211 results on '"Blumen, A."'
Search Results
2. Excited State Dynamics in Low-Dimensional Systems
- Author
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Alexander Blumen, Joseph Klafter, and J. M. Drake
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Physics ,Excited state ,Dynamics (mechanics) ,Atomic physics - Published
- 2020
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3. NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities
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Brigitte Blumen, François Penin, Matthieu Fritz, Annette Martin, Célia Boukadida, Marie-Laure Fogeron, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by a grant (AM) from the ANRS (France REcherche, Nord & sud, Sida-hiv, Hépatites, The authors gratefully acknowledge Sylvie van der Werf for continuous support, Nicolas Escriou for helpful discussions, Florent Le Parc, Florian Bakoa and Emeline Simon for excellent technical assistance and the following colleagues for sharing valuable biological material: Takaji Wakita (JFH1 cDNA), Ralf Bartenschlager (JFH1-2EI3-adapt plasmid, anti-NS2JFH1 antibodies), Charles M. Rice (Huh-7.5 cells, FL-J6/JFH-5'C19Rluc2AUbi plasmid), and Darius Moradpour (pCMVNS2-GFP and pCMV-KEB-GFP plasmids)., and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP) more...
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Hepacivirus ,medicine.medical_treatment ,MESH: Rodentia ,MESH: Amino Acid Sequence ,Pathology and Laboratory Medicine ,Biochemistry ,Animal Cells ,Chiroptera ,MESH: Proteolysis ,MESH: Animals ,Enzyme Chemistry ,MESH: Phylogeny ,lcsh:QH301-705.5 ,Phylogeny ,Crystallography ,Physics ,virus diseases ,MESH: Chiroptera ,3. Good health ,Medical Microbiology ,Viral Pathogens ,Physical Sciences ,Cellular Types ,Proteases ,Bioinformatics ,Viral protein ,Immunology ,MESH: Sequence Alignment ,Rodentia ,Sequence alignment ,MESH: Viral Nonstructural Proteins / genetics ,MESH: Peptide Hydrolases / chemistry ,Microbiology ,MESH: Viral Nonstructural Proteins / chemistry ,03 medical and health sciences ,Protein Domains ,Catalytic triad ,Genetics ,Humans ,Amino Acid Sequence ,Horses ,MESH: Horses ,Microbial Pathogens ,Molecular Biology ,Protease ,MESH: Humans ,Flaviviruses ,Crystal structure ,Organisms ,Biology and Life Sciences ,Proteins ,Polypeptides ,biochemical phenomena, metabolism, and nutrition ,MESH: Peptide Hydrolases / metabolism ,030104 developmental biology ,Parasitology ,Cofactors (biochemistry) ,Peptides ,lcsh:RC581-607 ,RNA viruses ,0301 basic medicine ,viruses ,[SDV]Life Sciences [q-bio] ,Viral Nonstructural Proteins ,medicine.disease_cause ,MESH: Peptide Hydrolases / genetics ,Database and Informatics Methods ,Catalytic Domain ,MESH: Catalytic Domain* / genetics ,Medicine and Health Sciences ,MESH: Hepacivirus ,biology ,Hepatitis C virus ,Condensed Matter Physics ,Enzymes ,Viruses ,Pathogens ,Sequence Analysis ,Research Article ,lcsh:Immunologic diseases. Allergy ,Context (language use) ,Research and Analysis Methods ,Virology ,medicine ,Animals ,Solid State Physics ,NS3 ,MESH: Protein Domains / genetics ,030102 biochemistry & molecular biology ,Precursor cells ,Cell Biology ,biology.organism_classification ,MESH: Viral Nonstructural Proteins / metabolism ,Hepatitis viruses ,lcsh:Biology (General) ,Proteolysis ,Enzymology ,Peptide Hydrolases - Abstract
Over the recent years, several homologues with varying degrees of genetic relatedness to hepatitis C virus (HCV) have been identified in a wide range of mammalian species. HCV infectious life cycle relies on a first critical proteolytic event of its single polyprotein, which is carried out by nonstructural protein 2 (NS2) and allows replicase assembly and genome replication. In this study, we characterized and evaluated the conservation of the proteolytic mode of action and regulatory mechanisms of NS2 across HCV and animal hepaciviruses. We first demonstrated that NS2 from equine, bat, rodent, New and Old World primate hepaciviruses also are cysteine proteases. Using tagged viral protein precursors and catalytic triad mutants, NS2 of equine NPHV and simian GBV-B, which are the most closely and distantly related viruses to HCV, respectively, were shown to function, like HCV NS2 as dimeric proteases with two composite active sites. Consistent with the reported essential role for NS3 N-terminal domain (NS3N) as HCV NS2 protease cofactor via NS3N key hydrophobic surface patch, we showed by gain/loss of function mutagenesis studies that some heterologous hepacivirus NS3N may act as cofactors for HCV NS2 provided that HCV-like hydrophobic residues are conserved. Unprecedently, however, we also observed efficient intrinsic proteolytic activity of NS2 protease in the absence of NS3 moiety in the context of C-terminal tag fusions via flexible linkers both in transiently transfected cells for all hepaciviruses studied and in the context of HCV dicistronic full-length genomes. These findings suggest that NS3N acts as a regulatory rather than essential cofactor for hepacivirus NS2 protease. Overall, unique features of NS2 including enzymatic function as dimers with two composite active sites and additional NS3-independent proteolytic activity are conserved across hepaciviruses regardless of their genetic distances, highlighting their functional significance in hepacivirus life cycle., Author summary Despite remarkable progress in the development of therapeutic options, more than 70 million individuals are chronically infected by hepatitis C virus (HCV) worldwide and major challenges in basic and translational research remain. Phylogenetically-related HCV homologues have recently been identified in the wild in several mammalian species, whose host restriction and potential for zoonosis remain largely unknown. We comparatively characterized the functions and properties of nonstructural proteins 2 (NS2) from several animal hepaciviruses and HCV. We demonstrated that NS2 from animal hepaciviruses, like HCV NS2, are cysteine proteases, which function as dimers with two composite active sites to ensure a key proteolytic event of the single viral polyprotein at the NS2/NS3 junction. In addition to the activation of HCV NS2 protease by NS3 N-terminal domain, our data revealed a novel NS3-independent substrate specificity and efficient intrinsic proteolytic activity of NS2. The conservation of its properties and peculiar mode of action among distantly related hepaciviruses supports an important regulatory role for NS2 protein in the life cycle of these viruses. It also strengthens the value of animal, notably rodent hepaciviruses for the development of surrogate, immunocompetent models of HCV infection to address HCV-associated pathogenesis and vaccine strategies. more...
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- 2018
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4. Directed transport in quantum star graphs
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Alexander Blumen, Oliver Mülken, Maxim Dolgushev, and J. R. Yusupov
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Physics ,Network packet ,Wave packet ,Quantum dynamics ,Gaussian ,Statistical and Nonlinear Physics ,Complex network ,Topology ,01 natural sciences ,010305 fluids & plasmas ,Theoretical Computer Science ,Electronic, Optical and Magnetic Materials ,symbols.namesake ,Bifurcation theory ,Classical mechanics ,Modeling and Simulation ,Quantum graph ,0103 physical sciences ,Signal Processing ,symbols ,Electrical and Electronic Engineering ,010306 general physics ,Astrophysics::Galaxy Astrophysics ,Quantum computer - Abstract
We study the quantum dynamics of Gaussian wave packets on star graphs whose arms feature each a periodic potential and an external time-dependent field. Assuming that the potentials and the field can be manipulated separately for each arm of the star, we show that it is possible to manipulate the direction of the motion of a Gaussian wave packet through the bifurcation point by a suitable choice of the parameters of the external fields. In doing so, one can achieve a transmission of the wave packet into the desired arm with nearly 70 % while also keeping the shape of the wave packet approximately intact. Since a star graph is the simplest element of many other complex graphs, the obtained results can be considered as the first step to wave packet manipulations on complex networks. more...
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- 2016
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5. Molecular Dynamics Simulations of Hyperbranched PAMAM Vicsek Fractals
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Florian Fürstenberg, Maxim Dolgushev, Alexander Blumen, and Andrey A. Gurtovenko
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Physics ,Polymers and Plastics ,Organic Chemistry ,Hyperbranched polymers ,Poly(amidoamine) ,Condensed Matter Physics ,Condensed Matter::Soft Condensed Matter ,Inorganic Chemistry ,Molecular dynamics ,Fractal ,Computational chemistry ,Chemical physics ,Dendrimer ,Materials Chemistry ,Radius of gyration ,Radial density - Abstract
Within the broad class of hyperbranched polymers, highly symmetrical objects (such as dendrimers and Vicsek fractals) are of special theoretical interest. Here we study, using the MARTINI force-field, polyamidoamine Vicsek fractals (PVF) in silico, focusing on their structure and dynamics in dilute solution. Our extensive microsecond-long simulations show that the radius of gyration of PVF scales with the molecular weight as N0.54, behavior rather close to that of stars and considerably distinct from that of dendrimers. The study of the radial density profiles indicates that different parts of the PVF interpenetrate significantly, fact which stresses the soft and sparse character of PVF. These results are also supported by our findings for the rotational autocorrelation functions. more...
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- 2014
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6. Dynamics of end-linked star-polymer structures.
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Satmarel, C., von Ferber, C., and Blumen, A.
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POLYMERS ,MACROMOLECULES ,DENDRIMERS ,TOPOLOGY ,PHYSICS ,PHYSICAL sciences - Abstract
In this work we focus on the dynamics of macromolecular networks formed by end-linking identical polymer stars. The resulting macromolecular network can then be viewed as consisting of spacers which connect branching points (the cores of the stars). We succeed in analyzing exactly, in the framework of the generalized Gaussian model, the eigenvalue spectrum of such networks. As applications we focus on several topologies, such as regular networks and dendrimers; furthermore, we compare the results to those found for regular hyperbranched structures. In so doing, we also consider situations in which the beads of the cores differ from the beads of the spacers. The analytical procedure which we use involves an exact real-space renormalization, which allows to relate the star network to a (much simpler) network, in which each star is reduced to its core. It turns out that the eigenvalue spectrum of the star-polymer structure consists of two parts: one follows in terms of polynomial equations from the relaxation spectrum of the corresponding renormalized structure, while the second part involves the motion of the spacer chains themselves. Finally, we show exemplarily the situation for copolymeric dendrimers, calculate their spectra, and from them their storage and the loss moduli. [ABSTRACT FROM AUTHOR] more...
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- 2005
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7. Semiflexibility Highlights the Polymers' Topology: Monte Carlo Studies
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Maxim Dolgushev, Ganna Berezovska, and Alexander Blumen
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Physics ,Quantitative Biology::Biomolecules ,Polymers and Plastics ,Principle of maximum entropy ,Organic Chemistry ,Monte Carlo method ,Structure (category theory) ,Condensed Matter Physics ,Topology ,Gyration ,Stars ,Materials Chemistry ,Statistical physics ,Focus (optics) ,Topology (chemistry) ,Knot (mathematics) - Abstract
Summary: In this article we analyze in how far semiflexible behavior enhances the differences in the properties of classes of polymers whose topological structure varies. We focus on three pairs of macromolecular classes: stars vs. chains, unknotted rings vs. rings with one knot (trefoils), and stars vs. unknotted rings. For this we determine the mean-square radii of gyration and the bond-bond correlation functions through Monte Carlo simulations which use the bond fluctuation model. We show that introducing semiflexibility magnifies the differences between experimentally measurable quantities and may even lead to qualitative changes. Our simulation results are supported by theoretical studies which make use of the maximum entropy principle. more...
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- 2012
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8. Coherent exciton dynamics and trapping in topologically disordered systems
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Alexander Blumen and Oliver Mülken
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Condensed Matter::Quantum Gases ,Physics ,Condensed matter physics ,Exciton ,Dynamics (mechanics) ,Function (mathematics) ,Trapping ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials ,Quantum transport ,Survival probability ,High Energy Physics::Experiment ,Eigenvalues and eigenvectors - Abstract
We analyze the coherent dynamics of excitons in three-dimensional topologically disordered networks with traps. If the interactions between the nodes of the network are long ranged, i.e., algebraically decaying as a function of the distance between the nodes, the average survival probability of an exciton surprisingly shows a characteristic decay with features similar to the decay found for regular one-dimensional systems. We further show how this decay can be related to the eigenstates of the same system without a trap. more...
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- 2010
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9. Non-Markovian closure kinetics of flexible polymers with hydrodynamic interactions
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Thomas Guérin, Maxim Dolgushev, Alexander Blumen, Olivier Bénichou, Raphaël Voituriez, Nicolas Levernier, Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Theoretical Polymer Physics, University of Freiburg [Freiburg], Laboratoire Ondes et Matière d'Aquitaine (LOMA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Jean Perrin (LJP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Project: 277998,EC:FP7:ERC,ERC-2011-StG_20101014,FPTOPT(2011), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) more...
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Physics ,Quantitative Biology::Biomolecules ,Statistical Mechanics (cond-mat.stat-mech) ,Dynamics (mechanics) ,Kinetics ,General Physics and Astronomy ,Markov process ,FOS: Physical sciences ,Radius ,Condensed Matter::Soft Condensed Matter ,Nonlinear system ,symbols.namesake ,Closure (mathematics) ,symbols ,Tensor ,Statistical physics ,[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph] ,Physical and Theoretical Chemistry ,Scaling ,Condensed Matter - Statistical Mechanics - Abstract
International audience; This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete nonlinear dynamics. It is found that Markovian treatments based on a Wilemski-Fixman approximation significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects i n t he dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size N and capture radius b, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large N is given by T ∼ N 3/2 ln(N/b 2), which differs from the case of the Rouse dynamics where T ∼ N 2. The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented. more...
- Published
- 2015
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10. Contact Kinetics in Fractal Macromolecules
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Thomas Guérin, Maxim Dolgushev, Olivier Bénichou, Alexander Blumen, Raphaël Voituriez, Physikalisches Institut [Freiburg], Albert-Ludwigs-Universität Freiburg, Laboratoire Ondes et Matière d'Aquitaine (LOMA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), European Project: 277998,EC:FP7:ERC,ERC-2011-StG_20101014,FPTOPT(2011), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS) more...
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Kinetics ,FOS: Physical sciences ,General Physics and Astronomy ,Non-equilibrium thermodynamics ,Condensed Matter - Soft Condensed Matter ,chemistry.chemical_compound ,PACS numbers : 82.35.Lr, 05.40.-a, 36.20.Ey, 82.20.Uv ,Fractal ,Simple (abstract algebra) ,Physics - Chemical Physics ,Stochastic theories of rate constants ,Fluctuation phenomena ,Statistical physics ,Physical properties of polymers ,Scaling ,Condensed Matter - Statistical Mechanics ,Chemical Physics (physics.chem-ph) ,Physics ,Quantitative Biology::Biomolecules ,Statistical Mechanics (cond-mat.stat-mech) ,Stochastic process ,Conformation (statistics and dynamics) ,Condensed Matter::Soft Condensed Matter ,Monomer ,chemistry ,random processes ,noise and Brownian motion ,Soft Condensed Matter (cond-mat.soft) ,[PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft] ,Macromolecule - Abstract
International audience; We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the Mean First Contact Time (MFCT) for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the non-equilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the MFCT between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations. more...
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- 2015
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11. Models for the Dynamics of Hyperbranched Macromolecules
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Ch. Friedrich, Alexander Blumen, Aurel Jurjiu, and Th. Koslowski
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Physics ,Polymers and Plastics ,Gaussian ,Organic Chemistry ,Structure (category theory) ,Condensed Matter Physics ,Moduli ,Complex dynamics ,symbols.namesake ,Fractal ,Dendrimer ,Polymer chemistry ,Materials Chemistry ,symbols ,Statistical physics ,Scaling ,Macromolecule - Abstract
We focus on the motion of hyperbranched macromolecules in solution, paying particular attention to the relation between underlying topological structure and dynamics; we consider especially the mechanical moduli. Under the prominent representatives of hyperbranched polymers are both regular structures (such as the dendrimers) as well as disordered structures (such as irregular Cayley-trees). Evidently, batch-prepared hyperbranched macromolecules are closer to the latter. In order to theoretically determine their mechanical moduli we employ the method of generalized Gaussian structures (GGS), which allows us to study the situation including or excluding the hydrodynamic interactions (HI). Disordered hyperbranched structures display a complex dynamics; here we recall several analytical and numerical schemes for determining it and compare our theoretical results to the experimental data. more...
- Published
- 2006
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12. Fractional kinetics
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Sokolov, Igor M., Klafter, Joseph, and Blumen, Alexander
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Calculus -- Research ,System design -- Research ,Systems analysis ,Dynamics -- Analysis ,Diffusion -- Analysis ,System design ,Physics - Abstract
Fractional calculus can be used to formulate problems of strange kinetics as demonstrated by the Fick's law exceptions. Research shows that equations based on fractional derivatives can explain the anomalously slow diffusion in systems that exhibit a broad distribution of relaxation times. more...
- Published
- 2002
13. Scaling of star polymers: high order results
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C. von Ferber, Yu. Holovatch, V. Schulte-Frohlinde, and A. Blumen
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Physics ,chemistry.chemical_classification ,FOS: Physical sciences ,General Physics and Astronomy ,Polymer ,Condensed Matter - Soft Condensed Matter ,Renormalization group ,Star (graph theory) ,Random walk ,Condensed Matter::Soft Condensed Matter ,Loop (topology) ,chemistry ,Star polymer ,Copolymer ,Soft Condensed Matter (cond-mat.soft) ,Statistical physics ,Scaling - Abstract
We extend existing renormalization group calculations for the exponents describing scaling of star polymers and polymer networks constituted by chains of different species (the so-called copolymer star exponents). Our four loop results find application in the description of various phenomena involving self-avoiding and random walks that interact., Comment: 9 pages, 1 figure, style file included more...
- Published
- 2004
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14. Relaxation of Copolymeric Dendrimers Built from Alternating Monomers
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Cristian Satmarel, Alexander Blumen, and Andrey A. Gurtovenko
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Physics ,Polymers and Plastics ,Gaussian ,Organic Chemistry ,Relaxation (NMR) ,Composition (combinatorics) ,Condensed Matter Physics ,Moduli ,Inorganic Chemistry ,symbols.namesake ,Chemical physics ,Dendrimer ,Polymer chemistry ,Materials Chemistry ,symbols ,Copolymer ,Topology (chemistry) ,Macromolecule - Abstract
In this study we extend our previous work concerning the Rouse dynamics of linear alternating copolymers (Macromolecules 2003, 36, 486) to tree-like structures and focus on copolymeric dendrimers built from monomers of two kinds A and B; as before, we let the monomers differ in their interaction with the solvent. In the framework of generalized Gaussian structures (GGS), we consider alternating arrangements of monomers over the dendritic structures, we develop a semi-analytical method to determine for such structures (of arbitrary functionality, f, and number of generations, g), the eigenfrequencies (relaxation times). The method allows us to compute readily the storage, [G'(ω)] and the loss [G(ω)] moduli. These quantities show a multitude of features which mainly depend on the difference in the mobilities, or, equivalently, in the friction coefficients ζ A and ζ B of the A- and B-beads. These features range from the presence of large plateau-type regions in [G'(ω)] to the appearance of double-peaks in [G(ω)] In contrast to linear alternating copolymers, the behavior of the dynamic moduli of copolymeric systems with to dendritic topology can shed light into their composition, i.e. into the relative numbers of A- and B-beads. We discuss these aspects in view of their experimental relevance. more...
- Published
- 2004
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15. Network models and their dynamics: probes of topological structure
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Aurel Jurjiu, Thorsten Koslowski, and Alexander Blumen
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Physics ,Work (thermodynamics) ,Polymers and Plastics ,Scale (ratio) ,Organic Chemistry ,Eigenfunction ,Condensed Matter Physics ,Condensed Matter::Soft Condensed Matter ,Fractal ,Materials Chemistry ,Statistical physics ,Relaxation (approximation) ,Scaling ,Lattice model (physics) ,Network model - Abstract
In this work we focus on the mechanical relaxation of macromolecules. Based on linear response theory, this relaxation is in general related to the set of eigenmodes and eigenfunctions of the system. Of particular importance are situations which lead to scaling in the time and frequency domains. Thus the relaxation of star polymers, of dendrimers and of hyperbranched structures does not display scaling. On the other hand, one expects that the relaxation of fractals, as in fact that of linear chains, does scale. Here we numerically analyse the behavior of networks modelled through finite Sierpinski-type lattices, for which we have previously established that in the Rouse picture the mechanical relaxation scales in frequency and in time. As we show here, in the Zimm model based on the preaveraged Oseen-tensor, the picture changes drastically; taking the hydrodynamic interactions into account leads to relaxation forms which do not scale. more...
- Published
- 2003
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16. Dynamics of deterministic fractal polymer networks: Hydrodynamic interactions and the absence of scaling
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Th. Koslowski, A. Jurjiu, and A. Blumen
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Physics ,Work (thermodynamics) ,Fractal ,Scale (ratio) ,General Physics and Astronomy ,Relaxation (physics) ,Statistical physics ,Dielectric ,Tensor ,Physical and Theoretical Chemistry ,Flory–Huggins solution theory ,Scaling - Abstract
We numerically analyze the scaling behavior of experimentally accessible dynamical relaxation forms for networks modeled through finite Sierpinski-type lattices. Previous work has established unequivocally for such lattices that in the Rouse picture both the mechanical and the dielectric relaxation forms scale in frequency and in time. As we show here, in the Zimm model, based on the preaveraged Oseen tensor, the picture changes drastically; the introduction of the hydrodynamic interactions leads to relaxation patterns which do not scale. Our results show that the relaxation forms are very sensitive to the number of monomers in the network and to the strength of the hydrodynamic interaction parameter. more...
- Published
- 2003
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17. INTERACTIONS BETWEEN STAR POLYMERS: HIGH-ORDER CALCULATIONS OF THE SCALING EXPONENTS
- Author
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Schulte-Frohlinde, Blumen, von Ferber, and Holovatch
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chemistry.chemical_classification ,Physics ,Quantitative Biology::Biomolecules ,Physics and Astronomy (miscellaneous) ,Condensed matter physics ,Composite number ,Polymer ,Renormalization group ,Condensed Matter Physics ,lcsh:QC1-999 ,Condensed Matter::Soft Condensed Matter ,Stars ,chemistry ,Star polymer ,Colloidal particle ,fractals ,renormalization-group ,critical exponents ,High order ,Scaling ,polymers ,lcsh:Physics - Abstract
The scaling behavior of star polymers can be calculated in the m → 0 limit of an m -component spin system with an additional composite operator. The resulting scaling exponents describe the effective interaction of such polymer stars, i.e. objects whose behavior interpolates between that of polymer coils and that of hard sphere colloidal particles. We extend the existing renormalization group calculations from the third to the fourth order. Аналіз масштабної (скейлінгової) поведінки зіркових полімерів можна проводити на основі границі m → 0 m -компонентної спінової системи з додатковим композитним оператором. Скейлінгові показники, які при цьому отримуються, описують ефективну взаємодію полімерних зірок: об’єктів, поведінка яких інтерполює між поведінкою полімерних клубків та колоїдних частинок. Ми доповнюємо існуючі ренормгрупові обчислення третього порядку теорії збурень четвертим. more...
- Published
- 2003
18. Intermittent Turbulence Associated with a Density Current Passage in the Stable Boundary Layer
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Jielun Sun, Joan Cuxart, William Blumen, Sean P. Burns, Xin-Zhang Hu, Turker Ince, Rob K. Newsom, Stephen J. Frasier, Richard Coulter, Robert M. Banta, Carmen J. Nappo, Xuhui Lee, and Donald H. Lenschow more...
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Physics ,Atmospheric Science ,Boundary layer ,Meteorology ,Planetary boundary layer ,Turbulence ,Stratification (water) ,Mechanics ,Surface layer ,Stratified flow ,Surge ,Current density - Abstract
Using the unprecedented observational capabilities deployed duringthe Cooperative Atmosphere-Surface Exchange Study-99 (CASES-99),we found three distinct turbulence events on the night of 18October 1999, each of which was associated with differentphenomena: a density current, solitary waves, and downwardpropagating waves from a low-level jet. In this study, we focus onthe first event, the density current and its associatedintermittent turbulence. As the cold density current propagatedthrough the CASES-99 site, eddy motions in the upper part of thedensity current led to periodic overturning of the stratifiedflow, local thermal instability and a downward diffusion ofturbulent mixing. Propagation of the density current induced asecondary circulation. The descending motion following the head ofthe density current resulted in strong stratification, a sharpreduction in the turbulence, and a sudden increase in the windspeed. As the wind surge propagated toward the surface, shearinstability generated upward diffusion of turbulent mixing. Wedemonstrate in detail that the height and sequence of the localthermal and shear instabilities associated with the dynamics ofthe density current are responsible for the apparent intermittentturbulence. more...
- Published
- 2002
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19. Multifractal spectra and the relaxation of model polymer networks
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Aurel Jurjiu and A. Blumen
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Physics ,Fractal ,Computational chemistry ,Linear algebra ,General Physics and Astronomy ,Observable ,Multifractal system ,Statistical physics ,Relaxation (approximation) ,Physical and Theoretical Chemistry ,Eigenvalues and eigenvectors ,Spectral line ,Cole–Cole equation - Abstract
The mechanical and dielectric relaxation of polymer networks depends (especially in simple Gaussian-type approaches which extend the Rouse model) on the eigenvalues of the corresponding connectivity matrices. We use this to evaluate explicitly experimentally accessible relaxation forms for finite Sierpinski-type networks, whose eigenvalue spectra are multifractal. It turns out that the observable quantities are by far less singular than the eigenvalue spectra, since the underlying spectral structures get smoothed out. Our results establish unequivocally the spectral dimension as fundamental relaxation parameter; to see this, however, the finite fractal networks have to be sufficiently large. more...
- Published
- 2002
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20. Cyclization kinetics of Gaussian semiflexible polymer chains
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A. Blumen, Maxim Dolgushev, Olivier Bénichou, Raphaël Voituriez, Thomas Guérin, Laboratoire Ondes et Matière d'Aquitaine (LOMA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Theoretical Polymer Physics, University of Freiburg [Freiburg], Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), DFG : grant n° B1 142/11-1 et IRTG 'Soft Matter Science' (GRK 1642/1), Campus France (projet n° 28252XE), DAAD programme PROCOPE (projet n° 55853833), European Project: 277998,EC:FP7:ERC,ERC-2011-StG_20101014,FPTOPT(2011), and Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC) more...
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Physics ,Quantitative Biology::Biomolecules ,reactions ,010304 chemical physics ,Polymers ,Gaussian ,Kinetics ,PACS numbers: 82.35.-x, 05.40.-a ,Radius ,Eigenfunction ,Nonlinear dynamics and chaos ,01 natural sciences ,Combinatorics ,Mean squared displacement ,symbols.namesake ,Distribution (mathematics) ,properties ,polymerization ,0103 physical sciences ,symbols ,Statistical physics ,[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph] ,010306 general physics ,Finite set ,Eigenvalues and eigenvectors - Abstract
International audience; We consider the dynamics and the cyclization kinetics of Gaussian semiflexible chains, in which the interaction potential tends to align successive bonds. We provide asymptotic expressions for the cyclization time, for the eigenvalues and eigenfunctions, and for the mean square displacement at all time and length scales, with explicit dependence on the capture radius, on the positions of the reactive monomers in the chain, and on the finite number of beads. For the cyclization kinetics, we take into account non-Markovian effects by calculating the distribution of reactive conformations of the polymer, which are not taken into account in the classical Wilemski-Fixman theory. Comparison with numerical simulations confirms the accuracy of this non-Markovian theory. DOI: 10.1103/PhysRevE.90.052601 PACS number(s): 82.35.−x, 05.40.−a more...
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- 2014
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21. Gaussian semiflexible rings under angular and dihedral restrictions
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Thomas Guérin, Raphaël Voituriez, Olivier Bénichou, Alexander Blumen, Maxim Dolgushev, Theoretical Polymer Physics, University of Freiburg [Freiburg], Laboratoire Ondes et Matière d'Aquitaine (LOMA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Deutsche Forschungsgemeinschaft (DFG) : Grant No. Bl 142/11-1, DAAD : PROCOPE program (Project No. 55853833), Fonds der Chemischen Industrie, Campus France (Project No. 28252XE), European Project: 277998,EC:FP7:ERC,ERC-2011-StG_20101014,FPTOPT(2011), European Project: 295302,EC:FP7:PEOPLE,FP7-PEOPLE-2011-IRSES,SPIDER(2012), and Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC) more...
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Physics ,Ring (mathematics) ,Quantitative Biology::Biomolecules ,010304 chemical physics ,Polymers ,Gaussian ,Molecular Conformation ,Normal Distribution ,Closure (topology) ,General Physics and Astronomy ,Molecular Dynamics Simulation ,Dihedral angle ,Curvature ,01 natural sciences ,Displacement (vector) ,Normal distribution ,symbols.namesake ,Molecular dynamics ,Classical mechanics ,Computational chemistry ,0103 physical sciences ,symbols ,Physical and Theoretical Chemistry ,[PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech] ,010306 general physics - Abstract
International audience; Semiflexible polymer rings whose bonds obey both angular and dihedral restrictions [M. Dolgushev and A. Blumen, J. Chem. Phys.138, 204902 (2013)], are treated under exact closure constraints. This allows us to obtain semianalytic results for their dynamics, based on sets of Langevin equations. The dihedral restrictions clearly manifest themselves in the behavior of the mean-square monomer displacement. The determination of the equilibrium ring conformations shows that the dihedral constraints influence the ring curvature, leading to compact folded structures. The method for imposing such constraints in Gaussian systems is very general and it allows to account for heterogeneous (site-dependent) restrictions. We show it by considering rings in which one site differs from the others. more...
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- 2014
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22. Dynamics of annealed systems under external fields: CTRW and the fractional Fokker-Planck equations
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Igor M. Sokolov, Joseph Klafter, and Alexander Blumen
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Physics ,Statistical Mechanics (cond-mat.stat-mech) ,FOS: Physical sciences ,General Physics and Astronomy ,External field ,Fokker–Planck equation ,Disordered Systems and Neural Networks (cond-mat.dis-nn) ,Statistical physics ,Condensed Matter - Disordered Systems and Neural Networks ,Invariant (physics) ,Random walk ,Condensed Matter - Statistical Mechanics - Abstract
We consider the linear response of a system modelled by continuous-time random walks (CTRW) to an external field pulse of rectangular shape. We calculate the corresponding response function explicitely and show that it exhibits aging, i.e. that it is not translationally invariant in the time-domain. This result differs from that of systems which behave according to fractional Fokker-Planck equations. more...
- Published
- 2001
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23. Relaxation of disordered polymer networks: Regular lattice made up of small-world Rouse networks
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A. Blumen and Andrey A. Gurtovenko
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Physics ,chemistry.chemical_classification ,chemistry ,Computational chemistry ,Lattice (order) ,General Physics and Astronomy ,Regular lattice ,Polymer ,Statistical physics ,Physical and Theoretical Chemistry ,Pseudogap ,Eigenvalues and eigenvectors - Abstract
As models for inhomogeneous polymer networks, we investigate the Rouse dynamics of regular lattices built from subunits with arbitrary internal structure. We analyze as an example a two-dimensional lattice, consisting of small-world networks (SWNs). Using analytical and numerical calculations we study the stretching of such a structure under an external force. We find that the network shows interesting relaxation features and an unusual behavior in the intermediate time (frequency) domain, which lies in the region between the modes of the SWN subunits and those of the lattice. This behavior is related to the SWN-density of states, which leads to the appearance of a “pseudogap” between the highest lattice eigenvalue and the lowest SWN eigenvalue. more...
- Published
- 2001
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24. Unbalanced Frontogenesis. Part I: Zero Potential Vorticity
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R. T. Williams and William Blumen
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Physics::Fluid Dynamics ,Physics ,Rossby number ,Atmospheric Science ,Temperature gradient ,Frontogenesis ,Potential vorticity ,Barotropic fluid ,Mathematical analysis ,Frontolysis ,Thermodynamics ,Potential temperature ,Pressure gradient - Abstract
Unbalanced frontogenesis is studied in a two-dimensional, Boussinesq, rotating fluid that is constrained between two rigid, level surfaces. The potential vorticity is zero. The initial state is unbalanced because there is no motion and the potential temperature is given by the error function of x. An analytic solution is derived based on the neglect of the barotropic pressure gradient. The solution procedure uses momentum coordinates to obtain nonlinear solutions. When the initial Rossby number (Ro) is less than 1.435 the horizontal wind components display an inertial oscillation. During the first part of the inertial period (0 < ft < π) the isentropes develop a tilt and frontogenesis occurs, while in the second part (π < ft < 2π) the isentropes return to a vertical orientation and frontolysis brings the temperature gradient back to its original value at ft = 2π. For larger values of Ro a frontal discontinuity forms before ft = π. The importance of the barotropic pressure gradient is determined i... more...
- Published
- 2001
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25. Spin-up and spin-down in rotating fluid exhibiting inertial oscillations and frontogenesis
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Julie K. Lundquist and William Blumen
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Physics ,Atmospheric Science ,Ekman layer ,Baroclinity ,Geology ,Mechanics ,Oceanography ,Inertial wave ,Physics::Geophysics ,Physics::Fluid Dynamics ,Ocean dynamics ,Boundary layer ,Classical mechanics ,Barotropic fluid ,Computers in Earth Sciences ,Balanced flow ,Ekman number ,Physics::Atmospheric and Oceanic Physics - Abstract
Time-dependent, rotating flow in a finite depth of fluid is considered. Unbalanced initial conditions initiate flow in a shallow Ekman layer and in the inviscid interior, which is characterized by a state of zero potential vorticity. To determine the interior flow response to motion forced by the Ekman layer suction velocity, wB, an expansion of the flow to first-order in E1/2, where E is the Ekman number, is carried out. Frontogenesis, which occurs in both the baroclinic and barotropic parts of the geostrophic flow, modulates the inertial oscillation that enters at zero order. A baroclinic front (infinite relative vorticity) can occur in a finite-time, equal to or less than one-half the period of an inertial oscillation, πf−1 These fast-time processes are described in detail by Blumen (2000). Spin-up to the quasi-steady Ekman boundary layer solution also occurs during one-half the period of an inertial oscillation. Thereafter, wB varies on a slow-time scale, E−1/2f−1. Yet, a barotropic front may form in a finite-time if the initial anticyclonic relative vorticity exceeds f, a condition that favors nonlinear steepening in opposition to boundary layer dissipation. This analysis contributes to a theoretical understanding of the interplay between spin-down and frontogenesis in rotating fluid. Some values of the Ekman number, typical of mid-latitude flows, are introduced to compare theoretical predictions to observed conditions. It is concluded that the Ekman layer corrections are most likely smaller in magnitude than the magnitude of errors in current atmospheric wind measurement systems, and therefore, not verifiable. Oceanic flows are also difficult to measure at the required accuracy, and other processes compete with Ekman layer dissipation to explain slow-time spin-down in the oceans. more...
- Published
- 2001
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26. Stretch dynamics of flexible dendritic polymers in solution
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Alexander Blumen, Rama Kant, and Parbati Biswas
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chemistry.chemical_classification ,Physics ,Quantitative Biology::Biomolecules ,Work (thermodynamics) ,Dynamics (mechanics) ,Time evolution ,General Physics and Astronomy ,Polymer ,Condensed Matter::Soft Condensed Matter ,Stars ,Classical mechanics ,chemistry ,Chemical physics ,Center of mass ,Physical and Theoretical Chemistry ,Elastic modulus ,Topology (chemistry) - Abstract
We study the stretch dynamics of flexible dendritic polymers (dendrimers and stars) under external forces. We work in the framework of the bead-spring model with hydrodynamic interactions (HI) and take spacers of different length into account. The applied fields may, e.g., be of mechanical or electrical origin. We study the motion of a specific monomer, the time evolution of the stretch (the mean distance of the monomer on which the force acts from the center of mass of the polymer) and also the elastic moduli. We analyze how these dynamic properties depend on the underlying topology, i.e., on the number of generations for dendrimers and the length and number of branches for stars. As a special point we assess in how far the HI method utilized here (the Kirkwood–Riseman scheme) is stable for dendritic structures. Characteristic for the topology is the intermediate dynamics (between short and long times). It turns out that, different from stars, for dendrimers the stretch dynamics is for intermediate times close to logarithmic; hence the crossover in behavior at intermediate times is characteristic of the polymer’s topology. more...
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- 2001
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27. Front propagation in one-dimensional autocatalytic reactions: The breakdown of the classical picture at small particle concentrations
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J. Mai, Igor M. Sokolov, and A. Blumen
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Autocatalysis ,Physics ,Front propagation ,Dimension (vector space) ,Monte Carlo method ,Front (oceanography) ,Statistical physics ,Mechanics ,Small particles ,Limit (mathematics) ,Autocatalytic reaction - Abstract
The autocatalytic scheme A+B-->2A in a discrete particle system is studied in one dimension via Monte Carlo simulations. We find considerable differences in the results for the front velocities and front forms compared to the classical, continuous picture, which is only valid in the limit of very small reaction probabilities p. Interestingly, we also obtain front propagation velocities fairly below the classical minimal velocity. more...
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- 2000
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28. Ballistic versus diffusive pair dispersion in the Richardson regime
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A. Blumen, Igor M. Sokolov, and Joseph Klafter
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Fully developed ,Physics ,Turbulence ,Quantum mechanics ,Dispersion (optics) ,Probability density function ,Bulk Richardson number - Abstract
Two-particle dispersion in fully developed turbulence is modeled within an asymmetric L\'evy-walk framework which yields the Richardson ${t}^{3}$ law and which recovers recently observed results on the probability distribution function of pair separations in two-dimensional turbulence [M.C. Jullien, J. Paret, and P. Tabeling, Phys. Rev. Lett. 82, 2872 (1999)]. The ballistic nature of the Richardson dispersion is discussed in terms of the persistence parameter and compared with the Richardson diffusive behavior. more...
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- 2000
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29. Universal scaling and nonlinearity in surface layer fragmentation
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Igor M. Sokolov, Alexander Blumen, and U. A. Handge
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Physics ,Nonlinear system ,Fragmentation (mass spectrometry) ,Statistical physics ,Surface layer ,Molecular physics ,Scaling - Abstract
We analyze disordered one-dimensional bond-network models and investigate the influence of nonlinear force-elongation relations F proportional to/x/(m) on the fragmentation of coatings under tension. We aim to elucidate the interplay between the nonlinear forces and the random failure thresholds of the bonds. After an initial stage, the mean fragment length [L] scales with the applied strain epsilon, [L] proportional to epsilon(-alpha), where alpha=m/(m+1) for weakly disordered and alpha=m/(m+2) for strongly disordered coatings. more...
- Published
- 2000
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30. [Untitled]
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Sergei Nechaev, Alexander Blumen, and Gleb Oshanin
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chemistry.chemical_classification ,Physics ,Quantitative Biology::Biomolecules ,Anomalous diffusion ,Time evolution ,Anchoring ,Statistical and Nonlinear Physics ,Polymer ,Statistical mechanics ,Trapping ,chemistry ,Chain (algebraic topology) ,Chemical physics ,Line (geometry) ,Mathematical Physics - Abstract
We study the dynamics of a Rouse polymer chain which diffuses in a three-dimensional space under the constraint that one of its ends, referred to as the slip-link, may move only along a one-dimensional line containing randomly placed, immobile, perfect traps. Extensions of this model occur naturally in many fields, ranging from the spreading of polymer liquids on chemically active substrates to the binding of biomolecules by ligands. For our model we succeed in computing exactly the time evolution of the probability Psl(t) that the chain slip-link will not encounter any of the traps until time t and, consequently, that until this time the chain will remain mobile. more...
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- 2000
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31. Inertial Oscillations and Frontogenesis in a Zero Potential Vorticity Model
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William Blumen
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Physics ,Mathematical analysis ,Vorticity ,Oceanography ,Inertial wave ,Physics::Fluid Dynamics ,Rossby number ,Geostrophic current ,Frontogenesis ,Classical mechanics ,Potential vorticity ,Coriolis frequency ,Physics::Atmospheric and Oceanic Physics ,Geostrophic wind - Abstract
Geostrophic adjustment and frontogenesis are examined by means of a two-dimensional, inviscid, rotating and nonlinear fluid model that satisfies the condition of zero potential vorticity. The fluid is bounded top and bottom by level, rigid lids. The initial state is one of no motion, but an unbalanced horizontal temperature gradient is prescribed. The subsequent motion is represented as the sum of an inertial oscillation, with the frequency of the local Coriolis frequency f, and an evolving geostrophic flow. When a nondimensional parameter a, a Rossby number, satisfies a < 1, the gradient of the evolving geostrophic flow increases (frontogenesis) during the period 0 < t ⩽ π/f; the gradient decreases during the period π/f < t ⩽ 2π/f (frontolysis). When a ≥ 1, the relative vorticity of the evolving geostrophic flow becomes infinite: a discontinuity forms at the top and bottom boundaries during the period 0 < t ⩽ π/f. There is an equipartition of energy between the inertial oscillation and the geost... more...
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- 2000
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32. The Frontal Width Problem
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M. Piper and William Blumen
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Physics ,Atmospheric Science ,Frontogenesis ,Cold front ,Turbulence ,Inviscid flow ,Turbulence kinetic energy ,Dissipative system ,Thermodynamics ,Mechanics ,Dissipation ,Kinetic energy - Abstract
Observations of two low-level frontal passages by a hot-wire anemometer placed at 3 m above the ground provide evidence that frontal zones and the postfrontal regions exhibit enhanced kinetic energy dissipation. These observations support a postulated linear relationship between turbulent kinetic energy dissipation rate ϵ and a characteristic frontal width L. A rigorous theoretical development is not available to verify the postulate that an equilibrated frontal width is determined by a balance between frontogenetical forcing and turbulent dissipation of kinetic energy. Instead, a simple construct, based on a model of inviscid frontogenesis, is introduced. This model exhibits downscale spectral energy transfer that decreases with horizontal scale during frontogenesis. This model is invalid in the dissipative range of fully turbulent small-scale motions. In those cases, however, when frontal equilibration occurs at scales close to the scales where dissipation just begins to become significant, the... more...
- Published
- 1999
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33. Drude approach to anomalous diffusion: Application to Richardson dispersion in turbulent flows
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I. M. Sokolov. Blumen and Joseph Klafter
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Physics ,Flow (mathematics) ,Anomalous diffusion ,Turbulence ,Stochastic modelling ,Dispersion (optics) ,Time evolution ,Rare events ,General Physics and Astronomy ,Statistical physics ,Bulk Richardson number - Abstract
We investigate two-particle dispersion in fully developed turbulence within a Levy-walk stochastic model using a generalized Drude approach. Different from one-particle pictures we focus here on the time evolution of the relative distance between two particles. Based on the Kolmogorov-Obukhov energy spectrum and on the temporal correlations in the flow the Richardson t3-law follows as a Levy-type enhancement of rare events. more...
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- 1999
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34. Front propagation in the one-dimensional autocatalyticA+B→2Areaction with decay
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V. N. Kuzovkov, A. Blumen, Igor M. Sokolov, and J. Mai
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Autocatalysis ,Physics ,Front propagation ,Quantum mechanics ,A domain ,Beta (velocity) ,Atomic physics ,Critical value - Abstract
We consider front propagation in the autocatalytic scheme $A+\stackrel{\ensuremath{\rightarrow}}{B}2A,$ where we also allow the A particles to decay, $\stackrel{\ensuremath{\rightarrow}}{A}0,$ with a constant decay rate $\ensuremath{\beta}.$ In a one dimensional, discrete, situation the A domain moves as a pulse, and its dynamics differs from what is found in higher dimensions. Thus the velocity of the pulse tends to a finite value when $\ensuremath{\beta}$ approaches from below the critical value ${\ensuremath{\beta}}_{c},$ at which pulses die out. On the other hand, when approaching ${\ensuremath{\beta}}_{c}$ from above, the mean lifetime of the pulse grows as $T\ensuremath{\propto}(\ensuremath{\beta}\ensuremath{-}{\ensuremath{\beta}}_{c}{)}^{\ensuremath{-}2}.$ more...
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- 1999
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35. Discreteness effects on the front propagation in the A + B → 2 A reaction in 3 dimensions
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A. Blumen, Igor M. Sokolov, and J. Mai
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Chemical kinetics ,Physics ,Front propagation ,Classical mechanics ,Structure (category theory) ,General Physics and Astronomy ,Fisher equation ,Statistical physics ,Autocatalytic reaction - Abstract
We consider numerically the front propagation in a three-dimensional, diffusion-controlled A + B → 2A autocatalytic reaction. We show that the interplay between local and global ordering phenomena strongly affects the reaction kinetics, and that it leads to the breakdown of the classical continuous scheme (described by the Fisher equation) even at quite small concentrations of reactants. Discreteness aspects lead to considerable deviations of the simulated behavior of chemical fronts from the continuous scheme predictions, especially in what the fronts' structure and their propagation velocities are concerned. more...
- Published
- 1998
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36. Molecular-dynamics simulations of polyampholytes: Instabilities due to excess charges and external fields
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Helmut Schiessel, A. Blumen, and T. Soddemann
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Physics ,Hysteresis ,Molecular dynamics ,Classical mechanics ,Condensed matter physics ,Electric field ,Charge (physics) ,Electrostatics ,Critical value ,Critical field ,Scaling - Abstract
In this paper we study the conformational properties of polyampholytes ~PAs; polymers with positively and negatively charged monomers! by molecular-dynamics ~MD! simulations and by scaling arguments. As is well known, in the absence of external electrical fields PAs with a small total charge Qtot collapse into spherical globules, whereas PAs whose Qtot exceeds a critical value Qc are expanded; our MD simulations confirm this fact. For Qtot50 we study the influence of external electric fields on single PAs. We find that the PA globule is unstable above a critical field strength Ec1 ; for E.Ec1 the PA becomes highly stretched. Lowering the external field again, one observes hysteresis; the PA collapses back into a globule only for E,Ec2 where Ec2,Ec1 . In the weak coupling limit ~when the intrachain electrostatic interactions can be neglected ! the PA attains in an external field a trumpetlike shape, whose end-to-end distance obeys Pincus scaling. @S1063-651X~98!15102-4# more...
- Published
- 1998
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37. [Untitled]
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J. Mai, A. Blumen, and Igor M. Sokolov
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Physics ,chemistry.chemical_classification ,Euclidean space ,Exciton ,General Physics and Astronomy ,Motion (geometry) ,Nanotechnology ,Trapping ,Polymer ,Chain (algebraic topology) ,chemistry ,Chemical physics ,Diffusion (business) ,Excitation - Abstract
We consider energy transfer in polymers in dilute solutions and model it as a purely incoherent, hopping exciton motion which ends at permanent traps, whose positions along the polymer chain are fixed. The transport involves not only steps along the chain but also steps between sites which are far away along the chain's backbone but near to each other in Euclidean space. This possibility leads to very peculiar features of the excitation’s diffusion along the chain, due to strong correlations between subsequent steps. The process depends strongly on whether the chain is frozen or moves. We show that conformational changes influence trapping strongly, even if they are relatively slow on the time scale of the hopping motion. more...
- Published
- 1998
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38. A Model of Inertial Oscillations with Deformation Frontogenesis
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William Blumen
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Physics ,Atmospheric Science ,Classical mechanics ,Circular motion ,Inertial frame of reference ,Frontogenesis ,Hodograph ,Oscillation ,Mechanics ,Deformation (meteorology) ,Inertial wave ,Geostrophic wind - Abstract
A model of inertial oscillations that may occur with, and be modulated by, deformation frontogenesis is formulated. The deformation parameter is α ∼ 10−5 s−1 and the Coriolis parameter is f ∼ 10−4 s−1. This timescale separation, distinguished by the ratio α/f ∼ 10−1, provides the basis for application of a two-timescale analysis that separates the frontal evolution from the inertial frequency oscillations. To lowest order, the inertial oscillations do not influence frontogenesis, described by the classical Hoskins and Bretherton model. The frontal evolution, characterized by the alongfront geostrophic wind, does, however, provide an amplitude modulation of the inertial wind oscillation and of the temperature that also undergoes an oscillation at the inertial frequency. Parameter values are chosen to illustrate frontal contraction and translation characteristics that can distort the wind hodograph from circular motion. Ground-level temperature traces also exhibit unusual attributes, such as an ini... more...
- Published
- 1997
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39. Front form and velocity in a one-dimensional autocatalyticA+B→2Areaction
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V. N. Kuzovkov, A. Blumen, J. Mai, and Igor M. Sokolov
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Physics ,Autocatalysis ,Statistical physics ,Mechanics ,Front (military) - Published
- 1997
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40. Dynamics of a polyampholyte hooked around an obstacle
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A. Blumen, Helmut Schiessel, and Igor M. Sokolov
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Physics ,Mathematics::Logic ,Mathematics::Algebraic Geometry ,Field separation ,Condensed matter physics ,Electric field ,mental disorders ,Dynamics (mechanics) ,Charge density ,Charge (physics) ,Nanotechnology ,Computer Science::Distributed, Parallel, and Cluster Computing ,Physics::Geophysics - Abstract
We consider polyampholytes (PAs), which are polymers carrying positive and negative charges. The PAs are submitted to electric fields and collide with single obstacles. Field separation of PAs depends drastically on ${\ensuremath{\tau}}_{u},$ the time to unhook. Our analysis shows ${\ensuremath{\tau}}_{u}$ to be very sensitive to the charge distribution of the chains: Unhooking is diffusional for regular, multiblock PAs, with ${\ensuremath{\tau}}_{u}$ depending on the length of the blocks; for random charge distributions ${\ensuremath{\tau}}_{u}$ increases exponentially with the PAs' length and unhooking is subdiffusive. more...
- Published
- 1997
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41. Paradoxal Diffusion in Chemical Space for Nearest-Neighbor Walks over Polymer Chains
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Igor M. Sokolov, A. Blumen, and J. Mai
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Physics ,chemistry.chemical_classification ,Heterogeneous random walk in one dimension ,chemistry ,General Physics and Astronomy ,Statistical physics ,Polymer ,Diffusion (business) ,Chemical space ,k-nearest neighbors algorithm - Published
- 1997
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42. Non-equilibrium directed diffusion and inherently irreversible heat engines
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A. Blumen and Igor M. Sokolov
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Physics ,Work (thermodynamics) ,Ratchet ,General Physics and Astronomy ,Thermodynamics ,Statistical and Nonlinear Physics ,Mechanics ,symbols.namesake ,Thermal ,symbols ,Diffusion (business) ,Current (fluid) ,Carnot cycle ,Mathematical Physics ,Excitation ,Heat engine - Abstract
We consider models which are symmetric under time-reversal and which produce net currents under parametrical, dichotomous, thermal excitation. The simplest is based on a three-level system, which is the basic unit of a `minimal' thermally driven ratchet. We analyse the system's behaviour under periodic, dichotomous temperature changes and calculate the current, work and efficiency of the engine as functions of the upper and lower temperatures and of the modulation period. The system's behaviour differs greatly from a quasistatically working heat engine (such as based on a Carnot cycle). We discuss how this behaviour arises due to the inherently irreversible nature of the underlying process. more...
- Published
- 1997
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43. Polymer chains tethered to impenetrable interfaces: Broadening of relaxation spectra
- Author
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Martin Koch, Alexander Blumen, and Jens-Uwe Sommer
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chemistry.chemical_classification ,Physics ,Smoluchowski coagulation equation ,General Physics and Astronomy ,Polymer ,Dielectric ,Molecular physics ,Spectral line ,Condensed Matter::Soft Condensed Matter ,symbols.namesake ,Superposition principle ,chemistry ,Chain (algebraic topology) ,Quantum mechanics ,Perpendicular ,symbols ,Relaxation (physics) ,Physical and Theoretical Chemistry - Abstract
We investigate the dynamics of an ideal polymer chain which is tethered with one of its ends to an impenetrable interface. Due to the geometric restrictions the relaxation of modes perpendicular to the interface differs significantly from that of modes parallel to it. A superposition of both components leads to a marked broadening of the relaxation spectrum, which may find its signature in dielectric measurements. We obtain the relevant dynamical quantities for a polymer chain subject to geometric constraints by use of the Smoluchowski equation combined with a Rayleigh-Ritz variational scheme. more...
- Published
- 1997
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44. Continuous-time random-walk approach to supercooled liquids. II. Mean-square displacements in polymer melts
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Jean Farago, A. Blumen, Stephan Frey, Falko Ziebert, Hendrik Meyer, Jörg Baschnagel, and Julian Helfferich
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Physics ,Molecular dynamics ,Distribution (mathematics) ,Series (mathematics) ,Monte Carlo method ,Jump ,Statistical physics ,Function (mathematics) ,Random walk ,Continuous-time random walk - Abstract
The continuous-time random walk (CTRW) describes the single-particle dynamics as a series of jumps separated by random waiting times. This description is applied to analyze trajectories from molecular dynamics (MD) simulations of a supercooled polymer melt. Based on the algorithm presented by Helfferich et al. [Phys. Rev. E 89, 042603 (2014)], we detect jump events of the monomers. As a function of temperature and chain length, we examine key distributions of the CTRW: the jump-length distribution (JLD), the waiting-time distribution (WTD), and the persistence-time distribution (PTD), i.e., the distribution of waiting times for the first jump. For the equilibrium (polymer) liquid under consideration, we verify that the PTD is determined by the WTD. For the mean-square displacement (MSD) of a monomer, the results for the CTRW model are compared with the underlying MD data. The MD data exhibit two regimes of subdiffusive behavior, one for the early $\ensuremath{\alpha}$ process and another at later times due to chain connectivity. By contrast, the analytical solution of the CTRW yields diffusive behavior for the MSD at all times. Empirically, we can account for the effect of chain connectivity in Monte Carlo simulations of the CTRW. The results of these simulations are then in good agreement with the MD data in the connectivity-dominated regime, but not in the early $\ensuremath{\alpha}$ regime where they systematically underestimate the MSD from the MD. more...
- Published
- 2013
45. Continuous-time random-walk approach to supercooled liquids. I. Different definitions of particle jumps and their consequences
- Author
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Falko Ziebert, Julian Helfferich, A. Blumen, Stephan Frey, Jörg Baschnagel, Hendrik Meyer, and Jean Farago
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Physics ,Molecular dynamics ,Particle ,Context (language use) ,State (functional analysis) ,Statistical physics ,Continuous-time random walk ,Supercooling ,Random walk ,Bifurcation - Abstract
Single-particle trajectories in supercooled liquids display long periods of localization interrupted by "fast moves." This observation suggests a modeling by a continuous-time random walk (CTRW). We perform molecular dynamics simulations of equilibrated short-chain polymer melts near the critical temperature of mode-coupling theory Tc and extract "moves" from the monomer trajectories. We show that not all moves comply with the conditions of a CTRW. Strong forward-backward correlations are found in the supercooled state. A refinement procedure is suggested to exclude these moves from the analysis. We discuss the repercussions of the refinement on the jump-length and waiting-time distributions as well as on characteristic time scales, such as the average waiting time ("exchange time") and the average time for the first move ("persistence time"). The refinement modifies the temperature (T) dependence of these time scales. For instance, the average waiting time changes from an Arrhenius-type to a Vogel-Fulcher-type T dependence. We discuss this observation in the context of the bifurcation of the α process and (Johari) β process found in many glass-forming materials to occur near Tc. Our analysis lays the foundation for a study of the jump-length and waiting-time distributions, their temperature and chain-length dependencies, and the modeling of the monomer dynamics by a CTRW approach in the companion paper [J. Helfferich et al., Phys. Rev. E 89, 042604 (2014)]. more...
- Published
- 2013
46. Billiard dynamics of bouncing dumbbell
- Author
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Vadim Zharnitsky, Victoria Blumen, Ki Yeun Kim, and Yuliy Baryshnikov
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Physics ,Dynamics (mechanics) ,Boundary (topology) ,Statistical and Nonlinear Physics ,Dynamical Systems (math.DS) ,Condensed Matter Physics ,Nonlinear Sciences::Chaotic Dynamics ,Condensed Matter::Soft Condensed Matter ,Classical mechanics ,70F35, 70H11 ,Adiabatic invariant ,FOS: Mathematics ,Dumbbell ,Dynamical billiards ,Mathematics - Dynamical Systems - Abstract
A system of two masses connected with a weightless rod (called dumbbell in this paper) interacting with a flat boundary is considered. The sharp bound on the number of collisions with the boundary is found using billiard techniques. In case, the ratio of masses is large and the dumbbell rotates fast, an adiabatic invariant is obtained., 14 pages, 4 figures more...
- Published
- 2013
47. From Continuous-Time Random Walks to Continuous-Time Quantum Walks: Disordered Networks
- Author
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Alexander Blumen and Oliver Mülken
- Subjects
Physics ,Quantum system ,Quantum walk ,Statistical physics ,Complex network ,Eigenfunction ,Continuous-time random walk ,Random walk ,Quantum ,Eigenvalues and eigenvectors - Abstract
Recent years have seen a growing interest in dynamical quantum processes; thus it was found that the electronic energy transfer through photosynthetic antennae displays quantum features, aspects also known from the dynamics of charge carriers along polymer backbones. Hence, in modeling energy transfer one has to extend the classical, master-equation-type formalism and incorporate quantum-mechanical aspects, while still aiming to describe complex networks of molecules over which the transport takes place. The continuous time random walk (CTRW) scheme is widely employed in modeling transport in random environments (Sokolov et al, Phys Today 55:48, 2002) and is mathematically akin to quantum-mechanical Hamiltonians of tight-binding type (Mulken and Blumen, Phys Rep 502:37, 2011; Mulken and Blumen, Phys Rev E 73:066117, 2006); a simple way to see it is to focus on the time-evolution operators in statistical and in quantum mechanics: The transition to the quantal domain leads then to continuous-time quantum walks (CTQW). In this way the CTQW problem stays linear, and thus many results obtained in solving CTRW (such as eigenvalues and eigenfunctions) can be readily reutilized for CTQW. However, the physically relevant properties of the two models differ vastly: In the absence of traps CTQW are time-inversion symmetric and no energy equipartition takes place at long times. Also, the quantum system keeps memory of the initial conditions, a fact exemplified by the occurrence of quasi-revivals (Mulken and Blumen, Phys Rep 502:37, 2011). Here we will exemplify the vastly different behaviors of CTQW and CTRW on disordered networks , namely on small-world networks (Mulken et al, Phys Rev E 76:051125, 2007) and on star-graphs with randomly added bonds (Anishchenko et al, Quantum Inf Process 11:1273, 2012). more...
- Published
- 2013
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48. NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities.
- Author
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Boukadida, Célia, Fritz, Matthieu, Blumen, Brigitte, Fogeron, Marie-Laure, Penin, François, and Martin, Annette
- Subjects
HEPATITIS C virus ,PROTEOLYTIC enzymes ,VIRAL nonstructural proteins ,PROTEIN precursors ,GENOMES - Abstract
Over the recent years, several homologues with varying degrees of genetic relatedness to hepatitis C virus (HCV) have been identified in a wide range of mammalian species. HCV infectious life cycle relies on a first critical proteolytic event of its single polyprotein, which is carried out by nonstructural protein 2 (NS2) and allows replicase assembly and genome replication. In this study, we characterized and evaluated the conservation of the proteolytic mode of action and regulatory mechanisms of NS2 across HCV and animal hepaciviruses. We first demonstrated that NS2 from equine, bat, rodent, New and Old World primate hepaciviruses also are cysteine proteases. Using tagged viral protein precursors and catalytic triad mutants, NS2 of equine NPHV and simian GBV-B, which are the most closely and distantly related viruses to HCV, respectively, were shown to function, like HCV NS2 as dimeric proteases with two composite active sites. Consistent with the reported essential role for NS3 N-terminal domain (NS3
N ) as HCV NS2 protease co-factor via NS3N key hydrophobic surface patch, we showed by gain/loss of function mutagenesis studies that some heterologous hepacivirus NS3N may act as co-factors for HCV NS2 provided that HCV-like hydrophobic residues are conserved. Unprecedently, however, we also observed efficient intrinsic proteolytic activity of NS2 protease in the absence of NS3 moiety in the context of C-terminal tag fusions via flexible linkers both in transiently transfected cells for all hepaciviruses studied and in the context of HCV dicistronic full-length genomes. These findings suggest that NS3N acts as a regulatory rather than essential co-factor for hepacivirus NS2 protease. Overall, unique features of NS2 including enzymatic function as dimers with two composite active sites and additional NS3-independent proteolytic activity are conserved across hepaciviruses regardless of their genetic distances, highlighting their functional significance in hepacivirus life cycle. [ABSTRACT FROM AUTHOR] more...- Published
- 2018
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49. Front Propagation and Local Ordering in One-Dimensional Irreversible Autocatalytic Reactions
- Author
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J. Mai, Igor M. Sokolov, and A. Blumen
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Physics ,Front propagation ,General Physics and Astronomy ,Statistical physics ,Autocatalytic reaction - Published
- 1996
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50. Copolymers in asymmetric interface potentials: A Monte Carlo study
- Author
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Alexander Blumen, Gongwen Peng, and Jens-Uwe Sommer
- Subjects
Physics ,media_common.quotation_subject ,Monte Carlo method ,Crossover ,General Physics and Astronomy ,Asymmetry ,Critical point (mathematics) ,Copolymer ,Exponent ,Statistical physics ,Physical and Theoretical Chemistry ,Scaling ,Critical exponent ,media_common - Abstract
We investigate using scaling methods and Monte Carlo simulations random AB‐copolymers at the interface between two good solvents. The asymmetry of the interface potential gives rise to an adsorption–desorption transition which shows for infinitely long chains a critical point. For finite chains we analyze the crossover scaling behavior near this critical point. Two new interface exponents, namely the crossover exponent φ and the interface order parameter exponent β are proposed. Simulation results obtained using the bond fluctuation model agree well with the scaling predictions. From the simulation data we obtain as best estimates φ=1.3±0.1 and β=0.35±0.04. more...
- Published
- 1996
- Full Text
- View/download PDF
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