Pub Date : 2016-10-17DOI: 10.1142/S1793048016500053
P. Greene
The transverse thermal fluctuations of the myosin molecule are significant. This paper explores the contribution of lateral myosin bending to the developed crossbridge force and power stroke. The equipartition theorem is used to calculate the mode amplitudes for myosin bending. Crossbridge axial force Fx and power stroke Δx are developed by transverse in-plane fluctuations along the y- and z-axes. Practical applications include the effects of temperature on the flexibility of the myosin molecule stiffness and tension, relevant to man-made fabrication of synthetic muscle using micromachines and nanowires. Scaling laws for the S2 bending amplitude depend on filament length, mode number, and stiffness, as n−2,L2, and (EI)−1. This paper quantifies the effects of thermal motion on the mechanics of miniature molecular motors, including the muscle crossbridge.
{"title":"Effects of Thermal Tension Transients on the Muscle Crossbridge","authors":"P. Greene","doi":"10.1142/S1793048016500053","DOIUrl":"https://doi.org/10.1142/S1793048016500053","url":null,"abstract":"The transverse thermal fluctuations of the myosin molecule are significant. This paper explores the contribution of lateral myosin bending to the developed crossbridge force and power stroke. The equipartition theorem is used to calculate the mode amplitudes for myosin bending. Crossbridge axial force Fx and power stroke Δx are developed by transverse in-plane fluctuations along the y- and z-axes. Practical applications include the effects of temperature on the flexibility of the myosin molecule stiffness and tension, relevant to man-made fabrication of synthetic muscle using micromachines and nanowires. Scaling laws for the S2 bending amplitude depend on filament length, mode number, and stiffness, as n−2,L2, and (EI)−1. This paper quantifies the effects of thermal motion on the mechanics of miniature molecular motors, including the muscle crossbridge.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"30 1","pages":"117-126"},"PeriodicalIF":0.0,"publicationDate":"2016-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048016500053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047290","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 : 2016-10-17DOI: 10.1142/S1793048016010025
M. Chakroun, P. Greene
This is a commentary about the biophysics of muscle, presenting an introduction to the area, modeling muscles' biophysics, and this Issue's projects.
这是一篇关于肌肉生物物理学的评论，介绍了该领域，建模肌肉的生物物理学，以及本期的项目。
{"title":"Commentary About the Biophysics of Muscles","authors":"M. Chakroun, P. Greene","doi":"10.1142/S1793048016010025","DOIUrl":"https://doi.org/10.1142/S1793048016010025","url":null,"abstract":"This is a commentary about the biophysics of muscle, presenting an introduction to the area, modeling muscles' biophysics, and this Issue's projects.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"11 1","pages":"105-108"},"PeriodicalIF":0.0,"publicationDate":"2016-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048016010025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047622","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 : 2016-09-05DOI: 10.1142/S179304801650003X
M. Chakroun, M. H. B. Ghozlen
Agar gel is a linear viscoelastic material with low deformations ( < 0.01%). Here, characterization technique used is the rheometer-type Carri-Med “CSL 100”. This rheometer offers us the opportunity to study the gel in static and dynamic shear. The study is done at low frequencies (0.1–40Hz). Mechanical characterization of the agar gel in terms of dynamic modulus is performed for different concentrations. The dynamic rigidity of the gel decreases with increasing concentration. The 8% agar gel simulates very well the dynamic rigidity of brain tissue at low frequency. The range of low frequencies is rarely studied for this material (brain) in the literature. Most tests done on brain tissue are in a frequency range between 50Hz and 600Hz. Yet, the Maxwell–Kelvin–Voigt model simulates very well the 8% agar gel. The instant elasticity derived from mathematical modeling of agar gel is similar to that measured in the literature for the brain tissue. Hence agar gel can be used in the construction of physical models of the human head used to analyze the dynamic response of the head to shock or to an inertial load.
{"title":"Simulation of Dynamic Rigidity Modulus of Brain Matter by that of Agar Gel","authors":"M. Chakroun, M. H. B. Ghozlen","doi":"10.1142/S179304801650003X","DOIUrl":"https://doi.org/10.1142/S179304801650003X","url":null,"abstract":"Agar gel is a linear viscoelastic material with low deformations ( < 0.01%). Here, characterization technique used is the rheometer-type Carri-Med “CSL 100”. This rheometer offers us the opportunity to study the gel in static and dynamic shear. The study is done at low frequencies (0.1–40Hz). Mechanical characterization of the agar gel in terms of dynamic modulus is performed for different concentrations. The dynamic rigidity of the gel decreases with increasing concentration. The 8% agar gel simulates very well the dynamic rigidity of brain tissue at low frequency. The range of low frequencies is rarely studied for this material (brain) in the literature. Most tests done on brain tissue are in a frequency range between 50Hz and 600Hz. Yet, the Maxwell–Kelvin–Voigt model simulates very well the 8% agar gel. The instant elasticity derived from mathematical modeling of agar gel is similar to that measured in the literature for the brain tissue. Hence agar gel can be used in the construction of physical models of the human head used to analyze the dynamic response of the head to shock or to an inertial load.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"11 1","pages":"149-156"},"PeriodicalIF":0.0,"publicationDate":"2016-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S179304801650003X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047734","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 : 2016-07-25DOI: 10.1142/S1793048016300012
Yekbun Adiguzel
Biophysical economics is initiated with the long history of the relation of economics with ecological basis and biophysical perspectives of the physiocrats. It inherently has social, economic, biological, environmental, natural, physical, and scientific grounds. Biological entities in economy like the resources, consumers, populations, and parts of production systems, etc. could all be dealt by biophysical economics. Considering this wide scope, current work is a “biophysical economics at a glance” rather than a comprehensive review of the full range of topics that may just be adequately covered in a book-length work. However, the sense of its wide range of applications is aimed to be provided to the reader in this work. Here, modern approaches and biophysical growth theory are presented after the long history and an overview of the concepts in biophysical economics. Examples of the recent studies are provided at the end with discussions. This review is also related to the work by Cleveland, “Biophysical Economics: From Physiocracy to Ecological Economics and Industrial Ecology” [C. J. Cleveland, in Advances in Bioeconomics and Sustainability: Essay in Honor of Nicholas Gerogescu-Roegen, eds. J. Gowdy and K. Mayumi (Edward Elgar Publishing, Cheltenham, England, 1999), pp. 125–154.]. Relevant parts include critics and comments on the presented concepts in a parallelized fashion with the Cleveland’s work.
{"title":"Historical and Critical Review on Biophysical Economics","authors":"Yekbun Adiguzel","doi":"10.1142/S1793048016300012","DOIUrl":"https://doi.org/10.1142/S1793048016300012","url":null,"abstract":"Biophysical economics is initiated with the long history of the relation of economics with ecological basis and biophysical perspectives of the physiocrats. It inherently has social, economic, biological, environmental, natural, physical, and scientific grounds. Biological entities in economy like the resources, consumers, populations, and parts of production systems, etc. could all be dealt by biophysical economics. Considering this wide scope, current work is a “biophysical economics at a glance” rather than a comprehensive review of the full range of topics that may just be adequately covered in a book-length work. However, the sense of its wide range of applications is aimed to be provided to the reader in this work. Here, modern approaches and biophysical growth theory are presented after the long history and an overview of the concepts in biophysical economics. Examples of the recent studies are provided at the end with discussions. This review is also related to the work by Cleveland, “Biophysical Economics: From Physiocracy to Ecological Economics and Industrial Ecology” [C. J. Cleveland, in Advances in Bioeconomics and Sustainability: Essay in Honor of Nicholas Gerogescu-Roegen, eds. J. Gowdy and K. Mayumi (Edward Elgar Publishing, Cheltenham, England, 1999), pp. 125–154.]. Relevant parts include critics and comments on the presented concepts in a parallelized fashion with the Cleveland’s work.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"11 1","pages":"63-86"},"PeriodicalIF":0.0,"publicationDate":"2016-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048016300012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047665","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 : 2016-07-25DOI: 10.1142/S1793048016010013
O. Flomenbom, G. Çoban, Yekbun Adiguzel
In this Issue, papers in the area of socio-econo-physics and biophysical economics are presented. We have recently introduced socio-econo-physics and biophysical economics in Biophysical Reviews and Letters (BRL), yet saw 3 to 4 relevant papers just in these most recent three quarters. In this commentary, we therefore would like to elaborate on the topics of socio-econo-physics and biophysical economics and to introduce these concepts to the readers of BRL and the biophysical community of science, with the purpose of supporting many more publications here in BRL, in this evolving area.
{"title":"Commentary on “Biophysical Economics” and Evolving Areas","authors":"O. Flomenbom, G. Çoban, Yekbun Adiguzel","doi":"10.1142/S1793048016010013","DOIUrl":"https://doi.org/10.1142/S1793048016010013","url":null,"abstract":"In this Issue, papers in the area of socio-econo-physics and biophysical economics are presented. We have recently introduced socio-econo-physics and biophysical economics in Biophysical Reviews and Letters (BRL), yet saw 3 to 4 relevant papers just in these most recent three quarters. In this commentary, we therefore would like to elaborate on the topics of socio-econo-physics and biophysical economics and to introduce these concepts to the readers of BRL and the biophysical community of science, with the purpose of supporting many more publications here in BRL, in this evolving area.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"11 1","pages":"55-61"},"PeriodicalIF":0.0,"publicationDate":"2016-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048016010013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047618","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 : 2016-07-25DOI: 10.1142/S1793048016500016
S. Vijaya, E. Rekha
This paper presents three species harvesting model in which there is one predator species and two others are prey species. We derive boundedness and equilibrium point for this system. Also we derive the stability of this system analytically. We find bifurcation for this system. We have derived the binomic equilibrium point by using Pontryagin’s maximum principle (PMP). Presented are various suitable analytical and numerical examples with Maple 18 programming.
{"title":"Prey–Predator Three Species Model Using Predator Harvesting Holling Type II Functional","authors":"S. Vijaya, E. Rekha","doi":"10.1142/S1793048016500016","DOIUrl":"https://doi.org/10.1142/S1793048016500016","url":null,"abstract":"This paper presents three species harvesting model in which there is one predator species and two others are prey species. We derive boundedness and equilibrium point for this system. Also we derive the stability of this system analytically. We find bifurcation for this system. We have derived the binomic equilibrium point by using Pontryagin’s maximum principle (PMP). Presented are various suitable analytical and numerical examples with Maple 18 programming.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"11 1","pages":"87-104"},"PeriodicalIF":0.0,"publicationDate":"2016-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048016500016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047672","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 : 2016-07-18DOI: 10.1142/S1793048016500028
S. Hakobyan, M. Shahinyan, Y. Babayan
In the present work, the thermostabilities of mitoxantrone (MTX) complexes with DNA from sarcoma 45 and healthy rat liver were studied. DNAs from both sources were irradiated by resonant (64.5 GHz and 50.3 GHz) and nonresonant (48.3 GHz) frequencies of water. The obtained data showed that DNA solution irradiation by resonant frequencies of water induces a dehydration of nucleotides and Na+ ions in the solution. It is shown that at relatively low concentrations of MTX, when one MTX molecule binds to almost 100 pairs of bases of DNA, the thermostabilities of complexes decrease. Moreover, this change is more pronounced (∼0.8∘C) at the complex formation with DNA released from sarcoma 45 tumor.
{"title":"Stabilities of Irradiated DNA Complexes from Sarcoma 45 Tumors with Mitoxantrone at Small Fillings","authors":"S. Hakobyan, M. Shahinyan, Y. Babayan","doi":"10.1142/S1793048016500028","DOIUrl":"https://doi.org/10.1142/S1793048016500028","url":null,"abstract":"In the present work, the thermostabilities of mitoxantrone (MTX) complexes with DNA from sarcoma 45 and healthy rat liver were studied. DNAs from both sources were irradiated by resonant (64.5 GHz and 50.3 GHz) and nonresonant (48.3 GHz) frequencies of water. The obtained data showed that DNA solution irradiation by resonant frequencies of water induces a dehydration of nucleotides and Na+ ions in the solution. It is shown that at relatively low concentrations of MTX, when one MTX molecule binds to almost 100 pairs of bases of DNA, the thermostabilities of complexes decrease. Moreover, this change is more pronounced (∼0.8∘C) at the complex formation with DNA released from sarcoma 45 tumor.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"11 1","pages":"139-147"},"PeriodicalIF":0.0,"publicationDate":"2016-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048016500028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047681","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 : 2016-05-10DOI: 10.1142/S179304801602001X
O. Flomenbom, L. Baraban, V. Misko
This is a commentary on the Special Issue continuation involving “Single File Dynamics and Generalizations in Interdisciplinary Sciences”.
这是对《跨学科科学中的单文件动力学和概括》特刊续刊的评论。
{"title":"Commentary on the Special Issue Continuation on “Single File Dynamics and Generalizations in Interdisciplinary Sciences”","authors":"O. Flomenbom, L. Baraban, V. Misko","doi":"10.1142/S179304801602001X","DOIUrl":"https://doi.org/10.1142/S179304801602001X","url":null,"abstract":"This is a commentary on the Special Issue continuation involving “Single File Dynamics and Generalizations in Interdisciplinary Sciences”.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"11 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2016-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S179304801602001X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047634","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 : 2016-05-10DOI: 10.1142/S1793048015500083
O. Flomenbom
We derive the general scaling law of the mean first passage time (MFPT) in single file dynamics; the process where many real particles move in a channel of length L with absorbing boundaries, where the particles and the channel have about the same cross section. We derive the relation MFPT ∼ f(n)MFPTfree, here we compute the MFPT when the channel is free (all particles are absorbed, where the average is over many trajectories), n is the number of particles in the channel at initiation, f(n) is the many-particle effect and the quantity MFPTfree is the MFPT of the free particle. When at initiation the density is fixed in basic files f(n) ∼n and therefore e.g. MFPT ∼ L2.5 (basic stochastic dynamics). We also compute the MFPT in diverse files; for example, in a file with heterogeneous particles, in deterministic files, in slow files and in files with long-range interactions. When the particle density is not fixed yet scales with 1/length from the origin, f(n) < n; yet, interactions might increase (attractive) or decrease (repulsive) the many-particle effect relative to n. In slow files, MFPT ∼ L3 (in the number of jumps). We explain these valuable results with various methods and approaches, e.g., we derive a general mapping from the mean square displacement scaling law to the MFPT scaling law. We also connect the results with real life activities. Special Issue Comments: Mean first passage scaling law in single file dynamics and various particular results in files are derived in this project. The project is related to the Special Issue projects about heterogeneous files and slow files,27 expansions in files,26 files with force32 and the first passage time in files.23
{"title":"Mean First Passage Time in Single File Dynamics","authors":"O. Flomenbom","doi":"10.1142/S1793048015500083","DOIUrl":"https://doi.org/10.1142/S1793048015500083","url":null,"abstract":"We derive the general scaling law of the mean first passage time (MFPT) in single file dynamics; the process where many real particles move in a channel of length L with absorbing boundaries, where the particles and the channel have about the same cross section. We derive the relation MFPT ∼ f(n)MFPTfree, here we compute the MFPT when the channel is free (all particles are absorbed, where the average is over many trajectories), n is the number of particles in the channel at initiation, f(n) is the many-particle effect and the quantity MFPTfree is the MFPT of the free particle. When at initiation the density is fixed in basic files f(n) ∼n and therefore e.g. MFPT ∼ L2.5 (basic stochastic dynamics). We also compute the MFPT in diverse files; for example, in a file with heterogeneous particles, in deterministic files, in slow files and in files with long-range interactions. When the particle density is not fixed yet scales with 1/length from the origin, f(n) < n; yet, interactions might increase (attractive) or decrease (repulsive) the many-particle effect relative to n. In slow files, MFPT ∼ L3 (in the number of jumps). We explain these valuable results with various methods and approaches, e.g., we derive a general mapping from the mean square displacement scaling law to the MFPT scaling law. We also connect the results with real life activities. Special Issue Comments: Mean first passage scaling law in single file dynamics and various particular results in files are derived in this project. The project is related to the Special Issue projects about heterogeneous files and slow files,27 expansions in files,26 files with force32 and the first passage time in files.23","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"56 1","pages":"39-54"},"PeriodicalIF":0.0,"publicationDate":"2016-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048015500083","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047553","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 : 2015-12-01DOI: 10.1142/S1793048015500101
M. Shahinyan, A. Antonyan, M. Mikaelyan, P. O. Vardevanyan
In this work, the effect of electromagnetic waves of millimeter diapason (EMW MM) on both melting parameters of serum albumin from human blood and its solution density has been studied. It was shown that the irradiation of albumin solution results in protein denaturation at higher temperatures than in the case of nonirradiated samples, which indicates the increase of albumin packing degree. It was also shown that the enhancement of albumin solution density takes place which indicates the protein packing degree change as well. The obtained data show that the effect of EMW MM does not depend on frequency of these waves, because alterations are revealed at all studied frequencies — 41.8, 48 and 51.8GHz.
{"title":"Study of influence of millimeter range electromagnetic waves on water-saline solutions of albumin","authors":"M. Shahinyan, A. Antonyan, M. Mikaelyan, P. O. Vardevanyan","doi":"10.1142/S1793048015500101","DOIUrl":"https://doi.org/10.1142/S1793048015500101","url":null,"abstract":"In this work, the effect of electromagnetic waves of millimeter diapason (EMW MM) on both melting parameters of serum albumin from human blood and its solution density has been studied. It was shown that the irradiation of albumin solution results in protein denaturation at higher temperatures than in the case of nonirradiated samples, which indicates the increase of albumin packing degree. It was also shown that the enhancement of albumin solution density takes place which indicates the protein packing degree change as well. The obtained data show that the effect of EMW MM does not depend on frequency of these waves, because alterations are revealed at all studied frequencies — 41.8, 48 and 51.8GHz.","PeriodicalId":88835,"journal":{"name":"Biophysical reviews and letters","volume":"10 1","pages":"201-207"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/S1793048015500101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64047564","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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