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biological physics

GeneTech 知识引擎共收录 667 篇相关科研实体，横跨 29 个垂直领域。数据来自 OpenAlex、arXiv、Crossref、PubMed、Europe PMC 等公开学术源，全部可溯源到原文。

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代表性文献（按质量分排序，前 60 条）

• Dynamic Operations in Macromolecular Data Storage.
  2026 · 生物计算 · In recent years, numerous concepts have been reported for storing data on molecules, either small molecule mixtures, oligomer libraries or polymers. In the latter case, binary information is stored in a controlled monome…
• Reaching agreement in competitive microbial systems
  2026 · 生物计算 · Abstract We study distributed agreement in microbial distributed systems under stochastic population dynamics and competitive interactions. Motivated by recent applications in synthetic biology, we examine how the presen…
• Mathematical Modeling Of Substrate And Product Inhibition Kinetics With Diffusion Limitation In The Amperometric Biosensor At Spherical Micro Reactions
  2026 · 生物计算 · This study presents a mathematical model of a non-steady-state amperometric biosensor with combined enzyme kinetics and diffusion restrictions, under substrate and product inhibition. An enzymatic reaction with non-Micha…
• Smart Agricultural BOT for Automated Seed Sowing and Soil Monitoring in Organic Farming
  2025 · 智慧农业 · A variety of activities such as to sow seeds, to cut weeds and unwanted plants are performed in the fields on daily basis. The existing methods to do sowing, plowing and weed cutting are very time consuming and very hard…
• Were heterochiral polymers relevant in primordial and extraterrestrial life scenarios?
  2025 · 地外矿物 · Agent-based simulations are employed to describe the early biological selection of oligomers made of monomers with different chirality. These simulations consider the spatial distribution of agents and resources, the bal…
• Design Principles for Polymerase Strand Recycling Circuits
  2025 · 生物计算 · Cell-free biosensing systems are being engineered as versatile and programmable diagnostic technologies. A core component of cell-free biosensors are programmable molecular circuits that improve biosensor speed, sensitiv…
• Correcting force error-induced underestimation of lattice thermal conductivity in machine learning molecular dynamics.
  2024 · AI 驱动科学发现 · Machine learned potentials (MLPs) have been widely employed in molecular dynamics simulations to study thermal transport. However, the literature results indicate that MLPs generally underestimate the lattice thermal con…
• Improved prediction of site‐rates from structure with averaging across homologs
  2024 · AI 驱动科学发现 · Abstract Variation in mutation rates at sites in proteins can largely be understood by the constraint that proteins must fold into stable structures. Models that calculate site‐specific rates based on protein structure a…
• Spatial and dynamic distribution of Chrysoperla spp. and Leucoptera coffeella populations in coffee Coffea arabica L
  2023 · 智慧农业 · Leucoptera coffeella (Guérin-Mèneville, 1842) (Lepidoptera: Lyonetiidae) is one of the main pests of coffee. Controlling this insect requires effective management methods, prevention of insecticide resistance from overus…
• Analysis of Steady-State Amperometric Biosensor with the Carbon Paste Electrode Using Physics-Informed Neural Network, AGM and TSM
  2025 · 生物计算 · The analytical model of the mediated bioelectrocatalysis is proposed in this paper. This model is based on a coupled steady-state nonlinear reaction–diffusion equations. In this model, we have also considered the effect …
• Machine Learning-based High-Dimensional Text Document Classification and Clustering
  2025 · 医疗人工智能 · Text classification is a difficult technique. Many techniques have been developed to decrease the dimension of feature vectors for use in text classification due to their enormous size. This work provides a detailed disc…
• Islet: interpolation semi-Lagrangian element-based transport
  2022 · 生物计算 · Abstract. Advection of trace species, or tracers, also called tracer transport, in models of the atmosphere and other physical domains is an important and potentially computationally expensive part of a model's dynamical…
• Machine Learning of Atomic Forces from Quantum Mechanics: a Model Based on Pairwise Interatomic Forces
  2021 · AI 驱动科学发现 · We present a new chemically intuitive approach, pairF-Net, to directly predict the atomic forces in a molecule to quantum chemistry accuracy using machine learning techniques. A residual artificial neural network has bee…
• A Formal Account of Structuring Motor Actions With Sensory Prediction for a Naive Agent
  2020 · AI Agent 生态 · For naive robots to become truly autonomous, they need a means of developing their perceptive capabilities instead of relying on hand crafted models. The sensorimotor contingency theory asserts that such a way resides in…
• Analysis of Circuits for Dosage Control in Microbial Populations
  2020 · 生物计算 · Designing genetic circuits to control the behaviors of microbial populations is an ongoing challenge in synthetic biology. Here we analyze circuits which implement dosage control by controlling levels of a global signal …
• Structure prediction of alternative protein conformations
  2024 · AI 驱动科学发现 · Abstract Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations…
• Limits on the Evolutionary Rates of Biological Traits
  2024 · 生物计算 · This paper focuses on the maximum speed at which biological evolution can occur.I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift.These rate limi…
• Structure prediction of alternative protein conformations
  2023 · AI 驱动科学发现 · Abstract Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins in the conformatio…
• Multiple-Valued DNA Computing
  2023 · 生物计算 · Molecular computing, or DNA (Deoxyribose Nucleic Acid) computing, is a new discipline of computer science. It s a novel method for massively parallel computation that can tackle NP-complete or non-deterministic polynomia…
• Informed Self-organization
  2023 · 生物计算 · Abstract This chapter is a brief, non-orthodox introduction into molecular biology. As the Nobel Laureate Sidney Brenner wrote: ‘Biology is essentially (very low energy) physics with computations’. The chapter shows how …
• DNA Reservoir Computing: A Novel Molecular Computing Approach
  2013 · 生物计算 · We propose a novel molecular computing approach based on reservoir computing. In reservoir computing, a dynamical core, called a reservoir, is perturbed with an external input signal while a readout layer maps the reserv…
• Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction
  2019 · AI 驱动科学发现 · Due to the advancement in various sequencing technologies, the gap between the number of protein sequences and the number of experimental protein structures is ever increasing. Community-wide initiatives like CASP have r…
• Growth defects and loss-of-function in synthetic gene circuits
  2019 · 生物计算 · Abstract Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts the equilibrium of resource allocation in the host, leading to slow growth and reduced biosynt…
• Finite element analysis for turbine foundation under static loading condition with different soil model
  2018 · AI 驱动科学发现 · In recent year, the soil-structure interaction (SSI) has been the topic of considerable research interest. Many researchers have been targeted to study the response of the soil under different loading cases. In many situ…
• Computing framework in biological cells via stochastic methods
  2018 · 生物计算 · In this paper, we propose using stochastic framework for computations by biological cells. The key observation is that the input molecules activate receptors of a biological cell independently with probability p that is …
• Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel
  2018 · 生物计算 · Voltage-gated sodium channels undergo transitions between open, closed, and inactivated states, enabling regulation of the translocation of sodium ions across membranes. A recently published crystal structure of the full…
• Synthetic negative feedback circuits using engineered small RNAs
  2017 · 生物计算 · ABSTRACT Negative feedback is known to endow biological and man-made systems with robust performance in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have relied upon protein…
• Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox
  2012 · AI 驱动科学发现 · A protein molecule is a covalent chain of amino acid residues. Although it is topologically linear, in physiological conditions it folds into a unique (though flexible) three-dimensional structure. This structure, which …
• Relating Protein Structure and Function Through a Bijection and Its Implications on Protein Structure Prediction
  2012 · AI 驱动科学发现 · Proteins are studied by measuring different properties, typically the chemical structure and biochemical activity. Given that these measurements are done on the same protein molecule, they must be related. Despite the fa…
• Protein Structure Prediction by Protein Threading
  2010 · AI 驱动科学发现 · The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on “the inverse protein folding problem” laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness…
• On the lower bounds of DNA word sets for DNA computing
  2009 · 生物计算 · DNA computing is a new research field, which has been paid attention to by more and more experts with the DNA computing bringing the flying development of mathematics, computer science and other subjects. Because the DNA…
• Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment
  2008 · AI 驱动科学发现 · Primary amino acid content and the geometry of the folded protein 3D structure are major parameters of protein function. During the course of evolution the protein 3D structure is more preserved than its primary sequence…
• Symbolic representations of biological oscillations
  2008 · 生物计算 · The investigation of biological dynamics involves many interesting aspects such as abstraction, modelling and simulation, but a very important aspect to consider is the representation of such dynamics. A correct, flexibl…
• Biological Model of Flagella Motor
  2008 · 生物计算 · We proposed a sample of stochastic motor, which moved by using principle of stochastic resonance. First we introduced Lagrangian, having dissipative terms caused by water molecules. Using Eular-Lagrange method, we got th…
• Scoring Functions for ab initio Protein Structure Prediction
  2003 · AI 驱动科学发现 · The native conformation of a protein is generally assumed to be the one with the lowest free energy ( 1 ). The successful prediction of protein structure depends on the surmounting of three subproblems: (1) choosing a re…
• AI-derived Protein Structures Validation: AlphaFold2 Models in the Twilight Zone
  2026 · AI 安全与对齐 · In any field, unquestioningly accepting artificial intelligence (AI) results should be considered bad practise. Here, we devised a comparative modelling-based strategy for validating protein structures that exploits the …
• The accuracy of electrostatic interactions captured by AI protein structure prediction models.
  2026 · AI 驱动科学发现 · A variant of the U1A protein containing four substitutions to ionizable residues was generated serendipitously due to a miscommunication. Biophysical measurements reveal this variant has twice the helical structure of wi…
• Do AI Models for Protein Structure Prediction Get Electrostatics Right?
  2026 · AI 驱动科学发现 · A variant of the U1A protein containing four substitutions to ionizable residues was generated serendipitously due to a miscommunication. Biophysical measurements show that this variant has at least twice as much helical…
• Co-folding of Membrane Proteins and Lipid Molecules Improves Membrane-Protein Structure Prediction Accuracy
  2026 · AI 驱动科学发现 · Recent advances in deep-learning-based structure prediction have greatly improved the accuracy of protein structure modeling and enabled prediction of biomolecular complexes. However, the surrounding molecular environmen…
• Programmable 2D-to-3D structural transformation of DNA nanostructures triggered by single-stranded RNA.
  2026 · AI 驱动科学发现 · Controllable structural transformation of DNA nanostructures offers substantial potential for molecular devices. Toehold-mediated strand displacement, a common strategy for driving such rearrangements, generally requires…
• Learning Electronic Polarization in Molecular Systems: Vibrational Spectroscopy of Ethanol-Water Mixtures.
  2026 · AI 驱动科学发现 · Mixtures of water and ethanol are an important solvent for biochemical reactions, as well as being a model system for hydrophobic hydration, since the ethanol molecule consists of polar and nonpolar regions. Experiments …
• Transferable generative models bridge femtosecond to nanosecond time-step molecular dynamics.
  2026 · AI 驱动科学发现 · Understanding the molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated timescales. Conventional molecular dynamics simulations provide an atomistic resolution, but …
• Examining Genetic Variants Associated with FOXP1 Syndrome through Molecular Dynamics of Its DNA-Binding Domain and Self-Organizing Maps.
  2026 · AI 驱动科学发现 · Genetic mutations in the transcription factor FOXP1 (forkhead box protein P1) cause an autosomal dominant neurodevelopmental disorder called FOXP1 syndrome. To understand the structural impact of pathogenic variants asso…
• Ultrafast solvent-modulated roaming mechanism in bromoform revealed by femtosecond X-ray solution scattering.
  2026 · AI 驱动科学发现 · Roaming-mediated isomerization is a universal reaction mechanism in photochemistry, yet solvent-dependent pathways of roaming intermediates remain poorly understood, particularly for environmentally relevant halogen comp…
• Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.
  2026 · 生物计算 · Conformational and configurational states of the sugar-phosphate backbone play an important role in DNA transcriptional and RNA translational events. In particular, the geometric parameters of the sugar ring dictate the …
• Revisiting the Conformational Flexibility of DNA 3-Arm Junctions for Nanoconstruction.
  2026 · 生物计算 · Programmed DNA self-assembly, based on branched DNA structures, provides a general approach for constructing defined nanostructures for drug delivery, biosensing, nanofabrication, and information processing and storage. …
• Estimation of Absolute Protein-DNA Binding Free Energy Using Streamlined Geometric Formalism.
  2026 · 生物计算 · Protein-DNA complexes are involved in vital cellular functions such as gene regulation, replication, transcription, packaging, rearrangement, and damage repair. In this work, we proposed an intricate streamlined geometri…
• Codepoietic biological evolution: From the origin of life to eukaryogenesis.
  2026 · 生物计算 · Evolution is an intrinsic property of autopoietic systems performing natural computation, which is based on an internal formal self-description representing the arrangement of digital and analog coding structures. Autopo…
• Solvation Shapes the Conformational Landscape of a Therapeutically Relevant SMN2 Splice-Site Defect
  2026 · 生物计算 · The SMN2 exon 7 5’ splice-site/U1 snRNA duplex contains an A −1 bulge that weakens splice-site recognition and represents a therapeutically relevant RNA connectivity defect, yet its conformational landscape and coupling …
• Photocytotoxic action of cyanine dye with two chromophores. Formation of superoxide anion radical.
  2026 · 生物计算 · This study investigates how a bis-cyanine dye (BCD) induces light-triggered cytotoxicity in human colorectal cancer HCT116 cells. The photodynamic therapy mechanism was investigated using optical absorption, steady-state…
• Atomistic simulations reveal the photoactivation mechanism of a carotenoid-binding photoreceptor.
  2026 · 生物计算 · The orange carotenoid protein (OCP) is a key photoreceptor in the photoprotection of cyanobacterial antenna complexes. Its peculiar activity is governed by a bound keto-carotenoid that functions both as a light sensor an…
• Engineered Optogenetic Circuits In Yeast with Self-Sustained Outputs.
  2026 · 生物计算 · Optoswitches are of particular interest to the metabolic engineering community, as light has a superior advantage of tunability and reversibility. However, the light-shading effect at industrial scales remains an unsolve…
• Fast, long-range intercellular signal propagation through growth-assisted positive feedback.
  2026 · 生物计算 · Intercellular signaling in bacteria is often mediated by small molecules secreted by cells. These small molecules disperse via diffusion, which limits the speed and spatial extent of information transfer in spatially ext…
• Fuel-driven catalytic molecular templating
  2026 · 生物计算 · Catalytic molecular templating, wherein a copolymer molecule serves as a sequence-specific template to propagate genetic information to a daughter copolymer, is fundamental to cells. Templating underlies DNA replication,…
• Membrane Protein Insertion in Cells: Principles, Pathways, and Quality Control.
  2026 · 生物计算 · Integral membrane proteins comprise at least a quarter of every proteome. To fold and function properly, these proteins must insert into the correct membrane with the proper topology and orientation. Although their trans…
• Thiol post-translational modifications modulate allosteric regulation of the OpcA-G6PDH complex through conformational gate control.
  2026 · 生物计算 · In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux betwee…
• Dynamics of attractor transitions in Boolean networks under noise.
  2026 · 生物计算 · Biological systems operate under persistent noise, which can alter system states and induce transitions between attractors. Here, we study the attractor dynamics of Boolean networks focusing on the transitions between at…
• Probing the dark energy in the functional protein universe.
  2026 · 生物计算 · We show how to localize and quantify the functional evolutionary constraints on natural proteins. Protein folding has been one of the strongest constraints in sequence evolution. The method we propose compares the pertur…
• Harnessing biological variability for mechanistic inference: A stochastic framework applied to neural stem cell dynamics.
  2026 · 生物计算 · Inter-individual heterogeneity is often treated as noise, yet its temporal evolution can reveal regulatory mechanisms hidden from mean-field behavior. We present a stochastic framework that exploits variability for mecha…
• Etv5 Is Required for Proper Maturation and Dendritic Development of Adult-Born Granule Cells in the Dentate Gyrus.
  2026 · 脑科学 · Adult neurogenesis in the dentate gyrus (DG) of the hippocampus is a dynamic and tightly regulated process that is finely regulated by a diverse array of transcription factors. While the transcription factor Etv5, a memb…

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