Pub Date : 2013-07-02DOI: 10.4236/am.2013.410A2002
E. Catsigeras
We study a mathematical model of biological neuronal networks composed by any finite number $N geq 2$ of non necessarily identical cells. The model is a deterministic dynamical system governed by finite-dimensional impulsive differential equations. The statical structure of the network is described by a directed and weighted graph whose nodes are certain subsets of neurons, and whose edges are the groups of synaptical connections among those subsets. First, we prove that among all the possible networks such that their respective graphs are mutually isomorphic, there exists a dynamical optimum. This optimal network exhibits the richest dynamics: namely, it is capable to show the most diverse set of responses (i.e. orbits in the future) under external stimulus or signals. Second, we prove that all the neurons of a dynamically optimal neuronal network necessarily satisfy Dale's Principle, i.e. each neuron must be either excitatory or inhibitory, but not mixed. So, Dale's Principle is a mathematical necessary consequence of a theoretic optimization process of the dynamics of the network. Finally, we prove that Dale's Principle is not sufficient for the dynamical optimization of the network.
{"title":"Dale's Principle is necessary for an optimal neuronal network's dynamics","authors":"E. Catsigeras","doi":"10.4236/am.2013.410A2002","DOIUrl":"https://doi.org/10.4236/am.2013.410A2002","url":null,"abstract":"We study a mathematical model of biological neuronal networks composed by any finite number $N geq 2$ of non necessarily identical cells. The model is a deterministic dynamical system governed by finite-dimensional impulsive differential equations. The statical structure of the network is described by a directed and weighted graph whose nodes are certain subsets of neurons, and whose edges are the groups of synaptical connections among those subsets. First, we prove that among all the possible networks such that their respective graphs are mutually isomorphic, there exists a dynamical optimum. This optimal network exhibits the richest dynamics: namely, it is capable to show the most diverse set of responses (i.e. orbits in the future) under external stimulus or signals. Second, we prove that all the neurons of a dynamically optimal neuronal network necessarily satisfy Dale's Principle, i.e. each neuron must be either excitatory or inhibitory, but not mixed. So, Dale's Principle is a mathematical necessary consequence of a theoretic optimization process of the dynamics of the network. Finally, we prove that Dale's Principle is not sufficient for the dynamical optimization of the network.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"286 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131680876","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}
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80% constriction, which shows existence of maximum pressure that can be overcome by vessel wall.
{"title":"Modeling of blood vessel constriction in 2-D case using molecular dynamics method","authors":"M. Rendi, Suprijadi, S. Viridi","doi":"10.1063/1.4868829","DOIUrl":"https://doi.org/10.1063/1.4868829","url":null,"abstract":"Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80% constriction, which shows existence of maximum pressure that can be overcome by vessel wall.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127461917","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 propose a non-thermal mechanism of weak microwave field impact on a nerve fiber. It is shown that in the range of about 30 - 300 GHz there are strongly pronounced resonances associated with the excitation of ultrasonic vibrations in the membrane as a result of interaction with electromagnetic radiation. These vibrations create acoustic pressure which may lead to the redistribution of the protein transmembrane channels, and, thus, changing the threshold of the action potential excitation in the axons of the neural network. The influence of the electromagnetic microwave radiation on various specific areas of myelin nerve fibers was analyzed: the nodes of Ranvier, and the so-called initial segment - the area between the neuron hillock and the first part of the axon covered with the myelin layer. It is shown that the initial segment is the most sensitive area of the myelined nerve fibers from which the action potential normally starts.
{"title":"Non-Thermal Mechanism of Weak Microwave Fields Influence on Nerve Fiber","authors":"M. Shneider, M. Pekker","doi":"10.1063/1.4821027","DOIUrl":"https://doi.org/10.1063/1.4821027","url":null,"abstract":"We propose a non-thermal mechanism of weak microwave field impact on a nerve fiber. It is shown that in the range of about 30 - 300 GHz there are strongly pronounced resonances associated with the excitation of ultrasonic vibrations in the membrane as a result of interaction with electromagnetic radiation. These vibrations create acoustic pressure which may lead to the redistribution of the protein transmembrane channels, and, thus, changing the threshold of the action potential excitation in the axons of the neural network. The influence of the electromagnetic microwave radiation on various specific areas of myelin nerve fibers was analyzed: the nodes of Ranvier, and the so-called initial segment - the area between the neuron hillock and the first part of the axon covered with the myelin layer. It is shown that the initial segment is the most sensitive area of the myelined nerve fibers from which the action potential normally starts.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126859595","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 : 2013-05-07DOI: 10.1007/978-94-007-6232-9_29
T. Latychevskaia, J. Longchamp, C. Escher, H. Fink
{"title":"Coherent Diffraction and Holographic Imaging of Individual Biomolecules Using Low-Energy Electrons","authors":"T. Latychevskaia, J. Longchamp, C. Escher, H. Fink","doi":"10.1007/978-94-007-6232-9_29","DOIUrl":"https://doi.org/10.1007/978-94-007-6232-9_29","url":null,"abstract":"","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122287674","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}
Muhammad Abdul Hakim Shibghatallah, S. Khotimah, S. Suhandono, S. Viridi, T. Kesuma
Leaf colors of a plant can be used to identify stress level due to its adaptation to environmental change. For most leaves green-related colors are sourced from chlorophyll a and b. Chlorophyll concentration is normally measured using a spectrophotometer in laboratory. In some remote observation places, it is impossible to collect the leaves, preserve them, and bring them to laboratory to measure their chlorophyll content. Based on this need, measurement of chlorophyll content is observed through its color. Using CIE chromaticity diagram leaf_color information in RGB is transformed into wavelength (in nm). Paddy seed with variety name IR-64 is used in observation during its vegetation stage t (age of 0-10 days). Light exposure time τ is chosen as environmental change, which normally should be about 12 hours/day, is varied (0-12 hours/day). Each day sample from different exposure time is taken, its color is recorded using HP Deskjet 1050 scanner with 1200 dpi, and its chlorophyll content is obtained from a...
{"title":"Measuring leaf chlorophyll concentration from its color: A way in monitoring environment change to plantations","authors":"Muhammad Abdul Hakim Shibghatallah, S. Khotimah, S. Suhandono, S. Viridi, T. Kesuma","doi":"10.1063/1.4820322","DOIUrl":"https://doi.org/10.1063/1.4820322","url":null,"abstract":"Leaf colors of a plant can be used to identify stress level due to its adaptation to environmental change. For most leaves green-related colors are sourced from chlorophyll a and b. Chlorophyll concentration is normally measured using a spectrophotometer in laboratory. In some remote observation places, it is impossible to collect the leaves, preserve them, and bring them to laboratory to measure their chlorophyll content. Based on this need, measurement of chlorophyll content is observed through its color. Using CIE chromaticity diagram leaf_color information in RGB is transformed into wavelength (in nm). Paddy seed with variety name IR-64 is used in observation during its vegetation stage t (age of 0-10 days). Light exposure time τ is chosen as environmental change, which normally should be about 12 hours/day, is varied (0-12 hours/day). Each day sample from different exposure time is taken, its color is recorded using HP Deskjet 1050 scanner with 1200 dpi, and its chlorophyll content is obtained from a...","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"84 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126261691","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 : 2013-03-14DOI: 10.1615/PLASMAMED.2013006218
D. Dobrynin, G. Fridman, G. Friedman, A. Fridman
In this manuscript we present an in vitro model based on agarose gel that can be used to simulate a dirty, oily, bloody, and morphologically complex surface of, for example, an open wound. We show this models effectiveness in simulating depth of penetration of reactive species generated in plasma deep into tissue of a rat and confirm the penetration depths with agarose gel model. We envision that in the future such a model could be used to study plasma discharges (and other modalities) and minimize the use of live animals: plasma can be optimized on the agarose gel wound model and then finally verified using an actual wound.
{"title":"Penetration Deep into Tissues of Reactive Oxygen Species Generated in Floating-Electrode Dielectric Barrier Discharge (FE-DBD): in Vitro Agarose Gel Model Mimicking an Open Wound","authors":"D. Dobrynin, G. Fridman, G. Friedman, A. Fridman","doi":"10.1615/PLASMAMED.2013006218","DOIUrl":"https://doi.org/10.1615/PLASMAMED.2013006218","url":null,"abstract":"In this manuscript we present an in vitro model based on agarose gel that can be used to simulate a dirty, oily, bloody, and morphologically complex surface of, for example, an open wound. We show this models effectiveness in simulating depth of penetration of reactive species generated in plasma deep into tissue of a rat and confirm the penetration depths with agarose gel model. We envision that in the future such a model could be used to study plasma discharges (and other modalities) and minimize the use of live animals: plasma can be optimized on the agarose gel wound model and then finally verified using an actual wound.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"132 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115898663","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 have studied biomembranes with grafted polymer chains using a coarse-grained membrane simulation, where a meshless membrane model is combined with polymer chains. We focus on the polymer-induced entropic effects on mechanical properties of membranes. The spontaneous curvature and bending rigidity of the membranes increase with increasing polymer density. Our simulation results agree with the previous theoretical predictions.This original published article PDF was submitted in error and has been replaced with the version immediately following the text of this Corrigendum. The original paper is also attached but marked as WITHDRAWN.
{"title":"Effects of anchored flexible polymers on mechanical properties of model biomembranes","authors":"Hao Wu, H. Noguchi","doi":"10.1063/1.4794653","DOIUrl":"https://doi.org/10.1063/1.4794653","url":null,"abstract":"We have studied biomembranes with grafted polymer chains using a coarse-grained membrane simulation, where a meshless membrane model is combined with polymer chains. We focus on the polymer-induced entropic effects on mechanical properties of membranes. The spontaneous curvature and bending rigidity of the membranes increase with increasing polymer density. Our simulation results agree with the previous theoretical predictions.This original published article PDF was submitted in error and has been replaced with the version immediately following the text of this Corrigendum. The original paper is also attached but marked as WITHDRAWN.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129145553","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}
J. Lino, E. Gonz'alez, A. Deriabina, M. Velasco, V. Poltev
DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values obtained with QM. For Adenine and Thymine the QM local minima energy values are closer to those obtained by the PM potential (average of 0.72 kcal/mol) than by the AMBER force field (1.86 kcal/mol). The differences in energy between MM and QM results are more pronounced for Guanine and Cytosine, especially for minima with the water molecule forming H-bonds with two proton-acceptor centers of the base. Such minima are the deepest ones obtained via MM methods while QM calculations result in the global minima corresponding to water molecule H-bonded to one acceptor and one donor site of the base. Calculations for trimethylated bases with a water molecule corroborate the MM results. The energy profiles were obtained with some degrees of freedom of the water molecule being frozen. This data will contribute to the improvement of the molecular mechanics force fields.
{"title":"Comparative Molecular Mechanics and Quantum Mechanics Study of Microhydration of Nucleic Acid Bases","authors":"J. Lino, E. Gonz'alez, A. Deriabina, M. Velasco, V. Poltev","doi":"10.4236/JBPC.2016.72005","DOIUrl":"https://doi.org/10.4236/JBPC.2016.72005","url":null,"abstract":"DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values obtained with QM. For Adenine and Thymine the QM local minima energy values are closer to those obtained by the PM potential (average of 0.72 kcal/mol) than by the AMBER force field (1.86 kcal/mol). The differences in energy between MM and QM results are more pronounced for Guanine and Cytosine, especially for minima with the water molecule forming H-bonds with two proton-acceptor centers of the base. Such minima are the deepest ones obtained via MM methods while QM calculations result in the global minima corresponding to water molecule H-bonded to one acceptor and one donor site of the base. Calculations for trimethylated bases with a water molecule corroborate the MM results. The energy profiles were obtained with some degrees of freedom of the water molecule being frozen. This data will contribute to the improvement of the molecular mechanics force fields.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127616322","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}
In order to establish defined biomimetic systems, type I collagen was functionalised with 1,3-Phenylenediacetic acid (Ph) as aromatic, bifunctional segment. Following investigation on molecular organization and macroscopic properties, material functionalities, i.e. degradability and bioactivity, were addressed, aiming at elucidating the potential of this collagen system as mineralization template. Functionalised collagen hydrogels demonstrated a preserved triple helix conformation. Decreased swelling ratio and increased thermo-mechanical properties were observed in comparison to state-of-the-art carbodiimide (EDC)-crosslinked collagen controls. Ph-crosslinked samples displayed no optical damage and only a slight mass decrease (~ 4 wt.-%) following 1-week incubation in simulated body fluid (SBF), while nearly 50 wt.-% degradation was observed in EDC-crosslinked collagen. SEM/EDS revealed amorphous mineral deposition, whereby increased calcium phosphate ratio was suggested in hydrogels with increased Ph content. This investigation provides valuable insights for the synthesis of triple helical collagen materials with enhanced macroscopic properties and controlled degradation. In light of these features, this system will be applied for the design of tissue-like scaffolds for mineralized tissue formation.
{"title":"Structure-property-function relationships in triple helical collagen hydrogels","authors":"Giuseppe Tronci, A. Doyle, S. Russell, D. Wood","doi":"10.1557/opl.2012.1653","DOIUrl":"https://doi.org/10.1557/opl.2012.1653","url":null,"abstract":"In order to establish defined biomimetic systems, type I collagen was functionalised with 1,3-Phenylenediacetic acid (Ph) as aromatic, bifunctional segment. Following investigation on molecular organization and macroscopic properties, material functionalities, i.e. degradability and bioactivity, were addressed, aiming at elucidating the potential of this collagen system as mineralization template. Functionalised collagen hydrogels demonstrated a preserved triple helix conformation. Decreased swelling ratio and increased thermo-mechanical properties were observed in comparison to state-of-the-art carbodiimide (EDC)-crosslinked collagen controls. Ph-crosslinked samples displayed no optical damage and only a slight mass decrease (~ 4 wt.-%) following 1-week incubation in simulated body fluid (SBF), while nearly 50 wt.-% degradation was observed in EDC-crosslinked collagen. SEM/EDS revealed amorphous mineral deposition, whereby increased calcium phosphate ratio was suggested in hydrogels with increased Ph content. This investigation provides valuable insights for the synthesis of triple helical collagen materials with enhanced macroscopic properties and controlled degradation. In light of these features, this system will be applied for the design of tissue-like scaffolds for mineralized tissue formation.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124418148","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 formulate and explore a generic continuum model of a polarizable active layer with neo-Hookean elasticity and chemo-mechanical interactions. Homogeneous solutions of the model equations exhibit a stationary long-wave instability when the medium is activated by expansion, and an oscillatory short-wave instability in the case of compressive activation. Both regimes are investigated analytically and numerically. The long-wave instability initiates a coarsening process, which provides a possible mechanism for the establishment of permanent polarization in spherical geometry.
{"title":"Chemo-mechanical instabilities in polarizable active layers","authors":"M. Koepf","doi":"10.14288/1.0042953","DOIUrl":"https://doi.org/10.14288/1.0042953","url":null,"abstract":"We formulate and explore a generic continuum model of a polarizable active layer with neo-Hookean elasticity and chemo-mechanical interactions. Homogeneous solutions of the model equations exhibit a stationary long-wave instability when the medium is activated by expansion, and an oscillatory short-wave instability in the case of compressive activation. Both regimes are investigated analytically and numerically. The long-wave instability initiates a coarsening process, which provides a possible mechanism for the establishment of permanent polarization in spherical geometry.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"281 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127552006","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}