arXiv - PHYS - Biological Physics最新文献_第6页

A Comparative Study of Neutron Irradiation for Genetic Mutations: Spallation, Reactor, and Compact Neutron Source 中子辐照基因突变的比较研究：溅射、反应堆和紧凑型中子源

arXiv - PHYS - Biological Physics Pub Date : 2024-08-20 DOI: arxiv-2408.10929

May Sweet, Kenji Mishima, Masahide Harada, Keisuke Kurita, Hiroshi Iikura, Seiji Tasaki, Norio Kikuchi

{"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":null,"pages":null},"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}

引用次数: 0

Physical limits on chemical sensing in bounded domains 有界域中化学传感的物理限制

arXiv - PHYS - Biological Physics Pub Date : 2024-08-20 DOI: arxiv-2408.10745

Daniel R. McCusker, David K. Lubensky

{"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":null,"pages":null},"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}

引用次数: 0

Exploring the Thermostability of CRISPR Cas12b using Molecular Dynamics Simulations 利用分子动力学模拟探索 CRISPR Cas12b 的耐热性

arXiv - PHYS - Biological Physics Pub Date : 2024-08-20 DOI: arxiv-2408.11149

Yinhao Jia, Katelynn Horvath, Santosh R. Rananaware, Piyush K. Jain, Janani Sampath

{"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":null,"pages":null},"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}

引用次数: 0

Solution landscape of reaction-diffusion systems reveals a nonlinear mechanism and spatial robustness of pattern formation 反应-扩散系统的解景观揭示了模式形成的非线性机制和空间稳健性

arXiv - PHYS - Biological Physics Pub Date : 2024-08-19 DOI: arxiv-2408.10095

Shuonan Wu, Bing Yu, Yuhai Tu, Lei Zhang

引用次数: 0

Current rectification via Photosystem I monolayers induced by their orientation on hydrophilic self-assembled monolayers on titanium nitride 氮化钛上亲水自组装单层的取向诱导光系统 I 单层实现电流整流

arXiv - PHYS - Biological Physics Pub Date : 2024-08-17 DOI: arxiv-2408.09276

Jonathan Rojas, Zhe Wang, Feng Liu, Jerry A. Fereiro, Domenikos Chryssikos, Thomas Dittrich, Dario Leister, David Cahen, Marc Tornow

{"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":null,"pages":null},"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}

引用次数: 0

Tunable Hyperuniformity in Cellular Structures 细胞结构中的可调超均匀性

arXiv - PHYS - Biological Physics Pub Date : 2024-08-16 DOI: arxiv-2408.08976

Yiwen Tang, Xinzhi Li, Dapeng Bi

{"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":null,"pages":null},"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}

引用次数: 0

Active Liquid-Liquid Phase-Separation in a Confining Environment 密闭环境中的活性液-液相分离

arXiv - PHYS - Biological Physics Pub Date : 2024-08-15 DOI: arxiv-2408.07876

Chen Lin, Robijn Bruinsma

引用次数: 0

Enabling microrobotic chemotaxis via reset-free hierarchical reinforcement learning 通过无重置分层强化学习实现微机器人趋化

arXiv - PHYS - Biological Physics Pub Date : 2024-08-14 DOI: arxiv-2408.07346

Tongzhao Xiong, Zhaorong Liu, Chong Jin Ong, Lailai Zhu

{"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":null,"pages":null},"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}

引用次数: 0

Self-folding Self-replication 自我折叠自我复制

arXiv - PHYS - Biological Physics Pub Date : 2024-08-13 DOI: arxiv-2408.07154

Ralph P. Lano

{"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":null,"pages":null},"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}

引用次数: 0

Kinetoplast DNA: a polymer physicist's Olympic dream Kinetoplast DNA：高分子物理学家的奥运梦想

arXiv - PHYS - Biological Physics Pub Date : 2024-08-12 DOI: arxiv-2408.05978

Davide Michieletto

引用次数: 0