1/2}. Otherwise this underestimates L n_0 by an amount of order σ^2/n_0.

cond-mat.soft↗

arXiv2003

The Ultrasensitivity of Living Polymers

Synthetic and biological living polymers are self-assembling chains whose chain length distributions (CLDs) are dynamic. We show these dynamics are ultrasensitive: even a small perturbation (e.g. temperature jump) non-linearly distorts the CLD, eliminating or massively augmenting short chains. The origin is fast relaxation of mass variables (mean chain length, monomer concentration) which perturbs CLD shape variables before these can relax via slow chain growth rate fluctuations. Viscosity relaxation predictions agree with experiments on the best-studied synthetic system, alpha-methylstyrene.

cond-mat.soft↗

arXiv2002

Irreversibility and Polymer Adsorption

Physisorption or chemisorption from dilute polymer solutions often entails irreversible polymer-surface bonding. We present a theory of the non-equilibrium layers which result. While the density profile and loop distribution are the same as for equilibrium layers, the final layer comprises a tightly bound inner part plus an outer part whose chains make only fN surface contacts where N is chain length. The contact fractions f follow a broad distribution, P(f) ~ f^{-4/5}, in rather close agreement with strong physisorption experiments [H. M. Schneider et al, Langmuir v.12, p.994 (1996)].

cond-mat.soft↗

arXiv1999

Interfacial Reactions: Mixed Order Kinetics and Segregation Effects

We study A-B reaction kinetics at a fixed interface separating A and B bulks. Initially, the number of reactions ${\cal R}_t \sim t n_A^\infty n_B^\infty$ is 2nd order in the far-field densities $n_A^\infty,n_B^\infty$. First order kinetics, governed by diffusion from the dilute bulk, onset at long times: ${\cal R}_t\approx x_t n_A^\infty$ where $x_t\sim t^{1/z}$ is the rms molecular displacement. Below a critical dimension, $d<d_c=z-1$, mean field theory is invalid: a new regime appears, ${\cal R}_t\sim x_t^{d+1} n_A^\infty n_B^\infty$, and long time A-B segregation (similar to bulk $A+B\gt\emptyset$) leads to anomalous decay of interfacial densities. Numerical simulations for $z=2$ support the theory.

cond-mat.soft↗

arXiv1999

Interfacial Reaction Kinetics

We study irreversible A-B reaction kinetics at a fixed interface separating two immiscible bulk phases, A and B. We consider general dynamical exponent $z$, where $x_t\sim t^{1/z}$ is the rms diffusion distance after time $t$. At short times the number of reactions per unit area, $R_t$, is {\em 2nd order} in the far-field reactant densities $n_A^{\infty},n_B^{\infty}$. For spatial dimensions $d$ above a critical value $d_c=z-1$, simple mean field (MF) kinetics pertain, $R_t\sim Q_b t n_A^{\infty} n_B^{\infty}$ where $Q_b$ is the local reactivity. For low dimensions $d Q_b^* \sim (n_B^{\infty})^{[z-(d+1)]/d}$. Logarithmic corrections arise in marginal cases. At long times, a cross-over to {\em 1st order} DC kinetics occurs: $R_t \approx x_t n_A^{\infty}$. A density depletion hole grows on the more dilute A side. In the symmetric case ($n_A^{\infty}=n_B^{\infty}$), when $d d_c$ fluctuations are unimportant: local mean field theory applies at the interface (joint density distribution approximating the product of A and B densities) and $n_A^s \sim t^{(1-z)/(2z)}$. We apply our results to simple molecules (Fickian diffusion, $z=2$) and to several models of short-time polymer diffusion ($z>2$).

cond-mat.soft↗

arXiv1998

Kinetic Regimes and Cross-Over Times in Many-Particle Reacting Systems

We study kinetics of single species reactions ("A+A -> 0") for general local reactivity Q and dynamical exponent z (rms displacement x_t ~ t^{1/z}.) For small molecules z=2, whilst z=4,8 for certain polymer systems. For dimensions d above the critical value d_c=z, kinetics are always mean field (MF). Below d_c, the density n_t initially follows MF decay, n_0 - n_t ~ n_0^2 Q t. A 2-body diffusion-controlled regime follows for strongly reactive systems (Q>Qstar ~ n_0^{(z-d)/d}) with n_0 - n_t ~ n_0^2 x_t^d. For Q<Qstar, MF kinetics persist, with n_t ~ 1/Qt. In all cases n_t ~ 1/x_t^d at the longest times. Our analysis avoids decoupling approximations by instead postulating weak physically motivated bounds on correlation functions.

cond-mat.stat-mech↗

arXiv1998

Reactions at Polymer Interfaces: Transitions from Chemical to Diffusion-Control and Mixed Order Kinetics

We study reactions between end-functionalized chains at a polymer-polymer interface. For small chemical reactivities (the typical case) the number of diblocks formed, $R_t$, obeys 2nd order chemically controlled kinetics, $R_t \sim t$, until interfacial saturation. For high reactivities (e.g. radicals) a transition occurs at short times to 2nd order diffusion-controlled kinetics, with $R_t \sim t/\ln t$ for unentangled chains while $t/\ln t$ and $t^{1/2}$ regimes occur for entangled chains. Long time kinetics are 1st order and controlled by diffusion of the more dilute species to the interface: $R_t \sim t^{1/4}$ for unentangled cases, while $R_t \sim t^{1/4}$ and $t^{1/8}$ regimes arise for entangled systems. The final 1st order regime is governed by center of gravity diffusion, $R_t \sim t^{1/2}$.

cond-mat.soft↗

arXiv1998

Reaction Kinetics in Polymer Melts

We study the reaction kinetics of end-functionalized polymer chains dispersed in an unreactive polymer melt. Starting from an infinite hierarchy of coupled equations for many-chain correlation functions, a closed equation is derived for the 2nd order rate constant $k$ after postulating simple physical bounds. Our results generalize previous 2-chain treatments (valid in dilute reactants limit) by Doi, de Gennes, and Friedman and O'Shaughnessy, to arbitrary initial reactive group density $n_0$ and local chemical reactivity $Q$. Simple mean field (MF) kinetics apply at short times, $k \sim Q$. For high $Q$, a transition occurs to diffusion-controlled (DC) kinetics with $k \approx x_t^3/t$ (where $x_t$ is rms monomer displacement in time $t$) leading to a density decay $n_t \approx n_0 - n_0^2 x_t^3$. If $n_0$ exceeds the chain overlap threshold, this behavior is followed by a regime where $n_t \approx 1/x_t^3$ during which $k$ has the same power law dependence in time, $k \approx x_t^3/t$, but possibly different numerical coefficient. For unentangled melts this gives $n_t \sim t^{-3/4}$ while for entangled cases one or more of the successive regimes $n_t \sim t^{-3/4}$, $t^{-3/8}$ and $t^{-3/4}$ may be realized depending on the magnitudes of $Q$ and $n_0$. Kinetics at times longer than the longest polymer relaxation time $τ$ are always MF. If a DC regime has developed before $τ$ then the long time rate constant is $k \approx R^3/τ$ where $R$ is the coil radius. We propose measuring the above kinetics in a model experiment where radical end groups are generated by photolysis.

cond-mat.soft↗