We study the radial current driven vortex dynamics in the Corbino disk sample at zero field, by using a logarithmically interacting point vortex model involving effect of temperature, random pinning centers, and disk wall confinement force. We also take into account both the current induced vortex pair nucleation and the vortex pair annihilation processes in the model. Simulation results demonstrate that the vortex motion induced voltage exhibits almost periodic pulse behavior in time, observed experimentally, for a certain range of the model parameters. Such an anomalous behavior is thought to originate from large fluctuations of the vortex number due to the collective dynamics of this vortex system.
{"title":"Vortex Nucleation Effects on Vortex Dynamics in Corbino Disk at Zero Field","authors":"Y. Enomoto, M. Ohta, Y. Yamada","doi":"10.1063/1.2897900","DOIUrl":"https://doi.org/10.1063/1.2897900","url":null,"abstract":"We study the radial current driven vortex dynamics in the Corbino disk sample at zero field, by using a logarithmically interacting point vortex model involving effect of temperature, random pinning centers, and disk wall confinement force. We also take into account both the current induced vortex pair nucleation and the vortex pair annihilation processes in the model. Simulation results demonstrate that the vortex motion induced voltage exhibits almost periodic pulse behavior in time, observed experimentally, for a certain range of the model parameters. Such an anomalous behavior is thought to originate from large fluctuations of the vortex number due to the collective dynamics of this vortex system.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897900","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A model system is studied via Molecular Dynamics (MD) simulation. The system consists of 3,200 molecules placed in the rigid cubic cell with the periodic boundary condition. A molecule has 100 united atoms which are assumed the CH2. The molecule has the bonds between the united atoms nearby, the bends to the next bond, and the torsional potential. The motions of the united atoms in the model system have at least three time stages before the time region of the system relaxation. The first stage is marked by the ballistic motion. The second stage is marked by the motion in some cage. The third stage is marked by the collective motion with the surrounding united atoms. The fourth stage is marked by the elementary process which causes the system relaxation for long time.
{"title":"A Molecular Dynamics Simulation of a Supercooled System with 3,200 Model Polymers","authors":"T. Muranaka","doi":"10.1063/1.2897796","DOIUrl":"https://doi.org/10.1063/1.2897796","url":null,"abstract":"A model system is studied via Molecular Dynamics (MD) simulation. The system consists of 3,200 molecules placed in the rigid cubic cell with the periodic boundary condition. A molecule has 100 united atoms which are assumed the CH2. The molecule has the bonds between the united atoms nearby, the bends to the next bond, and the torsional potential. The motions of the united atoms in the model system have at least three time stages before the time region of the system relaxation. The first stage is marked by the ballistic motion. The second stage is marked by the motion in some cage. The third stage is marked by the collective motion with the surrounding united atoms. The fourth stage is marked by the elementary process which causes the system relaxation for long time.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897796","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
E. Hashimoto, Y. Aoki, Y. Seshimo, K. Sasanuma, Y. Ike, S. Kojima
Polymorphism and dehydration process are studied in lysozyme crystals. Three kinds of crystals with tetragonal, orthorhombic, monoclinic systems are successfully grown by two liquids method. The dehydration process of a tetragonal crystal is investigated by the micro‐Brillouin scattering techniques. This process is discussed by the Avrami–Erofe'ev equation.
{"title":"Micro‐Brillouin Scattering Study of Acoustic Properties of Protein Crystals","authors":"E. Hashimoto, Y. Aoki, Y. Seshimo, K. Sasanuma, Y. Ike, S. Kojima","doi":"10.1063/1.2897817","DOIUrl":"https://doi.org/10.1063/1.2897817","url":null,"abstract":"Polymorphism and dehydration process are studied in lysozyme crystals. Three kinds of crystals with tetragonal, orthorhombic, monoclinic systems are successfully grown by two liquids method. The dehydration process of a tetragonal crystal is investigated by the micro‐Brillouin scattering techniques. This process is discussed by the Avrami–Erofe'ev equation.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897817","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Richter, K. Niedźwiedź, M. Monkenbusch, A. Wischnewski, R. Biehl, B. Hoffmann, R. Merkel
High resolution neutron scattering together with a meticulous choice of the contrast conditions allows to access the large scale dynamics of soft materials including biological molecules in space and time. In this contribution we present two examples. One from the world of synthetic polymers, the other from biomolecules. First, we will address the peculiar dynamics of miscible polymer blends with very different component glass transition temperatures. Polymethylmetacrylate (PMMA), polyethyleneoxide (PEO) are perfectly miscible but exhibit a difference in the glass transition temperature by 200 K. We present quasielastic neutron scattering investigations on the dynamics of the fast component in the range from angstroms to nanometers over a time frame of five orders of magnitude. All data may be consistently described in terms of a Rouse model with random friction, reflecting the random environment imposed by the nearly frozen PMMA matrix on the fast mobile PEO. In the second part we touch on some new devel...
{"title":"Polymer Dynamics from Synthetic to Biological Macromolecules","authors":"D. Richter, K. Niedźwiedź, M. Monkenbusch, A. Wischnewski, R. Biehl, B. Hoffmann, R. Merkel","doi":"10.1063/1.2897833","DOIUrl":"https://doi.org/10.1063/1.2897833","url":null,"abstract":"High resolution neutron scattering together with a meticulous choice of the contrast conditions allows to access the large scale dynamics of soft materials including biological molecules in space and time. In this contribution we present two examples. One from the world of synthetic polymers, the other from biomolecules. First, we will address the peculiar dynamics of miscible polymer blends with very different component glass transition temperatures. Polymethylmetacrylate (PMMA), polyethyleneoxide (PEO) are perfectly miscible but exhibit a difference in the glass transition temperature by 200 K. We present quasielastic neutron scattering investigations on the dynamics of the fast component in the range from angstroms to nanometers over a time frame of five orders of magnitude. All data may be consistently described in terms of a Rouse model with random friction, reflecting the random environment imposed by the nearly frozen PMMA matrix on the fast mobile PEO. In the second part we touch on some new devel...","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897833","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We studied the secondary relaxation in galactose‐water mixtures by analyzing the dielectric loss spectra with two different fitting methods. The first method was the free fit without any constraint and the second method was the fit with the coupling relation in coupling model (CM) [1, 2, 3]. The behavior of the secondary relaxation process were very similar to that of the secondary relaxation process with changing the rotational‐traslational (RT) coupling constant in the schematic mode coupling theory (MCT) [4, 5]. The secondary relaxation times (τJG) obtained by the constrained fit contain a large uncertainty and were consistent with τsec within the experimental errors. We also found that the fitting quality of free fit was better.
{"title":"A Study of the Secondary Relaxation in Galactose‐Water Mixtures","authors":"Hyun-Joung Kwon, Jeong-Ah Seo, H. Kim, Y. Hwang","doi":"10.1063/1.2897888","DOIUrl":"https://doi.org/10.1063/1.2897888","url":null,"abstract":"We studied the secondary relaxation in galactose‐water mixtures by analyzing the dielectric loss spectra with two different fitting methods. The first method was the free fit without any constraint and the second method was the fit with the coupling relation in coupling model (CM) [1, 2, 3]. The behavior of the secondary relaxation process were very similar to that of the secondary relaxation process with changing the rotational‐traslational (RT) coupling constant in the schematic mode coupling theory (MCT) [4, 5]. The secondary relaxation times (τJG) obtained by the constrained fit contain a large uncertainty and were consistent with τsec within the experimental errors. We also found that the fitting quality of free fit was better.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897888","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. Botet, B. Cabane, M. Clifton, M. Meireles, Ryohei Seto
We have developed a novel computational scheme that allows direct numerical simulation of the mechanical behavior of sticky granular matter under stress. We present here the general method, with particular emphasis on the particle features at the nanometric scale. It is demonstrated that, although sticky granular material is quite complex and is a good example of a challenging computational problem (it is a dynamical problem, with irreversibility, self‐organization and dissipation), its main features may be reproduced on the basis of rather simple numerical model, and a small number of physical parameters. This allows precise analysis of the possible deformation processes in soft materials submitted to mechanical stress. This results in direct relationship between the macroscopic rheology of these pastes and local interactions between the particles.
{"title":"How a Colloidal Paste Flows—Scaling Behaviors in Dispersions of Aggregated Particles under Mechanical Stress—","authors":"R. Botet, B. Cabane, M. Clifton, M. Meireles, Ryohei Seto","doi":"10.1063/1.2897806","DOIUrl":"https://doi.org/10.1063/1.2897806","url":null,"abstract":"We have developed a novel computational scheme that allows direct numerical simulation of the mechanical behavior of sticky granular matter under stress. We present here the general method, with particular emphasis on the particle features at the nanometric scale. It is demonstrated that, although sticky granular material is quite complex and is a good example of a challenging computational problem (it is a dynamical problem, with irreversibility, self‐organization and dissipation), its main features may be reproduced on the basis of rather simple numerical model, and a small number of physical parameters. This allows precise analysis of the possible deformation processes in soft materials submitted to mechanical stress. This results in direct relationship between the macroscopic rheology of these pastes and local interactions between the particles.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897806","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58347958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tetsunori Yamamoto, K. Nishikawa, Ayumu Sugiyama, A. Purqon, T. Mizukami, H. Shimahara, H. Nagao, K. Nishikawa
The docking structure of the Azurin‐Cytochrome C551 is presented. We investigate a complex system of Azurin(II)‐Cytochrome C551(II) by using molecular dynamics simulation. We estimate some physical properties, such as root‐mean‐square deviation (RMSD), binding energy between Azurin and Cytochrome C551, distance between Azurin(II) and Cytochrome C551(II) through center of mass and each active site. We also discuss docking stability in relation to the configuration by free energy between Azurin(II)‐Cytochrome C551(II) and Azurin(I)‐Cytochrome C551(III).
{"title":"Theoretical Study of Free Energy in Docking Stability of Azurin(II)‐Cytochrome c551(II) Complex System","authors":"Tetsunori Yamamoto, K. Nishikawa, Ayumu Sugiyama, A. Purqon, T. Mizukami, H. Shimahara, H. Nagao, K. Nishikawa","doi":"10.1063/1.2897903","DOIUrl":"https://doi.org/10.1063/1.2897903","url":null,"abstract":"The docking structure of the Azurin‐Cytochrome C551 is presented. We investigate a complex system of Azurin(II)‐Cytochrome C551(II) by using molecular dynamics simulation. We estimate some physical properties, such as root‐mean‐square deviation (RMSD), binding energy between Azurin and Cytochrome C551, distance between Azurin(II) and Cytochrome C551(II) through center of mass and each active site. We also discuss docking stability in relation to the configuration by free energy between Azurin(II)‐Cytochrome C551(II) and Azurin(I)‐Cytochrome C551(III).","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897903","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Currently, the designations for the low‐frequency vibrational spectrum of liquid watrer are still diversified. In this paper, the water molecules simulated by the SPC/E model are classified into subensembles, characterized by their local structures, which are specified in two different ways: the geometry of Voronoi polyhedron or the H‐bond configuration. Using the instantaneous normal mode (INM) analysis for these subensembles, we investigate the effects of local structure on the low‐frequency INM spectrum of liquid water. From the contributions of these subensembles to the translational INM spectrum, our results provide insights into the geometric effects of local structure and the H‐bond configuration on intermolecular vibrations in liquid water.
{"title":"Local Structural Effects on Intermolecular Vibrations in Liquid Water: The Instantaneous‐Normal‐Mode Analysis","authors":"K. Tsai, Ten-Ming Wu","doi":"10.1063/1.2897830","DOIUrl":"https://doi.org/10.1063/1.2897830","url":null,"abstract":"Currently, the designations for the low‐frequency vibrational spectrum of liquid watrer are still diversified. In this paper, the water molecules simulated by the SPC/E model are classified into subensembles, characterized by their local structures, which are specified in two different ways: the geometry of Voronoi polyhedron or the H‐bond configuration. Using the instantaneous normal mode (INM) analysis for these subensembles, we investigate the effects of local structure on the low‐frequency INM spectrum of liquid water. From the contributions of these subensembles to the translational INM spectrum, our results provide insights into the geometric effects of local structure and the H‐bond configuration on intermolecular vibrations in liquid water.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897830","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Spreading and receding processes of water drops impacting on a stainless steel surface comprising rectangular shaped parallel grooves are studied experimentally. The study was confined to the impact of drops in inertia dominated flow regime with Weber number in the range 15–257. Measurements of spreading drop diameter and drop height were obtained during the impact process as function of time. Experimental measurements of spreading drop diameter and drop height obtained for the grooved surface were compared with those obtained for a smooth surface to elucidate the influence of surface grooves on the impact process. The grooves definitely influence both spreading and receding processes of impacting liquid drops. A more striking observation from this study is that the receding process of impacting liquid drops is dramatically changed by the groove structure for all droplet Weber number.
{"title":"Drop Impact on a Solid Surface Comprising Micro Groove Structure","authors":"R. Kannan, D. Sivakumar","doi":"10.1063/1.2897870","DOIUrl":"https://doi.org/10.1063/1.2897870","url":null,"abstract":"Spreading and receding processes of water drops impacting on a stainless steel surface comprising rectangular shaped parallel grooves are studied experimentally. The study was confined to the impact of drops in inertia dominated flow regime with Weber number in the range 15–257. Measurements of spreading drop diameter and drop height were obtained during the impact process as function of time. Experimental measurements of spreading drop diameter and drop height obtained for the grooved surface were compared with those obtained for a smooth surface to elucidate the influence of surface grooves on the impact process. The grooves definitely influence both spreading and receding processes of impacting liquid drops. A more striking observation from this study is that the receding process of impacting liquid drops is dramatically changed by the groove structure for all droplet Weber number.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897870","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Friction between the polymer network and the solvent water was measured under the conditions that the thermoresponsive hydrogel was mechanically constrained in a glass microcapillary. The water‐flow through the hydrogel could be continuously controlled by more than 1×102 times only by adjusting the temperature in the vicinity of the transition temperature. The principles to control the solvent flow and the switching velocity by the temperature jump were discussed on the basis of the material parameters and the experimental conditions.
{"title":"Water flow through a stimuli-responsive hydrogel under mechanical constraint","authors":"G. Kondo, T. Oda, A. Suzuki","doi":"10.1063/1.2897837","DOIUrl":"https://doi.org/10.1063/1.2897837","url":null,"abstract":"Friction between the polymer network and the solvent water was measured under the conditions that the thermoresponsive hydrogel was mechanically constrained in a glass microcapillary. The water‐flow through the hydrogel could be continuously controlled by more than 1×102 times only by adjusting the temperature in the vicinity of the transition temperature. The principles to control the solvent flow and the switching velocity by the temperature jump were discussed on the basis of the material parameters and the experimental conditions.","PeriodicalId":46935,"journal":{"name":"Complex Systems","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2008-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.2897837","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58348153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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