Y. Manabe, T. Wada, Y. Tsunoyama, Hiroo Nakajima, I. Nakamura, M. Bandō
We present a novel model to estimate biological effects caused by artificial radiation exposure, Whack-a-mole (WAM) model. It is important to take account of the recovery effects during the time course of the cellular reactions. The inclusion of the dose-rate dependence is essential in the risk estimation of low dose radiation, while nearly all the existing theoretical models relies on the total dose dependence only. By analyzing the experimental data of the relation between the radiation dose and the induced mutation frequency of 5 organisms, mouse, drosophila, chrysanthemum, maize and tradescantia, we found that all the data can be reproduced by WAM model. Most remarkably, a scaling function, which is derived from WAM model, consistently accounts for the observed mutation frequencies of 5 organisms. This is the first rationale to account for the dose rate dependence as well as to give a unified understanding of a general feature of organisms.
{"title":"Whack-A-Mole Model -Towards unified description of biological effect caused by radiation-exposure","authors":"Y. Manabe, T. Wada, Y. Tsunoyama, Hiroo Nakajima, I. Nakamura, M. Bandō","doi":"10.7566/JPSJ.84.044002","DOIUrl":"https://doi.org/10.7566/JPSJ.84.044002","url":null,"abstract":"We present a novel model to estimate biological effects caused by artificial radiation exposure, Whack-a-mole (WAM) model. It is important to take account of the recovery effects during the time course of the cellular reactions. The inclusion of the dose-rate dependence is essential in the risk estimation of low dose radiation, while nearly all the existing theoretical models relies on the total dose dependence only. By analyzing the experimental data of the relation between the radiation dose and the induced mutation frequency of 5 organisms, mouse, drosophila, chrysanthemum, maize and tradescantia, we found that all the data can be reproduced by WAM model. Most remarkably, a scaling function, which is derived from WAM model, consistently accounts for the observed mutation frequencies of 5 organisms. This is the first rationale to account for the dose rate dependence as well as to give a unified understanding of a general feature of organisms.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"115 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122438300","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}
Pub Date : 2014-09-09DOI: 10.4172/2161-0398.1000164
M. Shneider, M. Pekker
This paper presents a short selective review of the non-thermal weak microwave field impact on a nerve fiber. The published results of recent experiments are reviewed and analyzed. The theory of the authors is presented, according to which there are strongly pronounced resonances in the range of about 30-300 GHz associated with the excitation of ultrasonic vibrations in the membrane as a result of interactions with the microwave radiation. These forced vibrations create acoustic pressure, which may lead to the redistribution of the protein transmembrane channels, thus changing the threshold of the action potential excitation in the axons of the neural network. The problem of surface charge on the bilayer lipid membrane of the nerve fiber is discussed. Various experiments for observing the effects considered are also discussed.
{"title":"Non-thermal influence of a weak microwave on nerve fiber activity","authors":"M. Shneider, M. Pekker","doi":"10.4172/2161-0398.1000164","DOIUrl":"https://doi.org/10.4172/2161-0398.1000164","url":null,"abstract":"This paper presents a short selective review of the non-thermal weak microwave field impact on a nerve fiber. The published results of recent experiments are reviewed and analyzed. The theory of the authors is presented, according to which there are strongly pronounced resonances in the range of about 30-300 GHz associated with the excitation of ultrasonic vibrations in the membrane as a result of interactions with the microwave radiation. These forced vibrations create acoustic pressure, which may lead to the redistribution of the protein transmembrane channels, thus changing the threshold of the action potential excitation in the axons of the neural network. The problem of surface charge on the bilayer lipid membrane of the nerve fiber is discussed. Various experiments for observing the effects considered are also discussed.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124893574","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}
Pub Date : 2014-07-16DOI: 10.1007/978-3-319-10629-8_69
S. Klein, C. Appert-Rolland, L. Santen
{"title":"Stochastic Modeling of Cargo Transport by Teams of Molecular Motors","authors":"S. Klein, C. Appert-Rolland, L. Santen","doi":"10.1007/978-3-319-10629-8_69","DOIUrl":"https://doi.org/10.1007/978-3-319-10629-8_69","url":null,"abstract":"","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129012112","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 develop a kinetic reaction model for cells having irradiated DNA molecules due to ionizing radiation exposure. Our theory simultaneously accounts for the time-dependent reactions of the DNA damage, the DNA mutation, the DNA repair, and the proliferation and apoptosis of cells in a tissue with a minimal set of model parameters. In contrast to existing theories for radiation exposition, we do not assume the relationships between the total dose and the induced mutation frequency. Our theory provides a universal scaling function that reasonably explains the mega-mouse experiments in Ref.[W. L. Russell and E. M. Kelly, Proc. Natl. Acad. Sci. USA. {bf 79} (1982) 542.] with different dose rates. Furthermore, we have estimated the effective dose rate, which is biologically equivalent to the ionizing effects other than those caused by artificial irradiation. This value is $ 1.11 times 10^{-3} ~rm{[Gy/hr]}$, which is significantly larger than the effect caused by natural background radiation.
我们开发了一个动力学反应模型的细胞辐照DNA分子由于电离辐射暴露。我们的理论以最小的模型参数集同时解释了组织中DNA损伤、DNA突变、DNA修复以及细胞增殖和凋亡的时间依赖性反应。与现有的辐射暴露理论相反，我们没有假设总剂量与诱导突变频率之间的关系。我们的理论提供了一个普遍的缩放函数，合理地解释了参考文献[W]中的巨型小鼠实验。L. Russell和E. M. Kelly, Proc。学会科学。美国。{bf 79}(1982) 542。用不同的剂量率。此外，我们还估计了有效剂量率，它在生物学上与人工照射引起的电离效应相当。这个值是$ 1.11 乘以10^{-3}~rm{[Gy/hr]}$，明显大于自然本底辐射造成的影响。
{"title":"Reaction Rate Theory of Radiation Exposure and Scaling Hypothesis in Mutation Frequency","authors":"Y. Manabe, I. Nakamura, M. Bandō","doi":"10.7566/JPSJ.83.114003","DOIUrl":"https://doi.org/10.7566/JPSJ.83.114003","url":null,"abstract":"We develop a kinetic reaction model for cells having irradiated DNA molecules due to ionizing radiation exposure. Our theory simultaneously accounts for the time-dependent reactions of the DNA damage, the DNA mutation, the DNA repair, and the proliferation and apoptosis of cells in a tissue with a minimal set of model parameters. In contrast to existing theories for radiation exposition, we do not assume the relationships between the total dose and the induced mutation frequency. Our theory provides a universal scaling function that reasonably explains the mega-mouse experiments in Ref.[W. L. Russell and E. M. Kelly, Proc. Natl. Acad. Sci. USA. {bf 79} (1982) 542.] with different dose rates. Furthermore, we have estimated the effective dose rate, which is biologically equivalent to the ionizing effects other than those caused by artificial irradiation. This value is $ 1.11 times 10^{-3} ~rm{[Gy/hr]}$, which is significantly larger than the effect caused by natural background radiation.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123905470","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 simple model of the two dimensional collective motion of a group of mobile agents have been studied. Like birds, these agents travel in open free space where each of them interacts with the first $n$ neighbors determined by the topological distance with a free boundary condition. Using the same prescription for interactions used in the Vicsek model with scalar noise it has been observed that the flock, in absence of the noise, arrives at a number of interesting stationary states. In the `single sink state' the entire flock maintains perfect cohesion and coherence. In the `cyclic state' every agent executes a uniform circular motion, and the entire flock executes a pulsating dynamics i.e., expands and contracts periodically between a minimum and a maximum size of the flock. When refreshing rate of the interaction zone is the fastest, the entire flock gets fragmented into smaller clusters of different sizes. On introduction of scalar noise a crossover is observed when the agents cross over from a ballistic motion to a diffusive motion. Expectedly the crossover time is dependent on the strength of the noise $eta$ and diverges as $eta to 0$. In simpler version the translational degrees of freedom of the agents are suppressed but their angular motion are retained. Here agents are the spins, placed at the sites of a square lattice with periodic boundary condition. Every spin interacts with its $n$ = 2, 3 or 4 nearest neighbors. In the stationary state the entire spin pattern moves as a whole when interactions are anisotropic with $n$ = 2 and 3; but it is completely frozen when the interaction is isotropic with $n=4$. These spin configurations have vortex-antivortex pairs whose density increases as the noise $eta$ increases and follows an excellent finite-size scaling analysis.
{"title":"Cyclic and coherent states in flocks with topological distance","authors":"B. Bhattacherjee, K. Bhattacharya, S. S. Manna","doi":"10.3389/fphy.2013.00035","DOIUrl":"https://doi.org/10.3389/fphy.2013.00035","url":null,"abstract":"A simple model of the two dimensional collective motion of a group of mobile agents have been studied. Like birds, these agents travel in open free space where each of them interacts with the first $n$ neighbors determined by the topological distance with a free boundary condition. Using the same prescription for interactions used in the Vicsek model with scalar noise it has been observed that the flock, in absence of the noise, arrives at a number of interesting stationary states. In the `single sink state' the entire flock maintains perfect cohesion and coherence. In the `cyclic state' every agent executes a uniform circular motion, and the entire flock executes a pulsating dynamics i.e., expands and contracts periodically between a minimum and a maximum size of the flock. When refreshing rate of the interaction zone is the fastest, the entire flock gets fragmented into smaller clusters of different sizes. On introduction of scalar noise a crossover is observed when the agents cross over from a ballistic motion to a diffusive motion. Expectedly the crossover time is dependent on the strength of the noise $eta$ and diverges as $eta to 0$. In simpler version the translational degrees of freedom of the agents are suppressed but their angular motion are retained. Here agents are the spins, placed at the sites of a square lattice with periodic boundary condition. Every spin interacts with its $n$ = 2, 3 or 4 nearest neighbors. In the stationary state the entire spin pattern moves as a whole when interactions are anisotropic with $n$ = 2 and 3; but it is completely frozen when the interaction is isotropic with $n=4$. These spin configurations have vortex-antivortex pairs whose density increases as the noise $eta$ increases and follows an excellent finite-size scaling analysis.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"47 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131992681","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}
Application of computation in many fields are growing fast in last two decades. Increasing on computation performance helps researchers to understand natural phenomena in many fields of science and technology including in life sciences. Computational fluid dynamic is one of numerical methods which is very popular used to describe those phenomena. In this paper we propose moving particle semi-implicit (MPS) and molecular dynamics (MD) to describe different phenomena in blood vessel. The effect of increasing the blood pressure on vessel wall will be calculate using MD methods, while the two fluid blending dynamics will be discussed using MPS. Result from the first phenomenon shows that around 80% of constriction on blood vessel make blood vessel increase and will start to leak on vessel wall, while from the second phenomenon the result shows the visualization of two fluids mixture (drugs and blood) influenced by ratio of drugs debit to blood debit.
{"title":"Application of computational physics: Blood vessel constrictions and medical infuses","authors":"Suprijadi, M. Rendi, P. Subekti, S. Viridi","doi":"10.1063/1.4866523","DOIUrl":"https://doi.org/10.1063/1.4866523","url":null,"abstract":"Application of computation in many fields are growing fast in last two decades. Increasing on computation performance helps researchers to understand natural phenomena in many fields of science and technology including in life sciences. Computational fluid dynamic is one of numerical methods which is very popular used to describe those phenomena. In this paper we propose moving particle semi-implicit (MPS) and molecular dynamics (MD) to describe different phenomena in blood vessel. The effect of increasing the blood pressure on vessel wall will be calculate using MD methods, while the two fluid blending dynamics will be discussed using MPS. Result from the first phenomenon shows that around 80% of constriction on blood vessel make blood vessel increase and will start to leak on vessel wall, while from the second phenomenon the result shows the visualization of two fluids mixture (drugs and blood) influenced by ratio of drugs debit to blood debit.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122722916","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}
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements. Based on this method, a numerical model had been constructed to mimic the behaviour of malaria-infected red blood cells within capillary vessel. The model was governed by three forces namely Coulomb force, normal force, and Stokes force. By utilizing two dimensional four-cells scheme, theoretical observation was carried out to test its capability. Although the parameters were chosen deliberately, all of the quantities were given arbitrary value. Despite this fact, the results were quite satisfactory. Combined with the previous results, it can be said that the proposed model were sufficient enough to mimic the malaria-infected red blood cells motion within obstructed capillary vessel.
{"title":"Molecular dynamics simulation of soft grains: Malaria-infected red blood cells motion within obstructed 2-D capillary vessel","authors":"Luman Haris, S. Khotimah, F. Haryanto, S. Viridi","doi":"10.1063/1.4866530","DOIUrl":"https://doi.org/10.1063/1.4866530","url":null,"abstract":"Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements. Based on this method, a numerical model had been constructed to mimic the behaviour of malaria-infected red blood cells within capillary vessel. The model was governed by three forces namely Coulomb force, normal force, and Stokes force. By utilizing two dimensional four-cells scheme, theoretical observation was carried out to test its capability. Although the parameters were chosen deliberately, all of the quantities were given arbitrary value. Despite this fact, the results were quite satisfactory. Combined with the previous results, it can be said that the proposed model were sufficient enough to mimic the malaria-infected red blood cells motion within obstructed capillary vessel.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115255868","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}
Pub Date : 2013-11-27DOI: 10.1142/9789814518550_0028
M. Barbi, F. Paillusson
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and DNA, electrostatic interaction should play a crucial role during this search. In this paper, we explicitly derive the mean field theory allowing for a description of the protein-DNA electrostatics in solution. This approach leads to a unified model of the search process, where 1D and 3D diffusion appear as a natural consequence of the diffusion on an extended interaction energy profile.
{"title":"On the ion-mediated interaction between protein and DNA","authors":"M. Barbi, F. Paillusson","doi":"10.1142/9789814518550_0028","DOIUrl":"https://doi.org/10.1142/9789814518550_0028","url":null,"abstract":"The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and DNA, electrostatic interaction should play a crucial role during this search. In this paper, we explicitly derive the mean field theory allowing for a description of the protein-DNA electrostatics in solution. This approach leads to a unified model of the search process, where 1D and 3D diffusion appear as a natural consequence of the diffusion on an extended interaction energy profile.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123982403","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}
Cells are modeled with spherical grains connected each other. Each cell can shrink and swell by transporting its fluid content to other connected neighbor while still maintaining its density at constant value. As a spherical part of a cell swells it gains more pressure from its surrounding, while shrink state gains less pressure. Pressure difference between these two or more parts of cell will create motion force for the cell. For simplicity, cell is considered to have same density as its environment fluid and connections between parts of cell are virtually accommodated by a spring force. This model is also limited to 2-d case. Influence of parameters to cell motion will be presented. One grain cell shows no motion, while two and more grains cell can perform a motion.
{"title":"Self-motion mechanism of chained spherical grains cells","authors":"S. Viridi, N. Nuraini","doi":"10.1063/1.4866547","DOIUrl":"https://doi.org/10.1063/1.4866547","url":null,"abstract":"Cells are modeled with spherical grains connected each other. Each cell can shrink and swell by transporting its fluid content to other connected neighbor while still maintaining its density at constant value. As a spherical part of a cell swells it gains more pressure from its surrounding, while shrink state gains less pressure. Pressure difference between these two or more parts of cell will create motion force for the cell. For simplicity, cell is considered to have same density as its environment fluid and connections between parts of cell are virtually accommodated by a spring force. This model is also limited to 2-d case. Influence of parameters to cell motion will be presented. One grain cell shows no motion, while two and more grains cell can perform a motion.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114658532","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}
The theoretical and experimental study of energy transfer in photosynthesis has revealed an interesting transport regime, which lies at the borderline between classical transport dynamics and quantum-mechanical interference effects. Dissipation is caused by the coupling of electronic degrees of freedom to vibrational modes and leads to a directional energy transfer from the antenna complex to the target reaction-center. The dissipative driving is robust and does not rely on fine-tuning of specific vibrational modes. For the parameter regime encountered in the biological systems new theoretical tools are required to directly compare theoretical results with experimental spectroscopy data. The calculations require to utilize massively parallel graphics processor units (GPUs) for efficient and exact computations.
{"title":"Modelling excitonic-energy transfer in light-harvesting complexes","authors":"Tobias Kramer, C. Kreisbeck","doi":"10.1063/1.4861701","DOIUrl":"https://doi.org/10.1063/1.4861701","url":null,"abstract":"The theoretical and experimental study of energy transfer in photosynthesis has revealed an interesting transport regime, which lies at the borderline between classical transport dynamics and quantum-mechanical interference effects. Dissipation is caused by the coupling of electronic degrees of freedom to vibrational modes and leads to a directional energy transfer from the antenna complex to the target reaction-center. The dissipative driving is robust and does not rely on fine-tuning of specific vibrational modes. For the parameter regime encountered in the biological systems new theoretical tools are required to directly compare theoretical results with experimental spectroscopy data. The calculations require to utilize massively parallel graphics processor units (GPUs) for efficient and exact computations.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"2019 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116643993","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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