arXiv: Biological Physics最新文献_第2页

Effects of restrained degradation on gene expression and regulation 抑制降解对基因表达和调控的影响

arXiv: Biological Physics Pub Date : 2019-08-28 DOI: 10.1142/s0217984920501328

Yan-Ling Feng, Jingjun Sun, Yi-Fan Liu, Jianke Ren, Jian-Min Dong

{"title":"Effects of restrained degradation on gene expression and regulation","authors":"Yan-Ling Feng, Jingjun Sun, Yi-Fan Liu, Jianke Ren, Jian-Min Dong","doi":"10.1142/s0217984920501328","DOIUrl":"https://doi.org/10.1142/s0217984920501328","url":null,"abstract":"The effects of carrying capacity of environment $K$ for degradation (the $K$ effect for short) on the constitutive gene expression and a simple genetic regulation system, are investigated by employing a stochastic Langevin equation combined with the corresponding Fokker-Planck equation for the two stochastic systems subjected to internal and external noises. This $K$ effect characterizes the limited degradation ability of the environment for RNA or proteins, such as insufficient catabolic enzymes. The $K$ effect could significantly change the distribution of mRNA copy-number in constitutive gene expression, and interestingly, it leads to the Fano factor slightly larger than 1 if only the internal noise exists. Therefore, that the recent experimental measurements suggests the Fano factor deviates from 1 slightly (Science {bf 346} (2014) 1533), probably originates from the $K$ effect. The $K$ effects on the steady and transient properties of genetic regulation system, have been investigated in detail. It could enhance the mean first passage time significantly especially when the noises are weak and reduce the signal-to-noise ratio in stochastic resonance substantially.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126723167","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: 0

On mechanisms of electromechanophysiological interactions between the components of signals in axons 轴突各信号组分间电生理相互作用机制的研究

arXiv: Biological Physics Pub Date : 2019-07-09 DOI: 10.3176/PROC.2020.2.03

J. Engelbrecht, K. Tamm, T. Peets

引用次数: 15

Membrane-Mediated Interactions Membrane-Mediated交互

arXiv: Biological Physics Pub Date : 2019-03-13 DOI: 10.1007/978-3-030-00630-3_13

Anne-Florence Bitbol, D. Constantin, J. Fournier

引用次数: 5

Ti2NiCu based composite nanotweezers with a shape memory effect and its use for DNA bunches 3D manipulation 具有形状记忆效应的Ti2NiCu基复合纳米镊子及其在DNA束三维操作中的应用

arXiv: Biological Physics Pub Date : 2019-01-21 DOI: 10.1063/1.5087672

A. Orlov, A. Frolov, A. Smolovich, P. Lega, P. V. Chung, A. Irzhak, N.A.Barinov, D. Klinov, V. Vlasenko, V. Koledov

引用次数: 5

Mechanical Factors Affecting the Mobility of Membrane Proteins 影响膜蛋白迁移的机械因素

arXiv: Biological Physics Pub Date : 2018-10-23 DOI: 10.1007/978-3-030-00630-3_8

V. D'emery, D. Lacoste

引用次数: 1

The outer hair cell of the organ of Corti possesses a voltage-dependent motile frequency response: evidence for the frequency-dependent compliance of prestin. Corti器官的外毛细胞具有电压依赖性的运动频率响应:prestin频率依赖性依从性的证据。

arXiv: Biological Physics Pub Date : 2018-09-29 DOI: 10.1085/jgp.201812280.

J. Santos-Sacchi, K. Iwasa, Winston J. T. Tan

{"title":"The outer hair cell of the organ of Corti possesses a voltage-dependent motile frequency response: evidence for the frequency-dependent compliance of prestin.","authors":"J. Santos-Sacchi, K. Iwasa, Winston J. T. Tan","doi":"10.1085/jgp.201812280.","DOIUrl":"https://doi.org/10.1085/jgp.201812280.","url":null,"abstract":"The outer hair cell (OHC) of the organ of Corti underlies a mechanically based process that enhances hearing, termed cochlear amplification. The cell possesses a unique motor protein, prestin, which senses voltage and consequently changes conformation to cause large cell length changes, termed electromotility (eM). In OHCs studied in vitro, the prestin voltage sensor generates a capacitance that is both voltage and frequency dependent, peaking in magnitude at a characteristic membrane voltage (Vh), which can be greater than the linear capacitance of the cell. Consequently, the OHC membrane time constant is multifarious depending upon resting potential and frequency of AC evaluation. After precisely correcting for this influence on the whole-cell voltage clamp time constant, we find that OHC eM is low pass in nature, substantially attenuating in magnitude within the frequency bandwidth of human speech. The frequency response is slowest at Vh, with a cut-off near 1.5 kHz, but increases up to six-fold in a U shaped manner as holding voltage deviates from Vh. NLC measures follow this pattern. Viscous drag alone cannot account for such eM behavior; nor can it arise from viscous drag in combination with a sigmoidal voltage-dependent OHC stiffness. However, viscous drag combined with kinetics of prestin, likely corresponding to its bell-shaped conformational gating compliance (Iwasa, 2000), is in line with our observations. How OHC eM influences cochlear amplification at higher frequencies needs reconsideration.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"434 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133207704","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: 0

COMPUTATIONAL STUDY OF GEOMETRIC EFFECTS OF BOTTOM WALL MICROGROOVES ON CELL DOCKING INSIDE MICROFLUIDIC DEVICES 微流控装置内底壁微槽对细胞对接几何效应的计算研究

arXiv: Biological Physics Pub Date : 2018-08-30 DOI: 10.1142/S0219519421500172

S. Ahandoust, M. Saadatmand

{"title":"COMPUTATIONAL STUDY OF GEOMETRIC EFFECTS OF BOTTOM WALL MICROGROOVES ON CELL DOCKING INSIDE MICROFLUIDIC DEVICES","authors":"S. Ahandoust, M. Saadatmand","doi":"10.1142/S0219519421500172","DOIUrl":"https://doi.org/10.1142/S0219519421500172","url":null,"abstract":"Single cell and regularly cells docking inside the microstructure of microfluidic systems are advantageous in different analyses of single cells exposed to equal drug concentration and mechanical stimulus. In this study, we investigated bottom wall microgrooves with semicircular and rectangular geometries with different sizes which are suitable for single cell docking along the length of the microgroove in x direction and numerous cells docking regularly in one line inside the microgroove in a 3D microchannel. We used computational fluid dynamics to analyze the fluid recirculation area inside different microgrooves. The height of recirculation area in the bottom of microgroove can affect the cell attachment, and also materials delivery to attached cells, so the height of recirculation area has to be optimum amount. In addition, we analyzed the fluid drag force on cell movement toward the microgroove. This parameter was proportional to the fluid velocities in x and y directions changing in different microgrooves geometries. In different microgrooves geometries the fluid velocity in y direction does not change. If the fluid velocity in x direction decreases inside the microgroove, the cell movement time inside the microgroove will increase, and also the drag force in y direction can push the cells toward the bottom due to the lower drag force in x direction. The percentages of negative shear stress and average shear stress on the adhered cell surface were also calculated. The lower average shear stress, and negative shear stress around 50% on the cell surface are against cell detachment from the substrate. The results indicated that at the constant fluid inlet velocity and microchannel height, microgroove geometry and ratio of cell size to the microgroove size play pivotal roles in the cell initial adhesion to the substrate as well as the cell detachment.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121921157","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: 0

Diffusion theory for the infection pathway of virus in a living cell 病毒在活细胞内感染途径的扩散理论

arXiv: Biological Physics Pub Date : 2018-03-08 DOI: 10.2174/2210289201809010001

Y. Itto

引用次数: 2

Rapid calculation of maximum particle lifetime for diffusion in complex geometries 在复杂几何中扩散的最大粒子寿命的快速计算

arXiv: Biological Physics Pub Date : 2018-01-09 DOI: 10.1063/1.5019180

E. Carr, M. Simpson

引用次数: 3

Protein Pattern Formation 蛋白质模式形成

arXiv: Biological Physics Pub Date : 2018-01-04 DOI: 10.1007/978-3-030-00630-3_10

Erwin Frey, J. Halatek, Simon Kretschmer, P. Schwille

引用次数: 26