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Strange Nonchaotic Bursting in A Quasiperiodially-Forced Hindmarsh-Rose Neuron 拟周期强迫Hindmarsh-Rose神经元的奇异非混沌爆发
arXiv: Biological Physics Pub Date : 2010-12-15 DOI: 10.3938/jkps57.1356
W. Lim, Sang-Yoon Kim
{"title":"Strange Nonchaotic Bursting in A Quasiperiodially-Forced Hindmarsh-Rose Neuron","authors":"W. Lim, Sang-Yoon Kim","doi":"10.3938/jkps57.1356","DOIUrl":"https://doi.org/10.3938/jkps57.1356","url":null,"abstract":"We study the transition from a silent state to a bursting state by varying the dc stimulus in the Hindmarsh-Rose neuron under quasiperiodic stimulation. For this quasiperiodically forced case, a new type of strange nonchaotic (SN) bursting state is found to occur between the silent state and the chaotic bursting state. This is in contrast to the periodically forced case where the silent state transforms directly to a chaotic bursting state. Using a rational approximation to the quasiperiodic forcing, the mechanism for the appearance of such an SN bursting state is investigated. Thus, a smooth torus (corresponding to a silent state) is found to transform to an SN bursting attractor through a phase-dependent subcritical period-doubling bifurcation. These SN bursting states, together with chaotic bursting states, are characterized in terms of the interburst interval, the bursting length, and the number of spikes in each burst. Both bursting states are found to be aperiodic complex ones. Consequently, aperiodic complex burstings may result from two dynamically different states with strange geometry (one is chaotic and the other one is nonchaotic). Thus, in addition to chaotic burstings, SN burstings may become a dynamical origin for complex physiological rhythms which are ubiquitous in organisms.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127343694","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}
引用次数: 2
Conformation changes and protein folding induced by φ4 interaction φ4相互作用引起的构象变化和蛋白质折叠
arXiv: Biological Physics Pub Date : 2010-11-01 DOI: 10.1142/9789814335614_0047
Mariska Januar, A. Sulaiman, L. T. Handoko
{"title":"Conformation changes and protein folding induced by φ4 interaction","authors":"Mariska Januar, A. Sulaiman, L. T. Handoko","doi":"10.1142/9789814335614_0047","DOIUrl":"https://doi.org/10.1142/9789814335614_0047","url":null,"abstract":"A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected non-linear sources are represented by the bosonic lagrangian with an additional phi^4 interaction for the sources. In the model the spring tension of protein representing the internal hydrogen bonds is realized as the interactions between individual amino acids and nonlinear sources. The folding pathway is determined by the strength of nonlinear sources that propagate through the protein backbone. It is also shown that the model reproduces the results in some previous works.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134239409","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}
引用次数: 3
Homochirality through Photon-Induced Melting of RNA/DNA: the Thermodynamic Dissipation Theory of the Origin of Life 光子诱导RNA/DNA熔融的同手性:生命起源的热力学耗散理论
arXiv: Biological Physics Pub Date : 2010-10-06 DOI: 10.1038/NPRE.2010.5177.1
K. Michaelian
{"title":"Homochirality through Photon-Induced Melting of RNA/DNA: the Thermodynamic Dissipation Theory of the Origin of Life","authors":"K. Michaelian","doi":"10.1038/NPRE.2010.5177.1","DOIUrl":"https://doi.org/10.1038/NPRE.2010.5177.1","url":null,"abstract":"","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"12 5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130348564","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}
引用次数: 6
Error-Control and Digitalization Concepts for Chemical and Biomolecular Information Processing Systems 化学和生物分子信息处理系统的误差控制和数字化概念
arXiv: Biological Physics Pub Date : 2010-04-26 DOI: 10.1166/JCTN.2011.1714
V. Privman
{"title":"Error-Control and Digitalization Concepts for Chemical and Biomolecular Information Processing Systems","authors":"V. Privman","doi":"10.1166/JCTN.2011.1714","DOIUrl":"https://doi.org/10.1166/JCTN.2011.1714","url":null,"abstract":"We consider approaches for controlling the buildup of noise by design of gates for chemical and biomolecular computing, in order to realize stable, scalable networks for multi-step information processing. Solvable rate-equation models are introduced and used to illustrate several recently developed concepts and methodologies. We also outline future challenges and possible research directions.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122591045","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}
引用次数: 14
Dynamic Principles of Center of Mass in Human Walking 人体行走的质心动力学原理
arXiv: Biological Physics Pub Date : 2010-04-20 DOI: 10.9734/BBJ/2013/4724
Yifang Fan, M. Loan, Yubo Fan, Zhiyu Li, C. Lv
{"title":"Dynamic Principles of Center of Mass in Human Walking","authors":"Yifang Fan, M. Loan, Yubo Fan, Zhiyu Li, C. Lv","doi":"10.9734/BBJ/2013/4724","DOIUrl":"https://doi.org/10.9734/BBJ/2013/4724","url":null,"abstract":"We present results of an analytic and numerical calculation that studies the relationship between the time of initial foot contact and the ground reaction force of human gait and explores the dynamic principle of center of mass. Assuming the ground reaction force of both feet to be the same in the same phase of a stride cycle, we establish the relationships between the time of initial foot contact and the ground reaction force, acceleration, velocity, displacement and average kinetic energy of center of mass. We employ the dispersion to analyze the effect of the time of the initial foot contact that imposes upon these physical quantities. Our study reveals that when the time of one foot's initial contact falls right in the middle of the other foot's stride cycle, these physical quantities reach extrema. An action function has been identified as the dispersion of the physical quantities and optimized analysis used to prove the least-action principle in gait. In addition to being very significant to the research domains such as clinical diagnosis, biped robot's gait control, the exploration of this principle can simplify our understanding of the basic properties of gait.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"122 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121012970","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}
引用次数: 2
The geometrical origin of the strain-twist coupling in double helices 双螺旋中应变-扭转耦合的几何起源
arXiv: Biological Physics Pub Date : 2010-03-28 DOI: 10.1063/1.3560851
K. Olsen, J. Bohr
{"title":"The geometrical origin of the strain-twist coupling in double helices","authors":"K. Olsen, J. Bohr","doi":"10.1063/1.3560851","DOIUrl":"https://doi.org/10.1063/1.3560851","url":null,"abstract":"The geometrical coupling between strain and twist in double helices is investigated. Overwinding, where strain leads to further winding, is shown to be a universal property for helices, which are stretched along their longitudinal axis when the initial pitch angle is below the zero-twist angle (39.4 deg). Unwinding occurs at larger pitch angles. The zero-twist angle is the unique pitch angle at the point between overwinding and unwinding, and it is independent of the mechanical properties of the double helix. This suggests the existence of zero-twist structures, i.e. structures that display neither overwinding, nor unwinding under strain. Estimates of the overwinding of DNA, chromatin, and RNA are given.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126619220","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}
引用次数: 20
Statistical Mechanics Model for Protein Folding 蛋白质折叠的统计力学模型
arXiv: Biological Physics Pub Date : 2009-12-02 DOI: 10.1063/1.3275681
A. Yakubovich, A. Solov'yov, W. Greiner
{"title":"Statistical Mechanics Model for Protein Folding","authors":"A. Yakubovich, A. Solov'yov, W. Greiner","doi":"10.1063/1.3275681","DOIUrl":"https://doi.org/10.1063/1.3275681","url":null,"abstract":"We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition function of a protein obeying two-stage-like folding kinetics. Using the statistical mechanics model of solvation of hydrophobic hydrocarbons we obtain the partition function of infinitely diluted solution of proteins in water environment. The calculated dependencies of the protein heat capacities upon temperature are compared with the corresponding results of experimental measurements for staphylococcal nuclease and metmyoglobin.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121430443","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}
引用次数: 3
Infrared Surface-Plasmon-Resonance -- a novel biophysical tool for studying living cell 红外表面等离子体共振——一种研究活细胞的新型生物物理工具
arXiv: Biological Physics Pub Date : 2009-10-15 DOI: 10.1063/1.3116143
M. Golosovsky, V. Lirtsman, V. Yashunsky, D. Davidov, B. Aroeti
{"title":"Infrared Surface-Plasmon-Resonance -- a novel biophysical tool for studying living cell","authors":"M. Golosovsky, V. Lirtsman, V. Yashunsky, D. Davidov, B. Aroeti","doi":"10.1063/1.3116143","DOIUrl":"https://doi.org/10.1063/1.3116143","url":null,"abstract":"We discuss the Surface-Plasmon-Resonance (SPR) technique based on Fourier -Transform - InfraRed (FTIR) spectrometry. We explore the potential of the infrared surface plasmon resonance technique for biological studies in aqueous solutions and compare it to the conventional surface plasmon technique operating in the visible range. We demonstrate that the sensitivity of the SPR technique in the infrared range is not lower and in fact is even higher. We show several examples of applying FTIR-SPR for biological studies: (i) monitoring D-glucose concentration in solution, and (ii) measuring D-glucose uptake by erythrocytes in suspension. We emphasize the advantages of infrared SPR for studying living cell cultures and show how this technique can be used for characterization of (i) cholesterol penetration into plasma membrane, and (ii) transferrin-induced clathrin-mediated endocytosis.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125539864","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}
引用次数: 57
Coupling of cytoplasm and adhesion dynamics determines cell polarization and locomotion 细胞质和粘附动力学的耦合决定了细胞的极化和运动
arXiv: Biological Physics Pub Date : 2009-07-29 DOI: 10.1201/9781420094558-c4
W. Alt, M. Bock, Christoph Mohl
{"title":"Coupling of cytoplasm and adhesion dynamics determines cell polarization and locomotion","authors":"W. Alt, M. Bock, Christoph Mohl","doi":"10.1201/9781420094558-c4","DOIUrl":"https://doi.org/10.1201/9781420094558-c4","url":null,"abstract":"Observations of single epidermal cells on flat adhesive substrates have revealed two distinct morphological and functional states, namely a non-migrating symmetric unpolarized state and a migrating asymmetric polarized state. These states are characterized by different spatial distributions and dynamics of important biochemical cell components: F-actin and myosin-II form the contractile part of the cytoskeleton, and integrin receptors in the plasma membrane connect F-actin filaments to the substratum. In this way, focal adhesion complexes are assembled, which determine cytoskeletal force transduction and subsequent cell locomotion. So far, physical models have reduced this phenomenon either to gradients in regulatory control molecules or to different mechanics of the actin filament system in different regions of the cell. \u0000Here we offer an alternative and self-organizational model incorporating polymerization, pushing and sliding of filaments, as well as formation of adhesion sites and their force dependent kinetics. All these phenomena can be combined into a non-linearly coupled system of hyperbolic, parabolic and elliptic differential equations. Aim of this article is to show how relatively simple relations for the small-scale mechanics and kinetics of participating molecules may reproduce the emergent behavior of polarization and migration on the large-scale cell level.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127032075","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}
引用次数: 16
On the Possibility of Superfast Charge Transfer in DNA DNA中超高速电荷转移的可能性
arXiv: Biological Physics Pub Date : 2009-07-07 DOI: 10.17537/2009.4.46
V. Lakhno, V. B. Sultanov
{"title":"On the Possibility of Superfast Charge Transfer in DNA","authors":"V. Lakhno, V. B. Sultanov","doi":"10.17537/2009.4.46","DOIUrl":"https://doi.org/10.17537/2009.4.46","url":null,"abstract":"Numerous experiments on charge transfer in DNA yield a contradictory picture of the transfer: on the one hand they suggest that it is a very slow process and the charge is almost completely localized on one Watson-Crick pair, but on the other hand they demonstrate that the charge can travel a very large distance. To explain this contradiction we propose that superfast charge transitions are possible between base pairs on individual DNA fragments resulting in the establishment of a quasi-equilibrium charge distribution during the time less than that of charge solvation. In other words, we hypothesize these states irrespective of the nature of a mechanism responsible for their establishment, whether it be a hopping mechanism, or a band mechanism, or superexchange, or polaron transport, etc., leaving aside the debates of which one is more advantageous. We discuss qualitative differences between the charge transfer in a dry DNA and that in a solution. In a solution, of great importance is the charge solvation which decreases the transfer rate 10 7 ÷10 8 times as compared with a dry DNA. We consider the conditions under which the superfast charge transfer in a DNA leading to quasi- equilibrium distributions of polarons in a duplex is possible. Comparison of calculated quasi-equilibrium distributions with the experiment testifies to the possibility of superfast tunnel transitions of a hole in a DNA duplex in a solution.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"281 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134214608","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}
引用次数: 5
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