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 Physics , 2012, DOI: 10.1063/1.4718833 Abstract: We present an analysis of the mean-field kinetics of Brownian coagulation of droplets and polymers driven by input of monomers which aims to characterize the long time behavior of the cluster size distribution as a function of the inverse fractal dimension, $a$, of the aggregates. We find that two types of long time behavior are possible. For $0\leq a < 1/2$ the size distribution reaches a stationary state with a power law distribution of cluster sizes having exponent 3/2. The amplitude of this stationary state is determined exactly as a function of $a$. For $1/2 < a \leq 1$, the cluster size distribution never reaches a stationary state. Instead a bimodal distribution is formed in which a narrow population of small clusters near the monomer scale is separated by a gap (where the cluster size distribution is effectively zero) from a population of large clusters which continue to grow for all time by absorbing small clusters. The marginal case, $a=1/2$, is difficult to analyze definitively, but we argue that the cluster size distribution becomes stationary and there is a logarithmic correction to the algebraic tail.
 Physics , 2015, Abstract: The static and dynamic properties of ring polymers in concentrated solutions remains one of the last deep unsolved questions in Polymer Physics. At the same time, the nature of the glass transition in polymeric systems is also not well understood. In this work we study a novel glass transition in polymeric systems by exploiting the topological constraints that populate concentrated solutions of ring polymers. We show that such rings strongly inter-penetrate through one another, generating an extensive network of topological interactions that dramatically affects their dynamics. We show that a kinetically arrested state can be induced by randomly pinning a small fraction of the rings. This occurs well above the classical glass transition temperature at which microscopic mobility is lost. Our work demonstrates both the existence of long-lived inter-ring penetrations, the subject of much conjecture, and also realises a novel, topologically-induced glass transition.
 Statistics , 2008, DOI: 10.1088/1742-5468/2009/01/P01011 Abstract: In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and introducing a Lennard-Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion with a Gaussian uncorrelated noise. We find a nonmonotonic behaviour of the mean first passage time and the most probable translocation time, of the polymer centre of inertia, as a function of the polymer length at low noise intensity. We show how thermal fluctuations influence the motion of short polymers, by inducing two different regimes of translocation in the molecule transport dynamics. In this context, the role played by the length of the molecule in the translocation time is investigated.
 Computer Science , 2007, Abstract: We show that the space of polygonizations of a fixed planar point set S of n points is connected by O(n^2) moves'' between simple polygons. Each move is composed of a sequence of atomic moves called stretches'' and twangs''. These atomic moves walk between weakly simple polygonal wraps'' of S. These moves show promise to serve as a basis for generating random polygons.
 Quantitative Biology , 2012, DOI: 10.1063/1.4772658 Abstract: We investigate the translocation of stiff polymers in the presence of binding particles through a nanopore by two-dimensional Langevin dynamics simulations. We find that the mean translocation time shows a minimum as a function of the binding energy $\epsilon$ and the particle concentration $\phi$, due to the interplay of the force from binding and the frictional force. Particularly, for the strong binding the translocation proceeds with a decreasing translocation velocity induced by a significant increase of the frictional force. In addition, both $\epsilon$ and $\phi$ have an notable impact on the distribution of the translocation time. With increasing $\epsilon$ and $\phi$, it undergoes a transition from an asymmetric and broad distribution under the weak binding to a nearly Gaussian one under the strong binding, and its width becomes gradually narrower.
 Quantitative Biology , 2014, Abstract: We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the filament. The stochastic binding-unbinding of the motor proteins and their ability to move along the polymer, generates active forces. As the pulling force reaches a threshold value, the polymer eventually desorbs from the substrate. Performing molecular dynamics simulations of the polymer in presence of a Langevin heat bath, and stochastic motor activity, we obtain desorption phase diagrams. The correlation time for fluctuations in desorbed fraction increases as one approaches complete desorption, captured quantitatively by a power law spectral density. We present theoretical analysis of the phase diagram using mean field approximations in the weakly bending limit of the polymer and performing linear stability analysis. This predicts increase in the desorption force with the polymer bending rigidity, active velocity and processivity of the motor proteins to capture the main features of the simulation results.
 PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039369 Abstract: Amyloid fibrillar aggregates of polypeptides are associated with many neurodegenerative diseases. Short peptide segments in protein sequences may trigger aggregation. Identifying these stretches and examining their behavior in longer protein segments is critical for understanding these diseases and obtaining potential therapies. In this study, we combined machine learning and structure-based energy evaluation to examine and predict amyloidogenic segments. Our feature selection method discovered that windows consisting of long amino acid segments of ~30 residues, instead of the commonly used short hexapeptides, provided the highest accuracy. Weighted contributions of an amino acid at each position in a 27 residue window revealed three cooperative regions of short stretch, resemble the β-strand-turn-β-strand motif in A-βpeptide amyloid and β-solenoid structure of HET-s(218–289) prion (C). Using an in-house energy evaluation algorithm, the interaction energy between two short stretches in long segment is computed and incorporated as an additional feature. The algorithm successfully predicted and classified amyloid segments with an overall accuracy of 75%. Our study revealed that genome-wide amyloid segments are not only dependent on short high propensity stretches, but also on nearby residues.
 Physics , 1996, DOI: 10.1142/S0217732396002356 Abstract: We study an ensemble of branched polymers which are embedded on other branched polymers. This is a toy model which allows us to study explicitly the reaction of a statistical system on an underlying geometrical structure, a problem of interest in the study of the interaction of matter and quantized gravity. We find a phase transition at which the embedded polymers begin to cover the basis polymers. At the phase transition point the susceptibility exponent $\gamma$ takes the value 3/4 and the two-point function develops an anomalous dimension 1/2.
 Brazilian Archives of Biology and Technology , 2006, DOI: 10.1590/S1516-89132006000200002 Abstract: according to the technical regulation of measurement of petroleum and natural gas (approved in 2000 by anp - the petroleum national agency of brazil), the systems of measurement of natural gas should use ultra-sonic flow meters, turbines and, especially, the orifice plates, which represent the most expressive base of the flow systems, being used in the fiscal and operational measurements. this work aims to evaluate the parameters that should be accounted for during the dimensional inspection of orifice plate and roughness of the straight stretches of the tubing used for measurement of natural gas, with the objective of guiding the responsible professionals for the measurement of volumes of natural gas by orifice plate, as well as the professionals of calibration laboratories. in this work, minimum specifications are recommended, irrespective of the pressure tapping or orifice type, in agreement with the norms iso, aga and the anp regulations. the influence of these specifications on the parameters used in the calculation of the volumetric flow is also analyzed.
 Materials , 2009, DOI: 10.3390/ma2020307 Abstract: Biodegradable materials are used in packaging, agriculture, medicine and other areas. In recent years there has been an increase in interest in biodegradable polymers. Two classes of biodegradable polymers can be distinguished: synthetic or natural polymers. There are polymers produced from feedstocks derived either from petroleum resources (non renewable resources) or from biological resources (renewable resources). In general natural polymers offer fewer advantages than synthetic polymers. The following review presents an overview of the different biodegradable polymers that are currently being used and their properties, as well as new developments in their synthesis and applications.
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