Pub Date : 2020-11-08DOI: 10.21203/rs.3.rs-628277/v1
P. Yadav, Papia Chowdhury
The virus SARS-CoV-2 has created a situation of global emergency all over the world from the last few months. We are witnessing a helpless situation due to COVID-19 as no vaccine or drug is effective against the disease. In the present study, we have tested the repurposing efficacy of some currently used combination drugs against COVID-19. We have tried to understand the mechanism of action of some repurposed drugs:Favipiravir (F), Hydroxychloroquine (H) and Oseltamivir (O). The ADME analysis have suggested strong inhibitory possibility of F, H, O combination towards receptor protein of 3CLpro of SARS-CoV-2 virus. The strong binding affinity, number of hydrogen bond interaction between inhibitor, receptor and lower inhibition constant computed from molecular docking validated the better complexation possibility of F + H + O:3CLprocombination. Various thermodynamical output from Molecular dynamics (MD) simulations like potential energy (Eg), temperature (T), density, pressure, SASA energy, interaction energies, Gibbs free energy (ΔGbind) etc., also favored the complexation between F + H + O and CoV-2 protease. Our in-silico results have recommended the strong candidature of combination drugs Favipiravir, Hydroxychloroquine and Oseltamivir as a potential lead inhibitor for targeting SARS-CoV-2 infections.
从过去几个月开始，SARS-CoV-2病毒在世界各地造成了全球紧急状态。由于没有有效的疫苗或药物，我们正在目睹因COVID-19而陷入无助的局面。在本研究中，我们测试了一些目前使用的联合药物对COVID-19的再利用效果。我们试图了解一些重组药物的作用机制:Favipiravir (F)、Hydroxychloroquine (H)和Oseltamivir (O)。ADME分析表明，F、H、O组合对SARS-CoV-2病毒3CLpro受体蛋白有很强的抑制作用。结合亲和力强，抑制剂与受体之间的氢键相互作用数和分子对接计算的抑制常数较低，验证了F + H + O:3CLprocombination较好的络合可能性。分子动力学(MD)模拟的各种热力学输出，如势能(Eg)、温度(T)、密度、压力、SASA能、相互作用能、吉布斯自由能(ΔGbind)等，也有利于F + H + O与CoV-2蛋白酶之间的络合。我们的计算机结果表明，联合药物Favipiravir、Hydroxychloroquine和Oseltamivir具有很强的候选性，可以作为靶向SARS-CoV-2感染的潜在先导抑制剂。
{"title":"Repurposing the Combination Drug of Favipiravir, Hydroxychloroquine and Oseltamivir as a Potential Inhibitor Against SARS-CoV-2: A Computational Study","authors":"P. Yadav, Papia Chowdhury","doi":"10.21203/rs.3.rs-628277/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-628277/v1","url":null,"abstract":"\u0000 The virus SARS-CoV-2 has created a situation of global emergency all over the world from the last few months. We are witnessing a helpless situation due to COVID-19 as no vaccine or drug is effective against the disease. In the present study, we have tested the repurposing efficacy of some currently used combination drugs against COVID-19. We have tried to understand the mechanism of action of some repurposed drugs:Favipiravir (F), Hydroxychloroquine (H) and Oseltamivir (O). The ADME analysis have suggested strong inhibitory possibility of F, H, O combination towards receptor protein of 3CLpro of SARS-CoV-2 virus. The strong binding affinity, number of hydrogen bond interaction between inhibitor, receptor and lower inhibition constant computed from molecular docking validated the better complexation possibility of F + H + O:3CLprocombination. Various thermodynamical output from Molecular dynamics (MD) simulations like potential energy (Eg), temperature (T), density, pressure, SASA energy, interaction energies, Gibbs free energy (ΔGbind) etc., also favored the complexation between F + H + O and CoV-2 protease. Our in-silico results have recommended the strong candidature of combination drugs Favipiravir, Hydroxychloroquine and Oseltamivir as a potential lead inhibitor for targeting SARS-CoV-2 infections.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133480005","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 : 2020-10-19DOI: 10.1103/PHYSREVRESEARCH.3.023036
A. Fruleux, A. Boudaoud
Many media are divided into elementary units with irregular shape and size, as exemplified by domains in magnetic materials, bubbles in foams, or cells in biological tissues. Such media are essentially characterized by geometrical disorder of their elementary units, which we term cells. Cells set a reference scale at which parameters and fields reflecting material properties and state are often assessed. In these media, it is difficult to quantify spatial variations of cell-scale fields, because space discretization based on standard coordinate systems is not commensurate with the natural discretization into geometrically disordered cells. Here we consider the spectral analysis of spatially varying fields. We built a method, which we call Cellular Fourier Transform (CFT), to analyze cell-scale fields, which includes both discrete fields defined only at cell level and continuous fields smoothed out from their sub-cell variations. Our approach is based on the construction of a discrete operator suited to the disordered geometry and on the computation of its eigenvectors, which respectively play the same role as the Laplace operator and sine waves in Euclidean coordinate systems. We show that CFT has the expected behavior for sinusoidal fields and for random fields with long-range correlations. Our approach for spectral analysis is suited to any geometrically disordered material, such as biological tissue with complex geometry, opening the way to systematic multiscale analyses of material behavior.
{"title":"Cellular Fourier analysis for geometrically disordered materials","authors":"A. Fruleux, A. Boudaoud","doi":"10.1103/PHYSREVRESEARCH.3.023036","DOIUrl":"https://doi.org/10.1103/PHYSREVRESEARCH.3.023036","url":null,"abstract":"Many media are divided into elementary units with irregular shape and size, as exemplified by domains in magnetic materials, bubbles in foams, or cells in biological tissues. Such media are essentially characterized by geometrical disorder of their elementary units, which we term cells. Cells set a reference scale at which parameters and fields reflecting material properties and state are often assessed. In these media, it is difficult to quantify spatial variations of cell-scale fields, because space discretization based on standard coordinate systems is not commensurate with the natural discretization into geometrically disordered cells. Here we consider the spectral analysis of spatially varying fields. We built a method, which we call Cellular Fourier Transform (CFT), to analyze cell-scale fields, which includes both discrete fields defined only at cell level and continuous fields smoothed out from their sub-cell variations. Our approach is based on the construction of a discrete operator suited to the disordered geometry and on the computation of its eigenvectors, which respectively play the same role as the Laplace operator and sine waves in Euclidean coordinate systems. We show that CFT has the expected behavior for sinusoidal fields and for random fields with long-range correlations. Our approach for spectral analysis is suited to any geometrically disordered material, such as biological tissue with complex geometry, opening the way to systematic multiscale analyses of material behavior.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"99 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127165123","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 : 2020-10-02DOI: 10.46439/radiation.1.001
B. Roy, S. Niture, Marvin H. Wu, D. Kumar
Background and controlled electromagnetic radiation (EMR) on biological cells and tissues induces thermal, non-thermal, and dielectric property change. After EMR interaction with cells/tissues the resulting signal is used for imaging, bio-molecular response, and photo-biomodulation studies at infrared regime, and for therapeutic use. We attempt to present a review of current literature with a focus to present compilation of published experimental results for each regime viz. microwave (extremely low frequency, ELF to 3 GHz), to cellular communication frequencies (100 KHz to 300 GHz), millimeter wave (300 GHz- 1 THz), and the infra-red band extending up to 461 THz. A unique graphical representation of frequency effects and their relevant significance in detection of direct biological effects, therapeutic applications and biophysical interpretation is presented. A total of seventy research papers from peer-reviewed journals were used to compile a mixture of useful information, all presented in a narrative style. Out of the Journal articles used for this paper, 63 journal articles were published between 2000 to 2020. Physical, biological, and therapeutic mechanisms of thermal, non-thermal and complex dielectric effects of EMR on cells are all explained in relevant sections of this paper. A broad up to date review for the EMR range KHz-NIR (kilohertz to near infra-red) is prepared. Published reports indicate that number of biological cell irradiation impact studies fall off rapidly beyond a few THz EMR, leading to relatively a smaller number of studies in FIR and NIR bands covering most of the thermal effects and microthermal effects, and rotation-vibration effects.
{"title":"Biological effects of low power nonionizing radiation: A narrative review","authors":"B. Roy, S. Niture, Marvin H. Wu, D. Kumar","doi":"10.46439/radiation.1.001","DOIUrl":"https://doi.org/10.46439/radiation.1.001","url":null,"abstract":"Background and controlled electromagnetic radiation (EMR) on biological cells and tissues induces thermal, non-thermal, and dielectric property change. After EMR interaction with cells/tissues the resulting signal is used for imaging, bio-molecular response, and photo-biomodulation studies at infrared regime, and for therapeutic use. We attempt to present a review of current literature with a focus to present compilation of published experimental results for each regime viz. microwave (extremely low frequency, ELF to 3 GHz), to cellular communication frequencies (100 KHz to 300 GHz), millimeter wave (300 GHz- 1 THz), and the infra-red band extending up to 461 THz. A unique graphical representation of frequency effects and their relevant significance in detection of direct biological effects, therapeutic applications and biophysical interpretation is presented. A total of seventy research papers from peer-reviewed journals were used to compile a mixture of useful information, all presented in a narrative style. Out of the Journal articles used for this paper, 63 journal articles were published between 2000 to 2020. Physical, biological, and therapeutic mechanisms of thermal, non-thermal and complex dielectric effects of EMR on cells are all explained in relevant sections of this paper. A broad up to date review for the EMR range KHz-NIR (kilohertz to near infra-red) is prepared. Published reports indicate that number of biological cell irradiation impact studies fall off rapidly beyond a few THz EMR, leading to relatively a smaller number of studies in FIR and NIR bands covering most of the thermal effects and microthermal effects, and rotation-vibration effects.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"25 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120846513","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 : 2020-08-26DOI: 10.1103/PHYSREVRESEARCH.3.013020
S. Kostinski, S. Reuveni
Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria, whereas Bacteria have none. The greater complexity of Eukarya renders them difficult to study from both an experimental and theoretical perspective. However, encouraged by a recent experimental result showing that budding yeast (a unicellular eukaryote) obeys the same proportionality between ribosomal proteome fractions and cellular growth rates as Bacteria, we derive a set of relations describing eukaryotic growth from first principles of ribosome biogenesis. We recover the observed ribosomal protein proportionality, and then continue to obtain two growth-laws for the number of RNA polymerases synthesizing ribosomal RNA per ribosome in the cell. These growth-laws, in turn, reveal two invariants of eukaryotic growth, i.e. quantities predicted to be conserved by Eukarya regardless of growth conditions. The invariants, which are the first of their kind for Eukarya, clarify the coordination of transcription and translation kinetics as required by ribosome biogenesis, and link these kinetic parameters to cellular physiology. We demonstrate application of the relations to the yeast S. cerevisiae and find the predictions to be in good agreement with currently available data. We then outline methods to quantitatively deduce several unknown kinetic and physiological parameters. The analysis is not specific to S. cerevisiae and can be extended to other lower (unicellular) Eukarya when data become available. The relations may also have relevance to certain cancer cells which, like bacteria and yeast, exhibit rapid cell proliferation and ribosome biogenesis.
{"title":"Growth laws and invariants from ribosome biogenesis in lower Eukarya","authors":"S. Kostinski, S. Reuveni","doi":"10.1103/PHYSREVRESEARCH.3.013020","DOIUrl":"https://doi.org/10.1103/PHYSREVRESEARCH.3.013020","url":null,"abstract":"Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria, whereas Bacteria have none. The greater complexity of Eukarya renders them difficult to study from both an experimental and theoretical perspective. However, encouraged by a recent experimental result showing that budding yeast (a unicellular eukaryote) obeys the same proportionality between ribosomal proteome fractions and cellular growth rates as Bacteria, we derive a set of relations describing eukaryotic growth from first principles of ribosome biogenesis. We recover the observed ribosomal protein proportionality, and then continue to obtain two growth-laws for the number of RNA polymerases synthesizing ribosomal RNA per ribosome in the cell. These growth-laws, in turn, reveal two invariants of eukaryotic growth, i.e. quantities predicted to be conserved by Eukarya regardless of growth conditions. The invariants, which are the first of their kind for Eukarya, clarify the coordination of transcription and translation kinetics as required by ribosome biogenesis, and link these kinetic parameters to cellular physiology. We demonstrate application of the relations to the yeast S. cerevisiae and find the predictions to be in good agreement with currently available data. We then outline methods to quantitatively deduce several unknown kinetic and physiological parameters. The analysis is not specific to S. cerevisiae and can be extended to other lower (unicellular) Eukarya when data become available. The relations may also have relevance to certain cancer cells which, like bacteria and yeast, exhibit rapid cell proliferation and ribosome biogenesis.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130103628","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 : 2020-06-08DOI: 10.1103/PhysRevFluids.6.023602
M. Abbasi, A. Farutin, H. Ez‐zahraouy, A. Benyoussef, C. Misbah
Red blood cells (RBCs) -- erythrocytes -- suspended in plasma tend to aggregate and form rouleaux. During aggregation the first stage consists in the formation of RBC doublets [Blood cells, molecules, and diseases 25, 339 (1999)]. While aggregates are normally dissociated by moderate flow stresses, under some pathological conditions the aggregation becomes irreversible, which leads to high blood viscosity and vessel occlusion. We perform here two-dimensional simulations to study the doublet dynamics under shear flow in different conditions and its impact on rheology. We sum up our results on the dynamics of doublet in a rich phase diagram in the parameter space (flow strength, adhesion energy) showing four different types of doublet configurations and dynamics. We find that membrane tank-treading plays an important role in doublet disaggregation, in agreement with experiments on RBCs. A remarkable feature found here is that when a single cell performs tumbling (by increasing vesicle internal viscosity) the doublet formed due to adhesion (even very weak) remains stable even under a very strong shear rate. It is seen in this regime that an increase of shear rate induces an adaptation of the doublet conformation allowing the aggregate to resist cell-cell detachment. We show that the normalized effective viscosity of doublet suspension increases significantly with the adhesion energy, a fact which should affect blood perfusion in microcirculation.
{"title":"Erythrocyte-erythrocyte aggregation dynamics under shear flow","authors":"M. Abbasi, A. Farutin, H. Ez‐zahraouy, A. Benyoussef, C. Misbah","doi":"10.1103/PhysRevFluids.6.023602","DOIUrl":"https://doi.org/10.1103/PhysRevFluids.6.023602","url":null,"abstract":"Red blood cells (RBCs) -- erythrocytes -- suspended in plasma tend to aggregate and form rouleaux. During aggregation the first stage consists in the formation of RBC doublets [Blood cells, molecules, and diseases 25, 339 (1999)]. While aggregates are normally dissociated by moderate flow stresses, under some pathological conditions the aggregation becomes irreversible, which leads to high blood viscosity and vessel occlusion. We perform here two-dimensional simulations to study the doublet dynamics under shear flow in different conditions and its impact on rheology. We sum up our results on the dynamics of doublet in a rich phase diagram in the parameter space (flow strength, adhesion energy) showing four different types of doublet configurations and dynamics. We find that membrane tank-treading plays an important role in doublet disaggregation, in agreement with experiments on RBCs. A remarkable feature found here is that when a single cell performs tumbling (by increasing vesicle internal viscosity) the doublet formed due to adhesion (even very weak) remains stable even under a very strong shear rate. It is seen in this regime that an increase of shear rate induces an adaptation of the doublet conformation allowing the aggregate to resist cell-cell detachment. We show that the normalized effective viscosity of doublet suspension increases significantly with the adhesion energy, a fact which should affect blood perfusion in microcirculation.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130525408","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 : 2020-05-03DOI: 10.1016/j.matpr.2020.05.217
R. Paul, Sudip Suklabaidya, S. Hussain
{"title":"Fluorescence resonance energy transfer (FRET) as biomarkers","authors":"R. Paul, Sudip Suklabaidya, S. Hussain","doi":"10.1016/j.matpr.2020.05.217","DOIUrl":"https://doi.org/10.1016/j.matpr.2020.05.217","url":null,"abstract":"","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"195 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128921885","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 : 2020-05-01DOI: 10.1103/PHYSREVRESEARCH.2.043063
A. K. Dasanna, G. Gompper, D. Fedosov
Adhesion interactions mediated by multiple bond types are relevant for many biological and soft matter systems, including the adhesion of biological cells and functionalized colloidal particles to various substrates. To elucidate advantages and disadvantages of multiple bond populations for the stability of heterogeneous adhesion clusters of receptor-ligand pairs, a theoretical model for a homogeneous parallel adhesion bond cluster under constant loading is extended to several bond types. The stability of the entire cluster can be tuned by changing densities of different bond populations as well as their extensional rigidity and binding properties. In particular, bond extensional rigidities determine the distribution of total load to be shared between different sub-populations. Under a gradual increase of the total load, the rupture of a heterogeneous adhesion cluster can be thought of as a multistep discrete process, in which one of the bond sub-populations ruptures first, followed by similar rupture steps of other sub-populations or by immediate detachment of the remaining cluster. This rupture behavior is qualitatively independent of involved bond types, such as slip and catch bonds. Interestingly, an optimal stability is generally achieved when the total cluster load is shared such that loads on distinct bond populations are equal to their individual critical rupture forces. We also show that cluster heterogeneity can drastically affect cluster lifetime.
{"title":"Stability of heterogeneous parallel-bond adhesion clusters under load","authors":"A. K. Dasanna, G. Gompper, D. Fedosov","doi":"10.1103/PHYSREVRESEARCH.2.043063","DOIUrl":"https://doi.org/10.1103/PHYSREVRESEARCH.2.043063","url":null,"abstract":"Adhesion interactions mediated by multiple bond types are relevant for many biological and soft matter systems, including the adhesion of biological cells and functionalized colloidal particles to various substrates. To elucidate advantages and disadvantages of multiple bond populations for the stability of heterogeneous adhesion clusters of receptor-ligand pairs, a theoretical model for a homogeneous parallel adhesion bond cluster under constant loading is extended to several bond types. The stability of the entire cluster can be tuned by changing densities of different bond populations as well as their extensional rigidity and binding properties. In particular, bond extensional rigidities determine the distribution of total load to be shared between different sub-populations. Under a gradual increase of the total load, the rupture of a heterogeneous adhesion cluster can be thought of as a multistep discrete process, in which one of the bond sub-populations ruptures first, followed by similar rupture steps of other sub-populations or by immediate detachment of the remaining cluster. This rupture behavior is qualitatively independent of involved bond types, such as slip and catch bonds. Interestingly, an optimal stability is generally achieved when the total cluster load is shared such that loads on distinct bond populations are equal to their individual critical rupture forces. We also show that cluster heterogeneity can drastically affect cluster lifetime.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127687491","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}
Unfolding of a coarse grained COVN protein from its native configuration shows a linear response with increasing temperature followed by a nonmonotonic double peaks in its radius of gyration. The protein conforms to a random coil of folded segments in native state with increasing tenuous and globular structures in specific temperature regimes where the effective dimensions of corresponding structures D is about 1.6 to 2.4. Thermal agitation alone is not sufficient to fully eradicate its segmental folding as few folds are found to persist around such residues as 65W, 110Y, 224L, 374P even at high temperatures.
{"title":"Thermal-induced unfolding-refolding of a nucleocapsid COVN protein","authors":"Warin Rangubpit, P. Sompornpisut, R. Pandey","doi":"10.3934/BIOPHY.2021007","DOIUrl":"https://doi.org/10.3934/BIOPHY.2021007","url":null,"abstract":"Unfolding of a coarse grained COVN protein from its native configuration shows a linear response with increasing temperature followed by a nonmonotonic double peaks in its radius of gyration. The protein conforms to a random coil of folded segments in native state with increasing tenuous and globular structures in specific temperature regimes where the effective dimensions of corresponding structures D is about 1.6 to 2.4. Thermal agitation alone is not sufficient to fully eradicate its segmental folding as few folds are found to persist around such residues as 65W, 110Y, 224L, 374P even at high temperatures.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134529950","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 : 2019-10-31DOI: 10.1142/9789814415958_0056
Chen Li, Tingnan Zhang, D. Goldman
Compared to agile legged animals, wheeled and tracked vehicles often suffer large performance loss on granular surfaces like sand and gravel. Understanding the mechanics of legged locomotion on granular media can aid the development of legged robots with improved mobility on granular surfaces; however, no general force model yet exists for granular media to predict ground reaction forces during complex limb intrusions. Inspired by a recent study of sand-swimming, we develop a resistive force model in the vertical plane for legged locomotion on granular media. We divide an intruder of complex morphology and kinematics, e.g., a bio-inspired robot L-leg rotated through uniform granular media (loosely packed ~ 1 mm diameter poppy seeds), into small segments, and measure stresses as a function of depth, orientation, and direction of motion using a model leg segment. Summation of segmental forces over the intruder predicts the net forces on both an L-leg and a reversed L-leg rotated through granular media with better accuracy than using simple one-dimensional penetration and drag force models. A multi-body dynamic simulation using the resistive force model predicts the speeds of a small legged robot (15 cm, 150 g) moving on granular media using both L-legs and reversed L-legs.
{"title":"A resistive force model of legged locomotion on granular media","authors":"Chen Li, Tingnan Zhang, D. Goldman","doi":"10.1142/9789814415958_0056","DOIUrl":"https://doi.org/10.1142/9789814415958_0056","url":null,"abstract":"Compared to agile legged animals, wheeled and tracked vehicles often suffer large performance loss on granular surfaces like sand and gravel. Understanding the mechanics of legged locomotion on granular media can aid the development of legged robots with improved mobility on granular surfaces; however, no general force model yet exists for granular media to predict ground reaction forces during complex limb intrusions. Inspired by a recent study of sand-swimming, we develop a resistive force model in the vertical plane for legged locomotion on granular media. We divide an intruder of complex morphology and kinematics, e.g., a bio-inspired robot L-leg rotated through uniform granular media (loosely packed ~ 1 mm diameter poppy seeds), into small segments, and measure stresses as a function of depth, orientation, and direction of motion using a model leg segment. Summation of segmental forces over the intruder predicts the net forces on both an L-leg and a reversed L-leg rotated through granular media with better accuracy than using simple one-dimensional penetration and drag force models. A multi-body dynamic simulation using the resistive force model predicts the speeds of a small legged robot (15 cm, 150 g) moving on granular media using both L-legs and reversed L-legs.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126232102","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 : 2019-09-15DOI: 10.1103/PHYSREVRESEARCH.3.013107
Sakib Matin, T. Tenzin, W. Klein
Neural avalanches are collective firings of neurons that exhibit emergent scale-free behavior. Understanding the nature and distribution of these avalanches is an important element in understanding how the brain functions. We study a model of the brain for which the dynamics are governed by neutral theory. The neural avalanches are defined using causal connections between the firing neurons. We analyze the scaling of causal neural avalanches as the critical point is approached from the absorbing phase. By using cluster analysis tools from percolation theory, we characterize the critical properties of the neural avalanches. We identify the tuning parameters consistent with experiments. The scaling hypothesis provides a unified explanation of the power laws which characterize the critical point. The critical exponents characterizing the avalanche distributions and divergence of the response functions are consistent with the predictions of the scaling hypothesis. We use an universal scaling function for the avalanche profile to find that the firing rate for avalanches of different sizes shows data collapse after appropriate rescaling. We also find data collapse for the avalanche distribution functions, which is a stronger evidence of criticality than just the existence of power laws. Critical slowing-down and power law relaxation of avalanches is observed as the system is tuned to its critical point. We discuss how our results motivate future empirical studies of criticality in the brain.
{"title":"Scaling of causal neural avalanches in a neutral model","authors":"Sakib Matin, T. Tenzin, W. Klein","doi":"10.1103/PHYSREVRESEARCH.3.013107","DOIUrl":"https://doi.org/10.1103/PHYSREVRESEARCH.3.013107","url":null,"abstract":"Neural avalanches are collective firings of neurons that exhibit emergent scale-free behavior. Understanding the nature and distribution of these avalanches is an important element in understanding how the brain functions. We study a model of the brain for which the dynamics are governed by neutral theory. The neural avalanches are defined using causal connections between the firing neurons. We analyze the scaling of causal neural avalanches as the critical point is approached from the absorbing phase. By using cluster analysis tools from percolation theory, we characterize the critical properties of the neural avalanches. We identify the tuning parameters consistent with experiments. The scaling hypothesis provides a unified explanation of the power laws which characterize the critical point. The critical exponents characterizing the avalanche distributions and divergence of the response functions are consistent with the predictions of the scaling hypothesis. We use an universal scaling function for the avalanche profile to find that the firing rate for avalanches of different sizes shows data collapse after appropriate rescaling. We also find data collapse for the avalanche distribution functions, which is a stronger evidence of criticality than just the existence of power laws. Critical slowing-down and power law relaxation of avalanches is observed as the system is tuned to its critical point. We discuss how our results motivate future empirical studies of criticality in the brain.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123183269","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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