Neutron beam, being electrically neutral and highly penetrating, offers unique advantages for irradiation of biological species such as plants, seeds, and microorganisms. We comprehensively investigate the potential of neutron irradiation for inducing genetic mutations using simulations of J-PARC BL10, JRR-3 TNRF, and KUANS for spallation, reactor, and compact neutron sources. We analyze neutron flux, energy deposition rates, and Linear Energy Transfer (LET) distributions. KUANS demonstrated the highest dose rate of 17 Gy/h, significantly surpassing BL10, due to the large solid angle by the optimal sample placement. The findings highlight KUANS's suitability for efficient genetic mutations and neutron breeding, particularly for inducing targeted mutations in biological samples. The LET range of KUANS is concentrated in 20-70 keV/{mu}m, which is potentially ideal for inducing specific genetic mutations. The importance of choosing neutron sources based on LET requirements to maximize mutation induction efficiency is emphasized. This research shows the potential of compact neutron sources like KUANS for effective biological irradiation and neutron breeding, offering a viable alternative to larger facilities. The neutron filters used in BL10 and TNRF effectively excluded low-energy neutrons with keeping the high LET component. The neutron capture reaction, 14N(n,p)14C, was found to be the main dose under thermal neutron-dominated conditions.
中子束是电中性的，穿透力强，在辐照植物、种子和微生物等生物物种方面具有独特的优势。我们通过模拟 J-PARC BL10、JRR-3 TNRF 和 KUANS 的溅射、反应堆和紧凑型中子源，全面研究了中子辐照诱导基因突变的潜力。我们分析了中子通量、能量沉积率和线性能量传递（LET）分布。KUANS 的剂量率最高，达到 17 Gy/h，大大超过 BL10，这得益于优化的样品放置所产生的大固着角。这些研究结果突出表明，KUANS 适用于高效基因突变和中子培育，特别是在生物样本中诱导靶向突变。KUANS 的 LET 范围集中在 20-70 keV/{/mu}m，这可能是诱导特定基因突变的理想选择。强调了根据 LET 要求选择中子源以最大限度地提高突变诱导效率的重要性。这项研究表明，像 KUANS 这样的紧凑型中子源具有进行有效生物辐照和中子育种的潜力，为大型设施提供了可行的替代方案。BL10 和 TNRF 使用的中子滤波器在保留高 LET 成分的同时，有效地排除了低能中子。研究发现，在热中子主导条件下，中子俘获反应 14N(n,p)14C 是主要剂量。
{"title":"A Comparative Study of Neutron Irradiation for Genetic Mutations: Spallation, Reactor, and Compact Neutron Source","authors":"May Sweet, Kenji Mishima, Masahide Harada, Keisuke Kurita, Hiroshi Iikura, Seiji Tasaki, Norio Kikuchi","doi":"arxiv-2408.10929","DOIUrl":"https://doi.org/arxiv-2408.10929","url":null,"abstract":"Neutron beam, being electrically neutral and highly penetrating, offers\u0000unique advantages for irradiation of biological species such as plants, seeds,\u0000and microorganisms. We comprehensively investigate the potential of neutron\u0000irradiation for inducing genetic mutations using simulations of J-PARC BL10,\u0000JRR-3 TNRF, and KUANS for spallation, reactor, and compact neutron sources. We\u0000analyze neutron flux, energy deposition rates, and Linear Energy Transfer (LET)\u0000distributions. KUANS demonstrated the highest dose rate of 17 Gy/h,\u0000significantly surpassing BL10, due to the large solid angle by the optimal\u0000sample placement. The findings highlight KUANS's suitability for efficient\u0000genetic mutations and neutron breeding, particularly for inducing targeted\u0000mutations in biological samples. The LET range of KUANS is concentrated in\u000020-70 keV/{mu}m, which is potentially ideal for inducing specific genetic\u0000mutations. The importance of choosing neutron sources based on LET requirements\u0000to maximize mutation induction efficiency is emphasized. This research shows\u0000the potential of compact neutron sources like KUANS for effective biological\u0000irradiation and neutron breeding, offering a viable alternative to larger\u0000facilities. The neutron filters used in BL10 and TNRF effectively excluded\u0000low-energy neutrons with keeping the high LET component. The neutron capture\u0000reaction, 14N(n,p)14C, was found to be the main dose under thermal\u0000neutron-dominated conditions.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213218","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 respond to chemical cues, and the precision with which they can sense these cues is fundamentally limited by the stochastic nature of diffusion and ligand binding. Berg and Purcell famously investigated how well a small sensor in an infinite ligand bath can determine the ligand concentration, and a number of subsequent analyses have refined and built upon their classical estimates. Not all concentration sensing problems, however, occur in such an infinite geometry. At different scales, subcellular sensors and cells in tissues are both often confronted with signals whose diffusion is affected by confining boundaries. It is thus valuable to understand how basic limits on chemosensation depend on the sensor's size and on its position in the domain in which ligand diffuses. Here we compute how sensor size and proximity to reflecting boundaries affect the diffusion-limited precision of chemosensation for various geometries in one and three dimensions. We derive analytical expressions for the sensing limit in these geometries. Among our conclusions is the surprising result that, in certain circumstances, smaller sensors can be more effective than larger sensors. This effect arises from a trade-off between spatial averaging and time averaging that we analyze in detail. We also find that proximity to confining boundaries can degrade a sensor's precision significantly compared to the precision of the same sensor far from any boundaries.
{"title":"Physical limits on chemical sensing in bounded domains","authors":"Daniel R. McCusker, David K. Lubensky","doi":"arxiv-2408.10745","DOIUrl":"https://doi.org/arxiv-2408.10745","url":null,"abstract":"Cells respond to chemical cues, and the precision with which they can sense\u0000these cues is fundamentally limited by the stochastic nature of diffusion and\u0000ligand binding. Berg and Purcell famously investigated how well a small sensor\u0000in an infinite ligand bath can determine the ligand concentration, and a number\u0000of subsequent analyses have refined and built upon their classical estimates.\u0000Not all concentration sensing problems, however, occur in such an infinite\u0000geometry. At different scales, subcellular sensors and cells in tissues are\u0000both often confronted with signals whose diffusion is affected by confining\u0000boundaries. It is thus valuable to understand how basic limits on\u0000chemosensation depend on the sensor's size and on its position in the domain in\u0000which ligand diffuses. Here we compute how sensor size and proximity to\u0000reflecting boundaries affect the diffusion-limited precision of chemosensation\u0000for various geometries in one and three dimensions. We derive analytical\u0000expressions for the sensing limit in these geometries. Among our conclusions is\u0000the surprising result that, in certain circumstances, smaller sensors can be\u0000more effective than larger sensors. This effect arises from a trade-off between\u0000spatial averaging and time averaging that we analyze in detail. We also find\u0000that proximity to confining boundaries can degrade a sensor's precision\u0000significantly compared to the precision of the same sensor far from any\u0000boundaries.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213216","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}
Yinhao Jia, Katelynn Horvath, Santosh R. Rananaware, Piyush K. Jain, Janani Sampath
CRISPR (clustered regularly interspaced short palindromic repeat)- based diagnostics are at the forefront of rapid detection platforms of infectious diseases. The integration of reverse transcription-loop-mediated isothermal amplification (RT-LAMP) with CRISPR-Cas protein systems has led to the creation of advanced one-pot assays. The sensitivity of these assays has been bolstered by the utilization of a thermophilic Cas12 protein, BrCas12b, and its engineered variant, which exhibits enhanced thermal stability and allows for broader operation temperatures of the assay. Here, we perform all-atom molecular dynamics (MD) simulations on wild-type and mutant BrCas12b to reveal the mechanism of stabilization conferred by the mutation. High-temperature simulations reveal a small structural change along with greater flexibility in the PAM-interacting domain of the mutant BrCas12b, with marginal structural and flexibility changes in the other mutated domains. Comparative essential dynamics analysis between the wild-type and mutant BrCas12b at both ambient and elevated temperatures provides insights into the stabilizing effects of the mutations. Our findings not only offer a comprehensive insight into the dynamic alterations induced by mutations but reveal important motions in BrCas12b, important for the rational design of diagnostic and therapeutic platforms of Cas12 proteins.
{"title":"Exploring the Thermostability of CRISPR Cas12b using Molecular Dynamics Simulations","authors":"Yinhao Jia, Katelynn Horvath, Santosh R. Rananaware, Piyush K. Jain, Janani Sampath","doi":"arxiv-2408.11149","DOIUrl":"https://doi.org/arxiv-2408.11149","url":null,"abstract":"CRISPR (clustered regularly interspaced short palindromic repeat)- based\u0000diagnostics are at the forefront of rapid detection platforms of infectious\u0000diseases. The integration of reverse transcription-loop-mediated isothermal\u0000amplification (RT-LAMP) with CRISPR-Cas protein systems has led to the creation\u0000of advanced one-pot assays. The sensitivity of these assays has been bolstered\u0000by the utilization of a thermophilic Cas12 protein, BrCas12b, and its\u0000engineered variant, which exhibits enhanced thermal stability and allows for\u0000broader operation temperatures of the assay. Here, we perform all-atom\u0000molecular dynamics (MD) simulations on wild-type and mutant BrCas12b to reveal\u0000the mechanism of stabilization conferred by the mutation. High-temperature\u0000simulations reveal a small structural change along with greater flexibility in\u0000the PAM-interacting domain of the mutant BrCas12b, with marginal structural and\u0000flexibility changes in the other mutated domains. Comparative essential\u0000dynamics analysis between the wild-type and mutant BrCas12b at both ambient and\u0000elevated temperatures provides insights into the stabilizing effects of the\u0000mutations. Our findings not only offer a comprehensive insight into the dynamic\u0000alterations induced by mutations but reveal important motions in BrCas12b,\u0000important for the rational design of diagnostic and therapeutic platforms of\u0000Cas12 proteins.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213213","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}
Spontaneous pattern formation in homogeneous systems is ubiquitous in nature. Although Turing demonstrated that spatial patterns can emerge in reaction-diffusion (RD) systems when the homogeneous state becomes linearly unstable, it remains unclear whether the Turing mechanism is the only route for pattern formation. Here, we develop an efficient algorithm to systematically map the solution landscape to find all steady-state solutions. By applying our method to generic RD models, we find that stable spatial patterns can emerge via saddle-node bifurcations before the onset of Turing instability. Furthermore, by using a generalized action in functional space based on large deviation theory, our method is extended to evaluate stability of spatial patterns against noise. Applying this general approach in a three-species RD model, we show that though formation of Turing patterns only requires two chemical species, the third species is critical for stabilizing patterns against strong intrinsic noise in small biochemical systems.
{"title":"Solution landscape of reaction-diffusion systems reveals a nonlinear mechanism and spatial robustness of pattern formation","authors":"Shuonan Wu, Bing Yu, Yuhai Tu, Lei Zhang","doi":"arxiv-2408.10095","DOIUrl":"https://doi.org/arxiv-2408.10095","url":null,"abstract":"Spontaneous pattern formation in homogeneous systems is ubiquitous in nature.\u0000Although Turing demonstrated that spatial patterns can emerge in\u0000reaction-diffusion (RD) systems when the homogeneous state becomes linearly\u0000unstable, it remains unclear whether the Turing mechanism is the only route for\u0000pattern formation. Here, we develop an efficient algorithm to systematically\u0000map the solution landscape to find all steady-state solutions. By applying our\u0000method to generic RD models, we find that stable spatial patterns can emerge\u0000via saddle-node bifurcations before the onset of Turing instability.\u0000Furthermore, by using a generalized action in functional space based on large\u0000deviation theory, our method is extended to evaluate stability of spatial\u0000patterns against noise. Applying this general approach in a three-species RD\u0000model, we show that though formation of Turing patterns only requires two\u0000chemical species, the third species is critical for stabilizing patterns\u0000against strong intrinsic noise in small biochemical systems.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"280 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213217","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}
Jonathan Rojas, Zhe Wang, Feng Liu, Jerry A. Fereiro, Domenikos Chryssikos, Thomas Dittrich, Dario Leister, David Cahen, Marc Tornow
Photosystem I (PSI) is a photosynthetic protein which evolved to efficiently transfer electrons through the thylakoid membrane. This remarkable process attracted the attention of the biomolecular electronics community, which aims to study and understand the underlying electronic transport through these proteins by contacting ensembles of PSI with solid-state metallic contacts. This paper extends published work of immobilizing monolayers of PSI with a specific orientation, by using organophosphonate self-assembled molecules with hydrophilic heads on ultra-flat titanium nitride. Electrical measurements carried out with eutectic GaIn top contacts showed current rectification ratios of up to ~200. The previously proposed rectification mechanism, relying on the protein's internal electric dipole, was inquired by measuring shifts in the work function. Our straightforward bottom-up fabrication method may allow for further experimental studies on PSI molecules, such as embedding them in solid-state, transparent top contact schemes for optoelectronic measurements.
{"title":"Current rectification via Photosystem I monolayers induced by their orientation on hydrophilic self-assembled monolayers on titanium nitride","authors":"Jonathan Rojas, Zhe Wang, Feng Liu, Jerry A. Fereiro, Domenikos Chryssikos, Thomas Dittrich, Dario Leister, David Cahen, Marc Tornow","doi":"arxiv-2408.09276","DOIUrl":"https://doi.org/arxiv-2408.09276","url":null,"abstract":"Photosystem I (PSI) is a photosynthetic protein which evolved to efficiently\u0000transfer electrons through the thylakoid membrane. This remarkable process\u0000attracted the attention of the biomolecular electronics community, which aims\u0000to study and understand the underlying electronic transport through these\u0000proteins by contacting ensembles of PSI with solid-state metallic contacts.\u0000This paper extends published work of immobilizing monolayers of PSI with a\u0000specific orientation, by using organophosphonate self-assembled molecules with\u0000hydrophilic heads on ultra-flat titanium nitride. Electrical measurements\u0000carried out with eutectic GaIn top contacts showed current rectification ratios\u0000of up to ~200. The previously proposed rectification mechanism, relying on the\u0000protein's internal electric dipole, was inquired by measuring shifts in the\u0000work function. Our straightforward bottom-up fabrication method may allow for\u0000further experimental studies on PSI molecules, such as embedding them in\u0000solid-state, transparent top contact schemes for optoelectronic measurements.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213229","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}
Hyperuniform materials, characterized by their suppressed density fluctuations and vanishing structure factors as the wave number approaches zero, represent a unique state of matter that straddles the boundary between order and randomness. These materials exhibit exceptional optical, mechanical, and acoustic properties, making them of great interest in materials science and engineering. Traditional methods for creating hyperuniform structures, including collective-coordinate optimization and centroidal Voronoi tessellations, have primarily been computational and face challenges in capturing the complexity of naturally occurring systems. This study introduces a comprehensive theoretical framework to generate hyperuniform structures inspired by the collective organization of biological cells within an epithelial tissue layer. By adjusting parameters such as cell elasticity and interfacial tension, we explore a spectrum of hyperuniform states from fluid to rigid, each exhibiting distinct mechanical properties and types of density fluctuations. Our results not only advance the understanding of hyperuniformity in biological tissues but also demonstrate the potential of these materials to inform the design of novel materials with tailored properties.
{"title":"Tunable Hyperuniformity in Cellular Structures","authors":"Yiwen Tang, Xinzhi Li, Dapeng Bi","doi":"arxiv-2408.08976","DOIUrl":"https://doi.org/arxiv-2408.08976","url":null,"abstract":"Hyperuniform materials, characterized by their suppressed density\u0000fluctuations and vanishing structure factors as the wave number approaches\u0000zero, represent a unique state of matter that straddles the boundary between\u0000order and randomness. These materials exhibit exceptional optical, mechanical,\u0000and acoustic properties, making them of great interest in materials science and\u0000engineering. Traditional methods for creating hyperuniform structures,\u0000including collective-coordinate optimization and centroidal Voronoi\u0000tessellations, have primarily been computational and face challenges in\u0000capturing the complexity of naturally occurring systems. This study introduces\u0000a comprehensive theoretical framework to generate hyperuniform structures\u0000inspired by the collective organization of biological cells within an\u0000epithelial tissue layer. By adjusting parameters such as cell elasticity and\u0000interfacial tension, we explore a spectrum of hyperuniform states from fluid to\u0000rigid, each exhibiting distinct mechanical properties and types of density\u0000fluctuations. Our results not only advance the understanding of hyperuniformity\u0000in biological tissues but also demonstrate the potential of these materials to\u0000inform the design of novel materials with tailored properties.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"63 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213225","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}
Active liquid-liquid phase separation (LLPS) in a confining environment is believed to play an important role in cell biology. Recently, it was shown that when active noise at the microscopic level is included in the classical theory of nucleation and growth then this does not cause the breakdown of detailed balance at the textit{macroscopic} level provided that the droplet radius is the only collective coordinate. Here, we present a simple model for active LLPS in a confining environment, with the droplet location in a confining potential as a second collective coordinate, and find that detailed balance textit{is} broken at the macroscopic level in an unusual fashion, using the Fluctuation-Dissipation Theorem as a diagnostic.
{"title":"Active Liquid-Liquid Phase-Separation in a Confining Environment","authors":"Chen Lin, Robijn Bruinsma","doi":"arxiv-2408.07876","DOIUrl":"https://doi.org/arxiv-2408.07876","url":null,"abstract":"Active liquid-liquid phase separation (LLPS) in a confining environment is\u0000believed to play an important role in cell biology. Recently, it was shown that\u0000when active noise at the microscopic level is included in the classical theory\u0000of nucleation and growth then this does not cause the breakdown of detailed\u0000balance at the textit{macroscopic} level provided that the droplet radius is\u0000the only collective coordinate. Here, we present a simple model for active LLPS\u0000in a confining environment, with the droplet location in a confining potential\u0000as a second collective coordinate, and find that detailed balance textit{is}\u0000broken at the macroscopic level in an unusual fashion, using the\u0000Fluctuation-Dissipation Theorem as a diagnostic.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213226","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}
Tongzhao Xiong, Zhaorong Liu, Chong Jin Ong, Lailai Zhu
Microorganisms have evolved diverse strategies to propel in viscous fluids, navigate complex environments, and exhibit taxis in response to stimuli. This has inspired the development of synthetic microrobots, where machine learning (ML) is playing an increasingly important role. Can ML endow these robots with intelligence resembling that developed by their natural counterparts over evolutionary timelines? Here, we demonstrate chemotactic navigation of a multi-link articulated microrobot using two-level hierarchical reinforcement learning (RL). The lower-level RL allows the robot -- featuring either a chain or ring topology -- to acquire topology-specific swimming gaits: wave propagation characteristic of flagella or body oscillation akin to an ameboid. Such flagellar and ameboid microswimmers, further enabled by the higher-level RL, accomplish chemotactic navigation in prototypical biologically-relevant scenarios that feature conflicting chemoattractants, pursuing a swimming bacterial mimic, steering in vortical flows, and squeezing through tight constrictions. Additionally, we achieve reset-free, partially observable RL, where the robot observes only its joint angles and local scalar quantities. This advancement illuminates solutions for overcoming the persistent challenges of manual resets and partial observability in real-world microrobotic RL.
{"title":"Enabling microrobotic chemotaxis via reset-free hierarchical reinforcement learning","authors":"Tongzhao Xiong, Zhaorong Liu, Chong Jin Ong, Lailai Zhu","doi":"arxiv-2408.07346","DOIUrl":"https://doi.org/arxiv-2408.07346","url":null,"abstract":"Microorganisms have evolved diverse strategies to propel in viscous fluids,\u0000navigate complex environments, and exhibit taxis in response to stimuli. This\u0000has inspired the development of synthetic microrobots, where machine learning\u0000(ML) is playing an increasingly important role. Can ML endow these robots with\u0000intelligence resembling that developed by their natural counterparts over\u0000evolutionary timelines? Here, we demonstrate chemotactic navigation of a\u0000multi-link articulated microrobot using two-level hierarchical reinforcement\u0000learning (RL). The lower-level RL allows the robot -- featuring either a chain\u0000or ring topology -- to acquire topology-specific swimming gaits: wave\u0000propagation characteristic of flagella or body oscillation akin to an ameboid.\u0000Such flagellar and ameboid microswimmers, further enabled by the higher-level\u0000RL, accomplish chemotactic navigation in prototypical biologically-relevant\u0000scenarios that feature conflicting chemoattractants, pursuing a swimming\u0000bacterial mimic, steering in vortical flows, and squeezing through tight\u0000constrictions. Additionally, we achieve reset-free, partially observable RL,\u0000where the robot observes only its joint angles and local scalar quantities.\u0000This advancement illuminates solutions for overcoming the persistent challenges\u0000of manual resets and partial observability in real-world microrobotic RL.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213227","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}
Inspired by protein folding, we explored the construction of three-dimensional structures and machines from one-dimensional chains of simple building blocks. This approach not only allows us to recreate the self-replication mechanism introduced earlier, but also significantly simplifies the process. We introduced a new set of folding blocks that facilitate the formation of secondary structures such as {alpha}-helices and b{eta}-sheets, as well as more advanced tertiary and quaternary structures, including self-replicating machines. The introduction of rotational degrees of freedom leads to a reduced variety of blocks and, most importantly, reduces the overall size of the machines by a factor of five. In addition, we present a universal copier-constructor, a highly efficient self-replicating mechanism composed of approximately 40 blocks, including the restictions posed on it. The paper also addresses evolutionary considerations, outlining several steps on the evolutionary ladder towards more sophisticated self-replicating systems. Finally, this study offers a clear rationale for nature's preference for one-dimensional chains in constructing three-dimensional structures.
{"title":"Self-folding Self-replication","authors":"Ralph P. Lano","doi":"arxiv-2408.07154","DOIUrl":"https://doi.org/arxiv-2408.07154","url":null,"abstract":"Inspired by protein folding, we explored the construction of\u0000three-dimensional structures and machines from one-dimensional chains of simple\u0000building blocks. This approach not only allows us to recreate the\u0000self-replication mechanism introduced earlier, but also significantly\u0000simplifies the process. We introduced a new set of folding blocks that\u0000facilitate the formation of secondary structures such as {alpha}-helices and\u0000b{eta}-sheets, as well as more advanced tertiary and quaternary structures,\u0000including self-replicating machines. The introduction of rotational degrees of\u0000freedom leads to a reduced variety of blocks and, most importantly, reduces the\u0000overall size of the machines by a factor of five. In addition, we present a\u0000universal copier-constructor, a highly efficient self-replicating mechanism\u0000composed of approximately 40 blocks, including the restictions posed on it. The\u0000paper also addresses evolutionary considerations, outlining several steps on\u0000the evolutionary ladder towards more sophisticated self-replicating systems.\u0000Finally, this study offers a clear rationale for nature's preference for\u0000one-dimensional chains in constructing three-dimensional structures.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213228","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}
All life forms are miraculous, but some are more inexplicable than others. Trypanosomes are by far one of the most puzzling organisms on Earth: their mitochondrial genome, also called kinetoplast DNA (kDNA) forms an Olympic-ring-like network of interlinked DNA circles, challenging conventional paradigms in both biology and physics. In this review, I will discuss kDNA from the astonished perspective of a polymer physicist and tell a story of how a single sub-celluar structure from a blood-dwelling parasite is inspiring generations of polymer chemists and physicists to create new catenated materials.
锥虫是迄今为止地球上最令人费解的生物之一：它们的半软核基因组（又称动粒 DNA（kDNA））形成了一个由相互连接的 DNA 圈组成的奥林匹克环状网络，挑战了生物学和物理学的传统范式。在这篇综述中，我将从一个高分子物理学家的惊奇视角来讨论 kDNA，并讲述一个故事：一个来自血栖寄生虫的亚细胞结构是如何激励一代又一代的高分子化学家和物理学家去创造新的复合材料的。
{"title":"Kinetoplast DNA: a polymer physicist's Olympic dream","authors":"Davide Michieletto","doi":"arxiv-2408.05978","DOIUrl":"https://doi.org/arxiv-2408.05978","url":null,"abstract":"All life forms are miraculous, but some are more inexplicable than others.\u0000Trypanosomes are by far one of the most puzzling organisms on Earth: their\u0000mitochondrial genome, also called kinetoplast DNA (kDNA) forms an\u0000Olympic-ring-like network of interlinked DNA circles, challenging conventional\u0000paradigms in both biology and physics. In this review, I will discuss kDNA from\u0000the astonished perspective of a polymer physicist and tell a story of how a\u0000single sub-celluar structure from a blood-dwelling parasite is inspiring\u0000generations of polymer chemists and physicists to create new catenated\u0000materials.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213231","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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