bims-enlima Biomed News
on Engineered living materials
Issue of 2025–02–23
forty-nine papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Metabolite-Responsive Control of Transcription by Phase Separation-Based Synthetic Organelles.
  2. Light-Modulated Self-Assembly of Synthetic Nanotubes.
  3. Solving Challenges in Microalgae-Based Living Materials.
  4. Interfacing bacterial microcompartment shell proteins with genetically encoded condensates.
  5. Engineering multifunctional surface topography to regulate multiple biological responses.
  6. Highly Extensible Physically Crosslinked Hydrogels for High-Speed 3D Bioprinting.
  7. Logic-Gated Modulation of Cell Migration via Mesoscale Mechanical Uncaging Effects.
  8. Bioinspired Materials for Controlling Mineral Adhesion: From Innovation Design to Diverse Applications.
  9. Bio-inspired electronics: Soft, biohybrid, and "living" neural interfaces.
  10. Split-Small GTPase Reassembly as a Method to Control Cellular Signaling with User-Defined Inputs.
  11. Micromechanical finite element modeling of crystalline lipid-based materials: monoglyceride-based oleogels and their composites.
  12. An engineered aldolase enables the biocatalytic synthesis of 2'-functionalized nucleoside analogues.
  13. Contextual computation by competitive protein dimerization networks.
  14. Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria.
  15. Generalizable Molecular Switch Designs for In Vivo Continuous Biosensing.
  16. Bacterial microcompartment architectures as biomaterials for conversion of gaseous substrates.
  17. Why is it so hard to rewrite a genome?
  18. Mussel-inspired cross-linking mechanisms enhance gelation and adhesion of multifunctional mucin-derived hydrogels.
  19. Microfluidic 3D Bioprinting of Foamed Fibers with Controlled Micromorphology.
  20. Spatio-temporal control of mitosis using light via a Plk1 inhibitor caged for activity and cellular permeability.
  21. Biodegradable Chitosan-Based Stretchable Electronics with Recyclable Silver Nanowires.
  22. Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage.
  23. Oblique line scan illumination enables expansive, accurate and sensitive single-protein measurements in solution and in living cells.
  24. Charge density on fracture surfaces and contact electrification of identical materials.
  25. Multiplex mapping of protein-protein interaction interfaces.
  26. Coarse-grained fundamental forms for characterizing isometries of trapezoid-based origami metamaterials.
  27. A Retropepsin-Like Bacterial Protease Regulates Ribosome Modification and Polypeptide Production.
  28. Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves.
  29. Alpha ketoacid decarboxylases: Diversity, structures, reaction mechanisms, and applications for biomanufacturing of platform chemicals and fuels.
  30. Snapshots of acyl carrier protein shuttling in human fatty acid synthase.
  31. Proteomic Ligandability Maps of Phosphorus(V) Stereoprobes Identify Covalent TLCD1 Inhibitors.
  32. Flow of Energy and Information in Molecular Machines.
  33. Emergence of binding and catalysis from a designed generalist binding protein.
  34. Hydrogel-Based Strategies for Liver Tissue Engineering.
  35. Interparticle Crosslinked Ion-responsive Microgels for 3D and 4D (Bio)printing Applications.
  36. Origins of elasticity in molecular materials.
  37. Magnetic activation of electrically active cells.
  38. Characterizing heterologous protein burden in Komagataella phaffii.
  39. Conductive hydrophobic graphene oxide films via laser-scribed surface modification.
  40. Single-Step Fabrication of V-Shaped Polymeric Microwells to Enhance Cancer Spheroid Formation.
  41. Antibacterial Polymers Based on Two Orthogonal Binding Motifs Coalesce with Bacterial Matter.
  42. Redefining Metal Organic Frameworks in Biosensors: Where Are We Now?
  43. Liposome-Encapsulated Escherichia coli Lysates to Reconstitute Intracellular Macromolecular Crowding Effects.
  44. Two dimensional MoS2 accelerates mechanically controlled polymerization and remodeling of hydrogel.
  45. A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.
  46. Framing synthetic biology as an innovation-driven market.
  47. Genetically Encoded Single-Wavelength Sensor with High Specificity for Imaging ATP in Living Cells.
  48. The Biology of Natural Polymers Accelerates and Expands the Science of Biomacromolecules: A Focus on Structural Proteins.
  49. Scaling in Biological Systems: A Molecular-Ensemble Duality.
  1. ACS Synth Biol. 2025 Feb 15.
    Metabolite-Responsive Control of Transcription by Phase Separation-Based Synthetic Organelles.
    Carolina Jerez-Longres, Wilfried Weber.
      Living natural materials have remarkable sensing abilities that translate external cues into functional changes of the material. The reconstruction of such sensing materials in bottom-up synthetic biology provides the opportunity to develop synthetic materials with life-like sensing and adaptation ability. Key to such functions are material modules that translate specific input signals into a biomolecular response. Here, we engineer a synthetic organelle based on liquid-liquid phase separation that translates a metabolic signal into the regulation of gene transcription. To this aim, we engineer the pyruvate-dependent repressor PdhR to undergo liquid-liquid phase separation in vitro by fusion to intrinsically disordered regions. We demonstrate that the resulting coacervates bind DNA harboring PdhR-responsive operator sites in a pyruvate dose-dependent and reversible manner. We observed that the activity of transcription units on the DNA was strongly attenuated following recruitment to the coacervates. However, the addition of pyruvate resulted in a reversible and dose-dependent reconstitution of transcriptional activity. The coacervate-based synthetic organelles linking metabolic cues to transcriptional signals represent a materials approach to confer stimulus responsiveness to minimal bottom-up synthetic biological systems and open opportunities in materials for sensor applications.
    Keywords:  coacervate; in vitro transcription; intrinsically disordered region; liquid−liquid phase separation; repressor protein
    DOI:  https://doi.org/10.1021/acssynbio.4c00633
  2. Nano Lett. 2025 Feb 17.
    Light-Modulated Self-Assembly of Synthetic Nanotubes.
    Mahdi Dizani, Siddharth Agarwal, Dino Osmanovic, Elisa Franco.
      Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to the development of living materials and synthetic cells. Here, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain so that UV irradiation activates nanotube self-assembly. We demonstrate that the nanotube formation speed can be tuned by adjusting the UV dose. We then couple the light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to building biomolecular scaffolds with controllable dynamics in response to multiple stimuli.
    Keywords:  Cytoskeleton; DNA nanotechnology; Nanotubes; Nucleic acids; Photoactivation; Synthetic cells
    DOI:  https://doi.org/10.1021/acs.nanolett.4c05452
  3. ACS Synth Biol. 2025 Feb 21. 14(2): 307-315
    Solving Challenges in Microalgae-Based Living Materials.
    Friedrich Hans Kleiner, Jeong-Joo Oh, Marie-Eve Aubin-Tam.
      Engineered living materials (ELMs) integrate aspects of material science and biology into a unique platform, leading to materials and devices with features of life. Among those, ELMs containing microalgae have received increased attention due to the many benefits photosynthetic organisms provide. Due to their relatively recent occurrence, photosynthetic ELMs still face many challenges related to reliability, lifetime, scalability, and more, often based on the complicated crosstalk of cellular, material-based, and environmental variables in time. This Viewpoint aims to summarize potential avenues for improving ELMs, beginning with an emphasis on understanding the cell's perspective and the potential stresses imposed on them due to recurring flaws in many current ELMs. Potential solutions and their ease of implementation will be discussed, ranging from choice of organism, adjustments to the ELM design, to various genetic modification tools, so as to achieve ELMs with longer lifetime and improved functionality.
    Keywords:  Microalgae; engineered living materials; genetic modification; living hydrogel; photosynthesis; stress responses
    DOI:  https://doi.org/10.1021/acssynbio.4c00683
  4. Protein Sci. 2025 Mar;34(3): e70061
    Interfacing bacterial microcompartment shell proteins with genetically encoded condensates.
    Michele Costantino, Eric J Young, Abesh Banerjee, Cheryl A Kerfeld, Giovanna Ghirlanda.
      Condensates formed by liquid-liquid phase separation are promising candidates for the development of synthetic cells and organelles. Here, we show that bacterial microcompartment shell proteins from Haliangium ochraceum (BMC-H) assemble into coatings on the surfaces of protein condensates formed by tandem RGG-RGG domains, an engineered construct derived from the intrinsically disordered region of the RNA helicase LAF-1. WT BMC-H proteins formed higher-order assemblies within RGG-RGG droplets; however, engineered BMC-H variants fused to RGG truncations formed coatings on droplet surfaces. These intrinsically disordered tags controlled the interaction with the condensed phase based on their length and sequence, and one of the designs, BMC-H-T2, assembled preferentially on the surface of the droplet and prevented droplet coalescence. The formation of the coatings is dependent on the pH and protein concentration; once formed, the coatings are stable and do not exchange with the dilute phase. Coated droplets could sequester and concentrate folded proteins, including TEV protease, with selectivity similar to uncoated droplets. Addition of TEV protease to coated droplets resulted in the digestion of RGG-RGG to RGG and a decrease in droplet diameter, but not in the dissolution of the coatings. BMC shell protein-coated protein condensates are entirely encodable and provide a way to control the properties of liquid-liquid phase-separated compartments in the context of synthetic biology.
    Keywords:  bacterial microcompartments; compartmentalization; liquid–liquid phase separation; self‐assembly; synthetic biology
    DOI:  https://doi.org/10.1002/pro.70061
  5. Biomaterials. 2025 Jan 28. pii: S0142-9612(25)00055-9. [Epub ahead of print]319 123136
    Engineering multifunctional surface topography to regulate multiple biological responses.
    Mohammad Asadi Tokmedash, Changheon Kim, Ajay P Chavda, Adrian Li, Jacob Robins, Jouha Min.
      Surface topography or curvature plays a crucial role in regulating cell behavior, influencing processes such as adhesion, proliferation, and gene expression. Recent advancements in nano- and micro-fabrication techniques have enabled the development of biomimetic systems that mimic native extracellular matrix (ECM) structures, providing new insights into cell-adhesion mechanisms, mechanotransduction, and cell-environment interactions. This review examines the diverse applications of engineered topographies across multiple domains, including antibacterial surfaces, immunomodulatory devices, tissue engineering scaffolds, and cancer therapies. It highlights how nanoscale features like nanopillars and nanospikes exhibit bactericidal properties, while many microscale patterns can direct stem cell differentiation and modulate immune cell responses. Furthermore, we discuss the interdisciplinary use of topography for combined applications, such as the simultaneous regulation of immune and tissue cells in 2D and 3D environments. Despite significant advances, key knowledge gaps remain, particularly regarding the effects of topographical cues on multicellular interactions and dynamic 3D contexts. This review summarizes current fabrication methods, explores specific and interdisciplinary applications, and proposes future research directions to enhance the design and utility of topographically patterned biomaterials in clinical and experimental settings.
    Keywords:  Biofilm control; Biomaterials; Cancer treatment; Immunomodulation; Surface topography; Tissue engineering
    DOI:  https://doi.org/10.1016/j.biomaterials.2025.123136
  6. Adv Healthc Mater. 2025 Feb 16. e2404988
    Highly Extensible Physically Crosslinked Hydrogels for High-Speed 3D Bioprinting.
    Ye Eun Song, Noah Eckman, Samya Sen, Carolyn K Jons, Olivia M Saouaf, Eric A Appel.
      Hydrogels have emerged as promising materials for bioprinting and many other biomedical applications due to their high degree of biocompatibility and ability to support and/or modulate cell viability and function. Yet, many hydrogel bioinks have suffered from low efficiency due to limitations on accessible printing speeds, often limiting cell viability and/or the constructs which can be generated. In this study, a highly extensible bioink system created by modulating the rheology of physically crosslinked hydrogels comprising hydrophobically-modified cellulosics and either surfactants or cyclodextrins is reported. It is demonstrated that these hydrogels are highly shear-thinning with broadly tunable viscoelasticity and stress-relaxation through simple modulation of the composition. Rheological experiments demonstrate that increasing concentration of rheology-modifying additives yields hydrogel materials exhibiting extensional strain-to-break values up to 2000%, which is amongst the most extensible examples of physically crosslinked hydrogels of this type. The potential of these hydrogels for use as bioinks is demonstrated by evaluating the relationship between extensibility and printability, demonstrating that greater hydrogel extensibility enables faster print speeds and smaller print features. The findings suggest that optimizing hydrogel extensibility can enhance high-speed 3D bioprinting capabilities, reporting over 5000 fold enhancement in speed index compared to existing works reported for hydrogel-based bioinks in extrusion-based printing.
    Keywords:  3D printing; extensibility; hydrogel; stress relaxation; viscoelasticity
    DOI:  https://doi.org/10.1002/adhm.202404988
  7. ACS Nano. 2025 Feb 20.
    Logic-Gated Modulation of Cell Migration via Mesoscale Mechanical Uncaging Effects.
    Deepak Karna, Shin Watanabe, Grinsun Sharma, Arpit Sharma, Yaorong Zheng, Ibuki Kawamata, Yuki Suzuki, Hanbin Mao.
      Mesoscopic objects ranging from molecular machinery to cells are prevalent in nature. Unlike atomic and nanoscopic objects that do not have pronounced mechanical properties due to their small sizes, mesoscale substances demonstrate their unique mechanical features that can interfere with cell functions, particularly those with a mechanical nature such as cell migrations. Here, we demonstrate mechanical caging/uncaging effects in a DNA origami nanospring system that precisely controls cancer cell migrations. By leveraging DNA as a programming language, our work demonstrates the creation of logic gates (Boolean AND and OR gates) responsive to various miRNA inputs, resulting in mechanical and structural changes in DNA origami nanosprings serving as processors, which uncage the arginyl-glycyl-aspartate (RGD) ligands to interact with integrins on the cell membrane surface. The mechanical uncaging effect inhibits the migration of cancer cells. The strategy can be readily harnessed for targeted drug delivery with minimal off-target effects. Our proof-of-concept mesoscale DNA origami self-assembly highlights the potential for exquisite multimodal control of mechanical functions of cells with future applications in synthetic biology and precision medicine.
    Keywords:  Boolean gates; DNA origami; caging/uncaging; mesoscale; metastasis; nanospring
    DOI:  https://doi.org/10.1021/acsnano.4c16194
  8. ACS Nano. 2025 Feb 20.
    Bioinspired Materials for Controlling Mineral Adhesion: From Innovation Design to Diverse Applications.
    Wei Chen, Jingxin Meng, Shutao Wang.
      The advancement of controllable mineral adhesion materials has significantly impacted various sectors, including industrial production, energy utilization, biomedicine, construction engineering, food safety, and environmental management. Natural biological materials exhibit distinctive and controllable adhesion properties that inspire the design of artificial systems for controlling mineral adhesion. In recent decades, researchers have sought to create bioinspired materials that effectively regulate mineral adhesion, significantly accelerating the development of functional materials across various emerging fields. Herein, we review recent advances in bioinspired materials for controlling mineral adhesion, including bioinspired mineralized materials and bioinspired antiscaling materials. First, a systematic overview of biological materials that exhibit controllable mineral adhesion in nature is provided. Then, the mechanism of mineral adhesion and the latest adhesion characterization between minerals and material surfaces are introduced. Later, the latest advances in bioinspired materials designed for controlling mineral adhesion are presented, ranging from the molecular level to micro/nanostructures, including bioinspired mineralized materials and bioinspired antiscaling materials. Additionally, recent applications of these bioinspired materials in emerging fields are discussed, such as industrial production, energy utilization, biomedicine, construction engineering, and environmental management, highlighting their roles in promoting or inhibiting aspects. Finally, we summarize the ongoing challenges and offer a perspective on the future of this charming field.
    Keywords:  antiscaling materials; bioinspired materials; biomineralization; controlled adhesion; inhibiting adhesion; mineral adhesion; mineralized materials; promoting adhesion
    DOI:  https://doi.org/10.1021/acsnano.4c16946
  9. Nat Commun. 2025 Feb 21. 16(1): 1861
    Bio-inspired electronics: Soft, biohybrid, and "living" neural interfaces.
    Dimitris Boufidis, Raghav Garg, Eugenia Angelopoulos, D Kacy Cullen, Flavia Vitale.
      Neural interface technologies are increasingly evolving towards bio-inspired approaches to enhance integration and long-term functionality. Recent strategies merge soft materials with tissue engineering to realize biologically-active and/or cell-containing living layers at the tissue-device interface that enable seamless biointegration and novel cell-mediated therapeutic opportunities. This review maps the field of bio-inspired electronics and discusses key recent developments in tissue-like and regenerative bioelectronics, from soft biomaterials and surface-functionalized bioactive coatings to cell-containing 'biohybrid' and 'all-living' interfaces. We define and contextualize key terminology in this emerging field and highlight how biological and living components can bridge the gap to clinical translation.
    DOI:  https://doi.org/10.1038/s41467-025-57016-0
  10. bioRxiv. 2025 Jan 28. pii: 2025.01.28.635345. [Epub ahead of print]
    Split-Small GTPase Reassembly as a Method to Control Cellular Signaling with User-Defined Inputs.
    Yuchen He, Benjamin M Faulkner, Emily Hyun, Cliff I Stains.
      Small GTPases are critical signaling enzymes that control diverse cellular functions such as cell migration and proliferation. However, dissecting the roles of these enzymes in cellular signaling is hindered by the lack of a plug-and-play methodology for the direct, temporal control of small GTPase activity using user-defined inputs. Herein, we present a method that pairs split-GTPases with user-defined chemical inducer of dimerization (CID) systems in a plug-and-play manner to directly control small GTPase signaling in living cells. The modularity of split-small GTPase systems allows for the selection of CIDs with minimal off-target effects on the pathway being studied. Our results highlight the ability to obtain consistent pathway activation with varying CID systems for direct control of MAPK signaling, filopodia formation, and cell retraction. Thus, split-small GTPase systems provide a customizable platform for development of temporally gated systems for directly controlling cellular signaling with user-defined inputs.
    DOI:  https://doi.org/10.1101/2025.01.28.635345
  11. Mater Horiz. 2025 Feb 17.
    Micromechanical finite element modeling of crystalline lipid-based materials: monoglyceride-based oleogels and their composites.
    Patrick Grahn, Petri Lassila, Fabio Valoppi.
      The mechanical properties of crystalline lipid-based materials are dependent on the microscale structure formed during the crystallization process. In this work, we show for the first time that the mechanical properties of such materials can be mathematically calculated by performing 3D mechanistic modeling on the exact microstructure obtained by non-destructive imaging. Initially, we obtained a digital twin of a monoglyceride-based oleogel from phase-contrast X-ray tomography. The microstructure was found to be composed of an interconnected network of crystalline platelets. Then, we applied micromechanical finite element modeling on the microstructure, which revealed that the effective shear modulus scales with the local solid fraction and also depends on the precise crystalline arrangement. Lastly, we designed composite materials in a digital environment by adding particle inclusions to the digital twin. The particle material, concentration and size are varied to demonstrate their effect on the composite's mechanical properties. The designed materials reveal that particle inclusions can either decrease or greatly increase the shear modulus of lipid-based materials. Our new micromechanical approach accelerates the design of lipid-based materials by leveraging virtual environments, leading the path towards materials with tailored mechanical properties.
    DOI:  https://doi.org/10.1039/d4mh01891e
  12. Nat Synth. 2025 ;4(2): 156-166
    An engineered aldolase enables the biocatalytic synthesis of 2'-functionalized nucleoside analogues.
    Matthew Willmott, William Finnigan, William R Birmingham, Sasha R Derrington, Rachel S Heath, Christian Schnepel, Martin A Hayes, Peter D Smith, Francesco Falcioni, Nicholas J Turner.
      Nucleosides functionalized at the 2'-position play a crucial role in therapeutics, serving as both small-molecule drugs and modifications in therapeutic oligonucleotides. However, the synthesis of these molecules often presents substantial synthetic challenges. Here we present an approach to the synthesis of 2'-functionalized nucleosides based on enzymes from the purine nucleoside salvage pathway. Initially, active-site variants of deoxyribose-5-phosphate aldolase were generated for the highly stereoselective synthesis of d-ribose-5-phosphate analogues with a broad range of functional groups at the 2-position. Thereafter, these 2-modified pentose phosphates were converted into 2'-modified purine analogues by construction of one-pot multienzyme cascade reactions, leading to the synthesis of guanosine (2'-OH) and adenosine (2'-OH, 2'-Me, 2'-F) analogues. This cascade allows for the control of the 2'-functional group alongside 2-stereochemistry. Our findings demonstrate the capability of these biocatalytic cascades to efficiently generate 2'-functionalized nucleosides, starting from simple starting materials.
    Keywords:  Biocatalysis; Synthetic chemistry methodology
    DOI:  https://doi.org/10.1038/s44160-024-00671-w
  13. Cell. 2025 Feb 11. pii: S0092-8674(25)00105-9. [Epub ahead of print]
    Contextual computation by competitive protein dimerization networks.
    Jacob Parres-Gold, Matthew Levine, Benjamin Emert, Andrew Stuart, Michael B Elowitz.
      Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations in which the concentrations of monomer inputs determine the concentrations of dimer outputs. Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks of 3-6 monomers are expressive, performing diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough, can perform nearly all potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing.
    Keywords:  biological computation; competitive dimerization; computational expressivity; computational modeling; protein-protein interaction networks
    DOI:  https://doi.org/10.1016/j.cell.2025.01.036
  14. ACS Omega. 2025 Feb 11. 10(5): 4548-4560
    Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria.
    Humbeline Paupelin-Vaucelle, Claire Boschiero, Christine Lazennec-Schurdevin, Emmanuelle Schmitt, Yves Mechulam, Philippe Marlière, Valérie Pezo.
      We report the construction of an alternative protein priming system to recode genetic translation in Escherichia coli by designing, through trial and error, a chimeric initiator whose sequence identity points partly to elongator tRNACys and partly to initiator tRNAf Met. The elaboration of a selection based on the N-terminal cysteine imperative for the function of glucosamine-6-phosphate synthase, an essential enzyme in bacterial cell wall synthesis, was a crucial step to achieve the engineering of this Cys-tRNAj. Iterative improvement of successive versions of Cys-tRNAj was corroborated in vitro by using a biochemical luciferase assay and in vivo by selecting for translation priming of E. coli thymidylate synthase. Condensation assays using specific fluorescent reagent FITC-Gly-cyanobenzothiazole provided biochemical evidence of cysteine coding at the protein priming stage. We showed that translation can be initiated, by N-terminal incorporation of cysteine, at a codon other than UGC by expressing a tRNAj with the corresponding anticodon. The optimized tRNAj is now available to recode the priming of an arbitrary subset of proteins in the bacterial proteome with absolute control of their expression and to evolve the use of xenonucleotides and the emergence of a tXNAj in vivo.
    DOI:  https://doi.org/10.1021/acsomega.4c08326
  15. Acc Chem Res. 2025 Feb 15.
    Generalizable Molecular Switch Designs for In Vivo Continuous Biosensing.
    Jason Saunders, Ian A P Thompson, Hyongsok Tom Soh.
      ConspectusContinuous biosensors have the potential to transform medicine, enabling healthcare to be more preventative and personalized as compared to the current standard of reactive diagnostics. Realizing this transformative potential requires biosensors that can function continuously in vivo without sample preparation and deliver molecular specificity, sensitivity, and high temporal resolution. Molecular switches stand out as a promising solution for creating such sensors for the continuous detection of many different types of molecules. Molecular switches are target-binding receptors designed such that binding causes a conformational change in the switch's structure. This structure switching induces a measurable signal change via reporters incorporated into the molecular switch, enabling highly specific, label-free sensing. However, there remains an outstanding need for generalizable switch designs that can be adapted for the detection of a wide range of molecular targets.In this Account, we chronicle the work our lab has done to develop generalizable molecular switch designs that allow more rapid development of high-performance biosensors across a broad range of biomarkers. Pioneering efforts toward molecular switch-based biosensing have employed aptamers─nucleic acid-based receptors with sequence-specific target affinity. However, most of these early demonstrations relied upon aptamers with intrinsic structure-switching capabilities. To accelerate aptamer switch design for more targets, we have applied rational design and knowledge of an aptamer's structure to engineer switching functionality into pre-existing aptamers. Our designs contained several structural parameters that enabled us to easily tune the sensitivity and binding kinetics of the resulting switches. Using such rationally designed aptamer switches, we demonstrated continuous optical detection of cortisol and dopamine at physiologically relevant concentrations in complex media. In an effort to move beyond aptamers with well-characterized structural properties, we developed a high-throughput screening method that allowed us to simultaneously screen millions of candidates derived from a single aptamer to find sensitive switches without any prior structural knowledge of the parent aptamer.In subsequent work, we reasoned that we could enhance our ability to design a broader range of biosensors by leveraging other classes of receptors besides aptamers. Antibodies offer excellent affinity and specificity for a wide range of targets, but lack the capacity for intrinsic structure switching. We therefore developed a set of strategies to augment antibodies with the capacity to act as molecular switches with a diverse range of target-binding properties. We combined both the high binding affinity of an antibody with the structure-switching capabilities of an aptamer to develop a chimeric switch with 100-fold enhanced sensitivity for a protein target and improved function in interferent-rich samples. In a second design, we developed a competitive immunoassay-inspired scheme to engineer switching behavior into an antibody for minutes-scale temporal resolution with nanomolar sensitivity. We used this competitive antibody-switch to demonstrate the first continuous detection of cortisol directly in whole blood. Together, these advances in molecular switch development have expanded our capability to rapidly engineer new continuous biosensors, thereby increasing opportunities to track health via a wide range of biomarkers to deliver more personalized and preventative medicine.
    DOI:  https://doi.org/10.1021/acs.accounts.4c00721
  16. Curr Opin Biotechnol. 2025 Feb 19. pii: S0958-1669(25)00012-6. [Epub ahead of print]92 103268
    Bacterial microcompartment architectures as biomaterials for conversion of gaseous substrates.
    Samuel N Snyder, Yali Wang, Matthew E Dwyer, Daipayan Sarkar, Cheryl A Kerfeld.
      Bacterial microcompartments (BMCs) are protein shells encapsulating multiple enzymes of a metabolic pathway. Interpretations of early experiments on carboxysomes led to the narrative that transport of small gases (CO2, O2) across the shell membrane is restricted. Since then, this notion has been largely contradicted by studies of engineered shells, although these shell constructs lack important proteins present in the native BMCs, altering the synthetic shells' topology, surface and mechanical properties. We discuss here an updated model of gas permeability that informs the design of engineered shells for catalysis on gas substrates and outline how nonshell suprastructures of BMC shell proteins could be used in formulating sustainable biomaterials for hydrogen generation via methane pyrolysis and for other greenhouse gas mitigations.
    DOI:  https://doi.org/10.1016/j.copbio.2025.103268
  17. Nature. 2025 Feb;638(8051): 848-850
    Why is it so hard to rewrite a genome?
    Michael Eisenstein.
      
    Keywords:  Biological techniques; Genomics; Synthetic biology; Technology
    DOI:  https://doi.org/10.1038/d41586-025-00462-z
  18. Proc Natl Acad Sci U S A. 2025 Feb 25. 122(8): e2415927122
    Mussel-inspired cross-linking mechanisms enhance gelation and adhesion of multifunctional mucin-derived hydrogels.
    George D Degen, Corey A Stevens, Gerardo Cárcamo-Oyarce, Jake Song, Raju Bej, Peng Tang, Katharina Ribbeck, Rainer Haag, Gareth H McKinley.
      Mucus supports human health by hydrating, lubricating, and preventing infection of wet epithelial surfaces. The beneficial material properties and bioactivity of mucus stem from glycoproteins called mucins, motivating the development of mucin-derived hydrogels for wound dressings and antifouling coatings. However, these applications require robust gelation and adhesion to a wide range of substrates. Inspired by the chemical cross-linking and water-tolerant adhesion of marine mussel adhesive structures, we use catechol-thiol bonding to drive gelation of native mucin proteins and synthetic mucin-inspired polymers, forming soft, adhesive hydrogels that can be coated onto diverse surfaces. The gelation dynamics and adhesive properties can be systematically tuned by varying the hydrogel composition, polymer architecture, and thiol availability, with gelation timescales adjustable from seconds to hours, and values of elastic modulus, failure stress, and debonding work spanning orders of magnitude. We demonstrate the functionality of these gels in two applications: as tissue adhesives, using porcine skin as a proxy for human skin, and as bioactive surface coatings to prevent bacterial colonization. The results highlight the potential of catechol-thiol cross-linking as a versatile platform for engineering multifunctional glycoprotein hydrogels with applications in wound repair and antimicrobial surface engineering.
    Keywords:  antifouling; biomaterials; catechol-thiol bond; mucus; tissue adhesive
    DOI:  https://doi.org/10.1073/pnas.2415927122
  19. ACS Appl Mater Interfaces. 2025 Feb 18.
    Microfluidic 3D Bioprinting of Foamed Fibers with Controlled Micromorphology.
    Federico Serpe, Francesco Nalin, Maria Celeste Tirelli, Pasquale Posabella, Nehar Celikkin, Jakub Jaroszewicz, Wojciech Święszkowski, Andrea Barbetta, Efsun Şentürk, Carlo Massimo Casciola, Giancarlo Ruocco, Gianluca Cidonio, Chiara Scognamiglio, Marco Costantini.
      The synergistic integration of microfluidic technologies with additive manufacturing systems is advancing the development of innovative platforms to 3D bioprint scaffolds for tissue engineering with unparalleled biological relevance. Significant interest is growing in realizing porous functionally graded materials (pFGMs) that can resemble the hierarchical organization of porosity found in bone tissue. This study introduces a method for fabricating porous scaffolds based on the real-time generation of a liquid foam, which is gelled, forming porous fibers that are organized into structured matrixes using a 3D bioprinting system. The primary advantage of this approach is the possibility to adjust bubble size during printing dynamically, modifying the characteristics of the deposited foamed filaments online and in one step. As a result, locally-defined and tailor-made pores can be distributed in 3D structures with high spatial accuracy. Besides the mechanical and morphological characterization of diverse microarchitectures, we also explored the biocompatibility of the proposed approach by directly embedding osteosarcoma cells within the biomaterial. Results demonstrated the biocompatibility of the proposed methodology and revealed the influence of the interior microporosity on cell proliferation, highlighting the potential for creating tailored tissue microenvironments. The findings underscore the versatility of the presented 3D bioprinting system and its potential in fabricating biomimetic scaffolds with tailored morphological gradients, representing a substantial advancement in pFGM synthesis, with direct implications in regenerative medicine and tissue engineering.
    Keywords:  3D bioprinting; foam; gradient; microfluidic; porous functionally graded materials; printhead
    DOI:  https://doi.org/10.1021/acsami.4c22450
  20. Nat Commun. 2025 Feb 19. 16(1): 1599
    Spatio-temporal control of mitosis using light via a Plk1 inhibitor caged for activity and cellular permeability.
    Victoria von Glasenapp, Ana C Almeida, Dalu Chang, Ivana Gasic, Nicolas Winssinger, Monica Gotta.
      The ability to control the activity of kinases spatially and temporally is essential to elucidate the role of signalling pathways in development and physiology. Progress in this direction has been hampered by the lack of tools to manipulate kinase activity in a highly controlled manner in vivo. Here we report a strategy to modify BI2536, the well characterized inhibitor of the conserved and essential mitotic kinase Polo-like kinase 1 (Plk1). We introduce the same coumarin photolabile protecting group (PPG) at two positions of the inhibitor. At one position, the coumarin prevents the interaction with Plk1, at the second it masks an added carboxylic acid, important for cellular retention. Exposure to light results in removal of both PPGs, leading to the activation of the inhibitor and its trapping inside cells. We demonstrate the efficacy of the caged inhibitor in three-dimensional spheroid cultures: by uncaging it with a single light pulse, we can inhibit Plk1 and arrest cell division, a highly dynamic process, with spatio-temporal control. Our design can be applied to other small molecules, providing a solution to control their activity in living cells with unprecedented precision.
    DOI:  https://doi.org/10.1038/s41467-025-56746-5
  21. ACS Appl Mater Interfaces. 2025 Feb 19.
    Biodegradable Chitosan-Based Stretchable Electronics with Recyclable Silver Nanowires.
    Mesbah Ahmad, Darpan Shukla, Yong Zhu, Orlin D Velev.
      The combination of biodegradability and biocompatibility makes chitosan a principal bioresourced material in biomedical engineering, wearable technology, and medical diagnostics, particularly for integration in human interfaces for soft electronic applications. However, this requires the introduction of soft electronic circuits with the capability of recycling the functional materials, while biodegrading the substrate. This paper presents the development and characterization of biodegradable soft circuits that are constructed using stretchable and flexible substrates from plasticized chitosan and conductive functional wiring from recyclable silver nanowires (AgNWs). The chitosan substrate demonstrates tunable mechanical properties with a maximum stretchability of ∼116%, in addition to desirable characteristics such as transparency, breathability, and controlled degradation. The plasticizing effect of glycerol reduces the rigidity associated with pure chitosan and imparts flexibility and stretchability to the AgNW-chitosan-glycerol (AgNW-Chi-Gly) composite. The AgNWs embedded in the Chi-Gly matrix are highly conductive, and their functionality in soft electronic devices such as strain sensors and electromyography (EMG) sensors is demonstrated. We show that the soft chitosan-based substrates can be subject to biodegradation at the end of their operational lifespan. The AgNWs can be recycled and reused, enhancing the overall sustainability of such soft electronic devices.
    Keywords:  biodegradable electronics; chitosan films; silver nanowires; soft circuits; stretchable electronics; sustainable electronic materials; wearable sensors
    DOI:  https://doi.org/10.1021/acsami.4c20193
  22. Nat Biotechnol. 2025 Feb 18.
    Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage.
    Zachary R Baker, Yao Zhang, Haiyan Zhang, Hollyn C Franklin, Priscila B S Serpa, Teresa Southard, Liwu Li, Bryan B Hsu.
      Oral administration of biologic drugs is challenging because of the degradative activity of the upper gastrointestinal tract. Strategies that use engineered microbes to produce biologics in the lower gastrointestinal tract are limited by competition with resident commensal bacteria. Here we demonstrate the engineering of bacteriophage (phage) that infect resident commensals to express heterologous proteins released during cell lysis. Working with the virulent T4 phage, which targets resident, nonpathogenic Escherichia coli, we first identify T4-specific promoters with maximal protein expression and minimal impact on T4 phage titers. We engineer T4 phage to express a serine protease inhibitor of a pro-inflammatory enzyme with increased activity in ulcerative colitis and observe reduced enzyme activity in a mouse model of colitis. We also apply the approach to reduce weight gain and inflammation in mouse models of diet-induced obesity. This work highlights an application of virulent phages in the mammalian gut as engineerable vectors to release therapeutics from resident gut bacteria.
    DOI:  https://doi.org/10.1038/s41587-025-02570-7
  23. Nat Methods. 2025 Feb 18.
    Oblique line scan illumination enables expansive, accurate and sensitive single-protein measurements in solution and in living cells.
    Amine Driouchi, Mason Bretan, Brynmor J Davis, Alec Heckert, Markus Seeger, Maité Bradley Silva, William S R Forrest, Jessica Hsiung, Jiongyi Tan, Hongli Yang, David T McSwiggen, Linda Song, Askhay Sule, Behnam Abaie, Hanzhe Chen, Bryant Chhun, Brianna Conroy, Liam A Elliott, Eric Gonzalez, Fedor Ilkov, Joshua Isaacs, George Labaria, Michelle Lagana, DeLaine D Larsen, Brian Margolin, Mai K Nguyen, Eugene Park, Jeremy Rine, Yangzhong Tang, Martin Vana, Andrew Wilkey, Zhengjian Zhang, Stephen Basham, Jaclyn J Ho, Stephanie Johnson, Aaron A Klammer, Kevin Lin, Xavier Darzacq, Eric Betzig, Russell T Berman, Daniel J Anderson.
      An ideal tool for the study of cellular biology would enable the measure of molecular activity nondestructively within living cells. Single-molecule localization microscopy (SMLM) techniques, such as single-molecule tracking (SMT), enable in situ measurements in cells but have historically been limited by a necessary tradeoff between spatiotemporal resolution and throughput. Here we address these limitations using oblique line scan (OLS), a robust single-objective light-sheet-based illumination and detection modality that achieves nanoscale spatial resolution and sub-millisecond temporal resolution across a large field of view. We show that OLS can be used to capture protein motion up to 14 μm2 s-1 in living cells. We further extend the utility of OLS with in-solution SMT for single-molecule measurement of ligand-protein interactions and disruption of protein-protein interactions using purified proteins. We illustrate the versatility of OLS by showcasing two-color SMT, STORM and single-molecule fluorescence recovery after photobleaching. OLS paves the way for robust, high-throughput, single-molecule investigations of protein function required for basic research, drug screening and systems biology studies.
    DOI:  https://doi.org/10.1038/s41592-025-02594-6
  24. Phys Rev E. 2025 Jan;111(1-2): 015502
    Charge density on fracture surfaces and contact electrification of identical materials.
    Toshihiko Kadono, Kazunori Ogawa, Kei Shirai, Hideyuki Kobayashi.
      Contact electrification of identical materials happens during collisions, rubbing, and mixing of granular materials. Fractures often accompany these processes, and the resulting fracture surfaces are typically charged. Based on visible-light and X-ray observations of fracture, we demonstrate that the charge density on fracture surfaces of organic and inorganic materials is consistent with those observed in collisions, rubbing, and mixing. This indicates that fractures involve contact electrification of identical materials.
    DOI:  https://doi.org/10.1103/PhysRevE.111.015502
  25. bioRxiv. 2025 Jan 29. pii: 2025.01.28.635392. [Epub ahead of print]
    Multiplex mapping of protein-protein interaction interfaces.
    Jingxuan He, Ling-Nan Zou, Vidhi Pareek, Stephen J Benkovic.
      We describe peptide mapping through Sp lit A ntibiotic R esistance C omplementation (SpARC-map), a method to identify the probable interface between two interacting proteins. Our method is based on in vivo affinity selection inside a bacterial host, and uses high throughput DNA sequencing results to infer the location of protein-protein interaction (PPI) interfaces. SpARC-map uses only routine microbiology techniques, with no reliance on specialized instrumentation or reconstituting protein complexes in vitro; it can be tuned to detect PPIs over a broad range of affinities; it can be multiplexed to probe multiple PPIs in parallel; its nonspecific background can be precisely measured, enabling the sensitive detection of weak PPIs. Using SpARC-map, we recover the known interface in the (p21-PCNA complex. We also use SpARC-map to probe the purinosome, the weakly bound complex of six purine biosynthetic enzymes, where no PPI interfaces are known. There, we identify interfaces that satisfy structural requirements for substrate channeling; we also identify protein surfaces that participate in multiple distinct interactions, which we validate using site-specific photocrosslinking in live human cells. Finally, we show that SpARC-map results can impose stringent constraints on outputs from machine learning based structure prediction.
    DOI:  https://doi.org/10.1101/2025.01.28.635392
  26. Nat Commun. 2025 Feb 20. 16(1): 1823
    Coarse-grained fundamental forms for characterizing isometries of trapezoid-based origami metamaterials.
    James P McInerney, Diego Misseroni, D Zeb Rocklin, Glaucio H Paulino, Xiaoming Mao.
      Investigations of origami tessellations as effective media reveal the ability to program the components of their elasticity tensor, and thus control the mechanical behavior of thin sheets. However, existing efforts focus on crease patterns that are composed of parallelogram faces where the parallel lines constrain the quasi-static elastic response. In this work, crease patterns composed of more general trapezoid faces are considered and their low-energy linear response is explored. Deformations of such origami tessellations are modeled as linear isometries that do not stretch individual panels at the small scale yet map to non-isometric changes of coarse-grained fundamental forms that quantify how the effective medium strains and curves at the large scale. Two distinct mode shapes, a rigid breathing mode and a nonrigid shearing mode, are identified in the continuum model. A specific example, which we refer to as Arc-Morph origami, is presented with analytical expressions for its deformations in both the discrete and continuous models. A developable specimen is fabricated and tested to validate the analytical predictions. This work advances the continuum modeling of origami tessellations as effective media with the incorporation of more generic faces and ground states, thereby enabling the investigation of novel designs and applications.
    DOI:  https://doi.org/10.1038/s41467-025-57089-x
  27. J Biol Chem. 2025 Feb 18. pii: S0021-9258(25)00178-4. [Epub ahead of print] 108329
    A Retropepsin-Like Bacterial Protease Regulates Ribosome Modification and Polypeptide Production.
    Richard H Little, Govind Chandra, Gerhard Saalbach, Carlo Martins, Catriona M A Thompson, Jacob G Malone.
      Adaptations to fluctuating environmental conditions require bacteria to make large scale proteomic shifts on short timescales. We previously characterised the tri-partite RimABK protein complex responsible for the post translational modification of the ribosome in response to environmental cues. Regulated control of RpsF polyglutamylation by RimK rapidly influenced the proteome of Pseudomonas fluorescens cells to facilitate colonisation of the plant rhizosphere. Here, we conduct a detailed investigation of the RimB protease. We show RimB to be a bifunctional retropepsin-like aspartic endopeptidase that uniquely recognises and removes glutamate residues from polyglutamated RpsF and stimulates poly-α-L-glutamate synthesis by RimK. We determine the minimal recognition requirements for RimB proteolysis and identify the catalytic aspartate residue required for function. Further, we identify a novel hybrid enzyme composed of RimB and RimK domains that also possesses protease activity. Phylogenetic analysis of accessions encoding either the hybrid or individual RimB and RimK proteins reveals a pattern of rim gene evolution that is distinct from that of the host organisms and reveals potential alternative targets of RimB.
    Keywords:  Aspartic peptidase; Poly-α-L-glutamate; Pseudomonas; Retropepsin protease; Ribosomal modification
    DOI:  https://doi.org/10.1016/j.jbc.2025.108329
  28. Biophys Physicobiol. 2024 ;21(4): e210022
    Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves.
    Sakura Takada, Kei Fujiwara.
      Intracellular positional information is crucial for the precise control of biological phenomena, including cell division, polarity, and motility. Intracellular reaction-diffusion (iRD) waves are responsible for regulating positional information within cells as morphogens in multicellular tissues. However, iRD waves are explained by the coupling of biochemical reactions and molecular diffusion which indicates nonlinear systems under far from equilibrium conditions. Because of this complexity, experiments using defined elements rather than living cells containing endogenous factors are necessary to elucidate their pattern formation mechanisms. In this review, we summarize the effectiveness of artificial cell systems for investigating iRD waves derived from their high controllability and ability to emulate cell-size space effects. We describe how artificial cell systems reveal the characteristics of iRD waves, including the mechanisms of wave generation, mode selection, and period regulation. Furthermore, we introduce remaining open questions and discuss future challenges even in Min waves and in applying artificial cell systems to various iRD waves.
    Keywords:  bottom-up synthetic biology; cell polarity; reconstitution; spatiotemporal pattern; synthetic cell
    DOI:  https://doi.org/10.2142/biophysico.bppb-v21.0022
  29. Biotechnol Adv. 2025 Feb 13. pii: S0734-9750(25)00017-5. [Epub ahead of print] 108531
    Alpha ketoacid decarboxylases: Diversity, structures, reaction mechanisms, and applications for biomanufacturing of platform chemicals and fuels.
    Khanh Ha, Seunghyun Ryu, Cong T Trinh.
      In living cells, alpha ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Finally, we discuss recent development in the modular cell engineering technology that can be potentially applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.
    Keywords:  Alcohols; Aldehydes; Alpha-ketoacid decarboxylase; Aromatic pathway; Biomanufacturing; C1 substrates; CO(2); Carboxylic acids; Consolidated bioprocessing; Esters; Lignocellulosic biomass; Methane; Modular cell engineering; Modular cells; One‑carbon recursive elongation pathway; Organic wastes
    DOI:  https://doi.org/10.1016/j.biotechadv.2025.108531
  30. Nature. 2025 Feb 20.
    Snapshots of acyl carrier protein shuttling in human fatty acid synthase.
    Kollin Schultz, Pedro Costa-Pinheiro, Lauren Gardner, Laura V Pinheiro, Julio Ramirez-Solis, Sarah M Gardner, Kathryn E Wellen, Ronen Marmorstein.
      The mammalian fatty acid synthase (FASN) enzyme is a dynamic multienzyme that belongs to the megasynthase family. In mammals, a single gene encodes six catalytically active domains and a flexibly tethered acyl carrier protein (ACP) domain that shuttles intermediates between active sites for fatty acid biosynthesis1. FASN is an essential enzyme in mammalian development through the role that fatty acids have in membrane formation, energy storage, cell signalling and protein modifications. Thus, FASN is a promising target for treatment of a large variety of diseases including cancer, metabolic dysfunction-associated fatty liver disease, and viral and parasite infections2,3. The multi-faceted mechanism of FASN and the dynamic nature of the protein, in particular of the ACP, have made it challenging to understand at the molecular level. Here we report cryo-electron microscopy structures of human FASN in a multitude of conformational states with NADPH and NADP+ plus acetoacetyl-CoA present, including structures with the ACP stalled at the dehydratase (DH) and enoyl-reductase (ER) domains. We show that FASN activity in vitro and de novo lipogenesis in cells is inhibited by mutations at the ACP-DH and ACP-ER interfaces. Together, these studies provide new molecular insights into the dynamic nature of FASN and the ACP shuttling mechanism, with implications for developing improved FASN-targeted therapeutics.
    DOI:  https://doi.org/10.1038/s41586-025-08587-x
  31. bioRxiv. 2025 Jan 31. pii: 2025.01.31.635883. [Epub ahead of print]
    Proteomic Ligandability Maps of Phosphorus(V) Stereoprobes Identify Covalent TLCD1 Inhibitors.
    Hayden A Sharma, Michael Bielecki, Meredith A Holm, Ty M Thompson, Yue Yin, Jacob B Cravatt, Timothy B Ware, Alex Reed, Molham Nassir, Tamara El-Hayek Ewing, Bruno Melillo, J Fernando Bazan, Phil S Baran, Benjamin F Cravatt.
      Activity-based protein profiling (ABPP) of stereoisomerically defined sets of electrophilic compounds ('stereoprobes') offers a versatile way to discover covalent ligands for proteins in native biological systems. Here we report the synthesis and chemical proteomic characterization of stereoprobes bearing a P(V)-oxathiaphospholane (OTP) reactive group. ABPP experiments identified numerous proteins in human cancer cells that showed stereoselective reactivity with OTP stereoprobes, and we confirmed several of these liganding events with recombinant proteins. OTP stereoprobes engaging the poorly characterized transmembrane protein TLCD1 impaired the incorporation of monounsaturated fatty acids into phosphatidylethanolamine lipids in cells, a lipidomic phenotype that mirrored genetic disruption of this protein. Using AlphaFold2, we found that TLCD1 structurally resembles the ceramide synthase and fatty acid elongase families of coenzyme A-dependent lipid processing enzymes. This structural similarity included conservation of catalytic histidine residues, the mutation of which blocked the OTP stereoprobe reactivity and lipid remodeling activity of recombinant TLCD1. Taken together, these data indicate that TLCD1 acts as a lipid acyltransferase in cells, and that OTP stereoprobes function as inhibitors of this enzymatic activity. Our findings thus illuminate how the chemical proteomic analysis of electrophilic compounds can facilitate the functional annotation and chemical inhibition of a key lipid metabolic enzyme in human cells.
    DOI:  https://doi.org/10.1101/2025.01.31.635883
  32. Annu Rev Phys Chem. 2025 Feb 14.
    Flow of Energy and Information in Molecular Machines.
    Matthew P Leighton, David A Sivak.
      Molecular machines transduce free energy between different forms throughout all living organisms. Unlike their macroscopic counterparts, molecular machines are characterized by stochastic fluctuations, overdamped dynamics, and soft components, and operate far from thermodynamic equilibrium. In addition, information is a relevant free energy resource for molecular machines, leading to new modes of operation for nanoscale engines. Toward the objective of engineering synthetic nanomachines, an important goal is to understand how molecular machines transduce free energy to perform their functions in biological systems. In this review, we discuss the nonequilibrium thermodynamics of free energy transduction within molecular machines, with a focus on quantifying energy and information flows between their components. We review results from theory, modeling, and inference from experiments that shed light on the internal thermodynamics of molecular machines, and ultimately explore what we can learn from considering these interactions.
    DOI:  https://doi.org/10.1146/annurev-physchem-082423-030023
  33. bioRxiv. 2025 Jan 31. pii: 2025.01.30.635804. [Epub ahead of print]
    Emergence of binding and catalysis from a designed generalist binding protein.
    Yuda Chen, Sagar Bhattacharya, Lena Bergmann, Galen J Correy, Sophia Tan, Kaipeng Hou, Justin Biel, Lei Lu, Ian Bakanas, Nicholas F Polizzi, James S Fraser, William F DeGrado.
      The evolution of proteins that bind to small molecules and catalyze chemical transformations played a central role in the emergence of life. While natural proteins have finely tuned affinity for their primary ligands, they also often have weak affinities for other molecules. These interactions serve as starting points for the evolution of new specificities and functions. Inspired by this concept, we determined the ability of a simple de novo protein to bind a set of diverse small molecules (< 300 Da) by crystallographic fragment screening. We then used this information to design one variant that binds fluorogenic molecule and another that acts as a highly efficient Kemp eliminase enzyme. Collectively, our work illuminates how the evolution of novel protein functions can emerge from existing proteins.
    DOI:  https://doi.org/10.1101/2025.01.30.635804
  34. Chem Bio Eng. 2024 Dec 26. 1(11): 887-915
    Hydrogel-Based Strategies for Liver Tissue Engineering.
    Yu Zhang, Luofei Li, Liang Dong, Yuanqi Cheng, Xiaoyu Huang, Bin Xue, Chunping Jiang, Yi Cao, Jiapeng Yang.
      The liver's role in metabolism, detoxification, and immune regulation underscores the urgency of addressing liver diseases, which claim millions of lives annually. Due to donor shortages in liver transplantation, liver tissue engineering (LTE) offers a promising alternative. Hydrogels, with their biocompatibility and ability to mimic the liver's extracellular matrix (ECM), support cell survival and function in LTE. This review analyzes recent advances in hydrogel-based strategies for LTE, including decellularized liver tissue hydrogels, natural polymer-based hydrogels, and synthetic polymer-based hydrogels. These materials are ideal for in vitro cell culture and obtaining functional hepatocytes. Hydrogels' tunable properties facilitate creating artificial liver models, such as organoids, 3D bioprinting, and liver-on-a-chip technologies. These developments demonstrate hydrogels' versatility in advancing LTE's applications, including hepatotoxicity testing, liver tissue regeneration, and treating acute liver failure. This review highlights the transformative potential of hydrogels in LTE and their implications for future research and clinical practice.
    DOI:  https://doi.org/10.1021/cbe.4c00079
  35. bioRxiv. 2025 Feb 02. pii: 2025.01.28.635095. [Epub ahead of print]
    Interparticle Crosslinked Ion-responsive Microgels for 3D and 4D (Bio)printing Applications.
    Vaibhav Pal, Deepak Gupta, Suihong Liu, Ilayda Namli, Syed Hasan Askari Rizvi, Yasar Ozer Yilmaz, Logan Haugh, Ethan Michael Gerhard, Ibrahim T Ozbolat.
      Microgels offer unique advantages over bulk hydrogels due to their improved diffusion limits for oxygen and nutrients. Particularly, stimuli-responsive microgels with inherently bioactive and self-supporting properties emerge as highly promising biomaterials. This study unveils the development of interparticle-crosslinked, self-supporting, ion-responsive microgels tailored for 3D and 4D (bio)printing applications. A novel strategy was proposed to develop microgels that enabled interparticle crosslinking, eliminating the need for filler hydrogels and preserving essential microscale void spaces to support cell migration and vascularization. Additionally, these microgels possessed unique, ion-responsive shrinking behavior primarily by the Hofmeister effect, reversible upon the removal of the stimulus. Two types of microgels, spherical (µS) and random-shaped (µR), were fabricated, with µR exhibiting superior mechanical properties and higher packing density. Fabricated microgel-based constructs supported angiogenesis with tunable vessel size based on interstitial void spaces while demonstrating excellent shear-thinning and self-healing properties and high print fidelity. Various bioprinting techniques were employed and validated using these microgels, including extrusion-based, embedded, intraembedded, and aspiration-assisted bioprinting, facilitating the biofabrication of scalable constructs. Multi-material 4D printing was achieved by combining ion-responsive microgels with non-responsive microgels, enabling programmable shape transformations upon exposure to ionic solutions. Utilizing 4D printing, complex, dynamic structures were generated such as coiling filaments, grippers, and folding sheets, providing a foundation for the development of advanced tissue models and devices for regenerative medicine and soft robotics, respectively.
    DOI:  https://doi.org/10.1101/2025.01.28.635095
  36. Nat Mater. 2025 Feb 21.
    Origins of elasticity in molecular materials.
    Amy J Thompson, Bowie S K Chong, Elise P Kenny, Jack D Evans, Joshua A Powell, Mark A Spackman, John C McMurtrie, Benjamin J Powell, Jack K Clegg.
      Elasticity is ubiquitous and produces a spontaneously reversible response to applied stress1. Despite the utility and importance of this property in regard to scientific and engineering applications, the atomic-scale location of the force that returns an object to its original shape remains elusive in molecular crystals. Here we use a series of density functional theory calculations to locate precisely where the energy is stored when single crystals of three molecular materials are placed under elastic stress. We show for each material that different intermolecular interactions are responsible for the restoring force under both expansive and compressive strain. These findings provide insight into the elastic behaviour of crystalline materials that is needed for more efficient design of flexible technologies and future smart devices.
    DOI:  https://doi.org/10.1038/s41563-025-02133-w
  37. bioRxiv. 2025 Feb 08. pii: 2025.02.07.636926. [Epub ahead of print]
    Magnetic activation of electrically active cells.
    Guillaume Duret, Samantha Coffler, Ben Avant, Wonjune Kim, Angel V Peterchev, Jacob Robinson.
      Magnetic control of cell activity has applications ranging from non-invasive neurostimulation to remote activation of cell-based therapies. Unlike other methods of regulating cell activity like heat and light, which are based on known receptors or proteins, no magnetically gated channel has been identified to date. As a result, effective approaches for magnetic control of cell activity are based on strong alternating magnetic fields able to induce electric fields or materials that convert magnetic energy into electrical, thermal, or mechanical energy to stimulate cells. In our investigations of magnetic cell responses, we found that a spiking HEK cell line with no other co-factors responds to a magnetic field that reaches a maximum of 500 mT within 200 ms using a permanent magnet. The response is rare, approximately 1 in 50 cells, but is fast and reproducible, generating an action potential within 200 ms of magnetic field stimulation. The magnetic field stimulation is over 10,000 times slower than the magnetic fields used in transcranial magnetic stimulation (TMS) and the induced electric field is more than an order of magnitude lower than necessary for neuromodulation, suggesting that induced electric currents do not drive the cell response. Instead, our calculation suggests that this response depends on mechanoreception pathways activated by the magnetic torque of TRP-associated lipid rafts. Despite the relatively rare response to magnetic stimulation, when cells form gap junctions, the magnetic stimulation can propagate to nearby cells, causing tissue-level responses. As an example, we co-cultured spiking HEK cells with beta-pancreatic MIN6 cells and found that this co-culture responds to magnetic fields by increasing insulin production. Together, these results point toward a method for the magnetic control of biological activity without the need for a material co-factor such as synthetic nanoparticles. By better understanding this mechanism and enriching for magneto-sensitivity it may be possible to adapt this approach to the rapidly expanding tool kit for wireless cell activity regulation.
    DOI:  https://doi.org/10.1101/2025.02.07.636926
  38. FEMS Yeast Res. 2025 Feb 19. pii: foaf007. [Epub ahead of print]
    Characterizing heterologous protein burden in Komagataella phaffii.
    Louise La Barbera Kastberg, Irene Hjorth Jacobsen, Emre Özdemir, Christopher T Workman, Michael Krogh Jensen, Jochen Förster.
      Yeast is a widely utilized chassis for heterologous protein production, with Komagataella phaffii well-established as a prominent non-conventional yeast in this field. Despite its widespread recognition, there remains considerable potential to further optimize these cell factories to meet high production demands in a cost-effective and sustainable manner. Understanding the cellular response to the challenges of heterologous protein production can equip genetic engineers with crucial knowledge to develop enhanced strategies for constructing more efficient cell factories. In this study, we explore the molecular response of various K. phaffii strains that produce either the human insulin precursor or Mambalgin-1, examining changes in transcription and changes in intra- and extracellular protein levels. Our findings provide valuable insights into the molecular mechanisms that regulate the behaviour of K. phaffii production strains under the stress of producing different heterologous proteins. We believe that these results will serve as a foundation for identifying new genetic targets to improve strain robustness and productivity. In conclusion, we present new cellular and molecular insights into the response of K. phaffii cell factories to the challenges of burdensome heterologous protein production and our findings point to different engineering strategies for improved cell factory performance.
    Keywords:   Komagataella phaffii ; Burden; Continuous cultivation; Heterologous protein production; Omics
    DOI:  https://doi.org/10.1093/femsyr/foaf007
  39. J Colloid Interface Sci. 2025 Feb 10. pii: S0021-9797(25)00406-0. [Epub ahead of print]687 189-196
    Conductive hydrophobic graphene oxide films via laser-scribed surface modification.
    Henry Apsey, Donald Hill, Thomas M McCoy, Marcos Villeda-Hernandez, Charl F J Faul, Shirin Alexander.
      Graphene oxide (GO) can be surface modified for various purposes, including enhancing its properties or tailoring its behaviour for specific applications such as biosensing. Herein we report the behaviour of a carboxylate functionalized graphene oxide that is both water repellent and electrically conductive. The GO is first produced using a modified Hummers method and then functionalized with a hyperbranched isostearic alcohol through an esterification reaction. The as-deposited functionalized GO films were observed to cause "petal-like" wetting of water, whereby droplets exhibited contact angles (CAs) greater than 150° and remaining pinned to the surface. To improve their conductivity, films of the functionalized GO deposited onto glass were laser-scribed to reduce some of the specific, adjoining regions of oxidic carbon to partially restore some of the sp2 C network. This improved the conductivity of the as-deposited GO films by approximately four orders of magnitude from 0.002 to ∼20 S/m using the low laser scan speed of 250 mm/min. It was observed that with a high laser scan speed of 500 mm/min some of the hydrophobic character was retained (CAs ∼110°), whilst maintaining conductivities of up to 0.17 S/m. Consequently, these materials show promise for applications such as biosensing materials, where tuneable hydrophobicity combined with conductivity are required characteristics.
    Keywords:  Biosensors; Carbon materials; Conductive; Water-repellent; Waterproof; Wearable electronics; Wettability
    DOI:  https://doi.org/10.1016/j.jcis.2025.02.055
  40. ACS Biomater Sci Eng. 2025 Feb 18.
    Single-Step Fabrication of V-Shaped Polymeric Microwells to Enhance Cancer Spheroid Formation.
    Omar M Rahman, Roberto Tarantino, Stephen D Waldman, Dae Kun Hwang.
      Traditional cancer research has long relied on two-dimensional (2D) cell cultures, which inadequately mimic the complex three-dimensional (3D) microenvironments of in vivo tumors. Recent advancements in 3D cell cultures, particularly cancer spheroids, have highlighted their superior physiological relevance. However, existing methods for spheroid generation often require complex, multistep fabrication processes that limit scalability and reproducibility. In this study, we present a novel single-step photolithographic technique to fabricate high-aspect-ratio V-slanted hydrogel microwells. By employing polyethylene glycol (PEG)-based hydrogels, we create biocompatible, extracellular matrix (ECM)-like scaffolds that enhance gas and nutrient exchange while promoting uniform spheroid formation. The hydrogel microwells allow precise control of spheroid size, achieving a physiologically relevant diameter of 425 μm within 12-24 h, and the resulting spheroids exhibiting high viability over 3 weeks. Moreover, the method facilitates the creation of scalable multiwell arrays for high-throughput applications, making it suitable for both small-scale and large-scale experimental needs. This platform addresses the limitations of traditional microwell fabrication, offering a robust, efficient, and reproducible system for generating physiologically relevant 3D models with valuable applications in cancer research, drug testing, and tissue engineering.
    Keywords:  PEG hydrogels; V-slant; cancer spheroids; fabrication; high-throughput culturing; photolithography; polymeric microwells
    DOI:  https://doi.org/10.1021/acsbiomaterials.4c02359
  41. ACS Appl Bio Mater. 2025 Feb 20.
    Antibacterial Polymers Based on Two Orthogonal Binding Motifs Coalesce with Bacterial Matter.
    Esteban Bautista, Eduardo Estrada, Jacob Deyell, Melody Sun, Albert R La Spada, Seunghyun Sim.
      Addressing the growing concern about antibiotic-resistant bacteria, we have developed a series of polymers exhibiting intrinsic antibacterial activities with a dual-targeting system that induces physical lysis upon copolymer coalescence with bacterial matter. These polymers are equipped with two orthogonal binding motifs that form electrostatic interactions and dynamic covalent complexes on bacterial surfaces and exhibit potent antibacterial activity against Gram-positive and Gram-negative bacteria. The effect of the chemical composition and architecture of copolymers incorporating phenylboronic acid and quaternary ammonium groups on the antimicrobial activities was systematically examined. This work expands the current chemical repertoire to combat antimicrobial resistance by intrinsically antibacterial polymers with a unique mode of action.
    Keywords:  antibacterial polymers; antimicrobial polymers; bactericidal activity; copolymers; self-assembly
    DOI:  https://doi.org/10.1021/acsabm.4c01872
  42. ACS Appl Mater Interfaces. 2025 Feb 21.
    Redefining Metal Organic Frameworks in Biosensors: Where Are We Now?
    Melisa Wei Ning Leoi, Xin Ting Zheng, Yong Yu, Jiajia Gao, Deborah Hui Shan Ong, Clarence Zhi Han Koh, Peng Chen, Le Yang.
      As a broad class of porous nanomaterials, metal organic frameworks (MOFs) exhibit unique properties, such as broad tunability, high stability, atomically well-defined structure, and ordered uniform porosity. These features facilitate the rational design of MOFs as an outstanding nanomaterial candidate in biosensing, therapeutics delivery, and catalysis applications. Recently, novel modifications of the MOF nanoarchitecture and incorporation of synergistic guest materials have been investigated to achieve well-tailored functional design, gradually bridging the fundamental gap between structure and targeted activity. Specifically, the burgeoning studies of MOF-based high-performance biosensors have aimed to achieve high sensitivity, selectivity, and stability for a large variety of analytes in different sensing matrices. In this review, we elaborate the key roles of MOF nanomaterials in biosensors, including their high stability as a protective framework for biomolecules, their intrinsic sensitivity-enhancing functionalities, and their contribution of catalytic activity as a nanozyme. By examining the main structures of MOFs, we further identify varied structural engineering approaches, such as precursor tuning and guest molecule incorporation, that elucidate the concept of the structure-activity relationship of MOFs. Furthermore, we highlight the unique applications of MOF nanomaterials in electrochemical and optical biosensors for enhanced sensor performances. Finally, the challenges and future perspectives of developing next-generation MOF nanomaterials for biosensor applications are discussed.
    Keywords:  MOF composites; biosensors; electrochemical sensors; enzymes; metal organic frameworks (MOFs); nanomaterials; nanozymes; optical sensors; structural engineering
    DOI:  https://doi.org/10.1021/acsami.4c19307
  43. ACS Synth Biol. 2025 Feb 20.
    Liposome-Encapsulated Escherichia coli Lysates to Reconstitute Intracellular Macromolecular Crowding Effects.
    Milara S Kalacheva, Nuno R da Silva, Arnold J Boersma.
      Intracellular macromolecular crowding impacts biomacromolecule behavior, including oligomerization, phase separation, and diffusion. However, understanding crowding effects in cells is challenging as cells respond and adapt to perturbations. Therefore, replicating in-cell crowding in liposomes would provide a good alternative to studying the consequences of macromolecular crowding. Here, we achieve physiological macromolecular crowding levels using Escherichia coli lysates in liposomes, as verified with a macromolecular crowding sensor. We shrink liposomes with a gradient-wise osmotic upshift to reach the high macromolecular crowding effects. We see that lysate induces higher macromolecular crowding than BSA at the same mg/mL, showing the need to use lysates to replicate in-cell behavior. We study the consequences of small cosolutes on macromolecular crowding and see that sugars and ATP modulate the lysate macromolecular crowding, implying they would also affect macromolecular crowding in cells. These artificial cells display the same crowding as E. coli at 220-300 mg/mL lysate and the same crowding as HEK293T at 50-100 mg/mL lysate. Hence, these artificial cells are a platform for obtaining information on physiologically relevant macromolecular crowding effects in a controlled environment.
    Keywords:  FRET sensor; cosolutes; giant unilamellar vesicles; hyperosmotic stress; lysate; macromolecular crowding
    DOI:  https://doi.org/10.1021/acssynbio.4c00824
  44. Nat Commun. 2025 Feb 16. 16(1): 1689
    Two dimensional MoS2 accelerates mechanically controlled polymerization and remodeling of hydrogel.
    Jian Wang, Zhijun Han, Longfei Zhang, Ran Ding, Chengqiang Ding, Kai Chen, Zhao Wang.
      Self-remodeling material can change their physical properties based on mechanical environment. Recently, mechanically controlled polymerization using mechanoredox catalyst enabled composite materials to undergo a permanent structural change, thereby enhancing their mechanical strength. However, a significant delay in material's response was observed due to the sluggish activation of the bulk catalyst for polymerization. Herein, we report a fast, mechanically controlled radical polymerization of water soluble monomers using 2D MoS2 as the mechanoredox catalyst, studied under various mechanical stimuli, including ultrasound, ball milling and low frequency vibrations. Our strategy enables complete polymerization within several minutes of work. This accelerated process can be utilized to create composite hydrogels with the ability to alter their mechanical and electrical properties in response to mechanical stimuli. This strategy has potential for applications in smart materials such as hydrogel sensors, artificial muscles, and implantable biomaterials.
    DOI:  https://doi.org/10.1038/s41467-025-57068-2
  45. bioRxiv. 2025 Feb 08. pii: 2025.02.03.635951. [Epub ahead of print]
    A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.
    Anna S Monzel, Jack Devine, Darshana Kapri, Jose Antonio Enriquez, Caroline Trumpff, Martin Picard.
      Mitochondria are a diverse family of organelles that specialize to accomplish complimentary functions 1-3 . All mitochondria share general features, but not all mitochondria are created equal 4 .Here we develop a quantitative pipeline to define the degree of molecular specialization among different mitochondrial phenotypes - or mitotypes . By distilling hundreds of validated mitochondrial genes/proteins into 149 biologically interpretable MitoPathway scores (MitoCarta 3.0 5 ) the simple mitotyping pipeline allows investigators to quantify and interpret mitochondrial diversity and plasticity from transcriptomics or proteomics data across a variety of natural and experimental contexts. We show that mouse and human multi-organ mitotypes segregate along two main axes of mitochondrial specialization, contrasting anabolic (liver) and catabolic (brain) tissues. In cultured primary human fibroblasts exhibiting robust time-dependent and treatment-induced metabolic plasticity 6-8 , we demonstrate how the mitotype of a given cell type recalibrates i) over time in parallel with hallmarks of aging, and ii) in response to genetic, pharmacological, and metabolic perturbations. Investigators can now use MitotypeExplorer.org and the associated code to visualize, quantify and interpret the multivariate space of mitochondrial biology.
    DOI:  https://doi.org/10.1101/2025.02.03.635951
  46. Trends Biotechnol. 2025 Feb 20. pii: S0167-7799(25)00040-X. [Epub ahead of print]
    Framing synthetic biology as an innovation-driven market.
    Jerome A Ramirez, Madeline Rose Smith, Robert E Speight, Ian O'Hara.
      Synthetic biology can create knowledge and tools that enable products with attributes that fit into a sustainable bioeconomy. The specialised synthetic biology market is often conflated with the broader enabled products market. Here, we propose a framework of the synthetic biology market for a common understanding of its commercial potential.
    Keywords:  bioeconomy; enabled products; markets; platforms; synthetic biology
    DOI:  https://doi.org/10.1016/j.tibtech.2025.02.003
  47. ACS Sens. 2025 Feb 17.
    Genetically Encoded Single-Wavelength Sensor with High Specificity for Imaging ATP in Living Cells.
    Lu Xiao, Xuexi Wang, Dujuan Liu, Chuang Yan, Xian-En Zhang, Minghai Chen.
      Adenosine 5'-triphosphate (ATP) plays an essential role in regulating many metabolic activities. Therefore, developing tools to directly measure ATP in real time will help us understand its underlying functions. Here, we report an optimized genetically encoded ATP sensor (OAS1.0) with a high specificity for ATP detection. OAS1.0 can be genetically targeted to specific cell types and subcellular compartments to monitor ATP production and consumption. We also used OAS1.0 to visualize metabolic-activity-dependent changes in ATP in normal and tumor cell lines and ATP consumption during the virus-host interaction process. OAS1.0 also worked well with a Ca2+ sensor to concurrently monitor ATP and Ca2+ dynamics in living cells. Thus, OAS1.0 represents a promising tool for ATP imaging under both physiological and pathophysiological conditions.
    Keywords:  ATP sensor; genetically encoded; high specificity; living cells; single wavelength
    DOI:  https://doi.org/10.1021/acssensors.4c03389
  48. Biomacromolecules. 2025 Feb 18.
    The Biology of Natural Polymers Accelerates and Expands the Science of Biomacromolecules: A Focus on Structural Proteins.
    Keiji Numata.
      This Perspective explores the use of biomacromolecules in natural materials synthesized by living organisms, such as spider silk, in the development of sustainable synthetic materials. Currently employed synthetic polymers lack the hierarchical complexity and unique properties of natural materials composed of biomacromolecules. By understanding the composition of these natural materials, it may be able to reproduce their properties synthetically. Additionally, research directions involving the use of renewable resources such as nitrogen and carbon dioxide from the air and seawater to develop biomacromolecules such as spider silk and biopolyester via photosynthetic organisms are reviewed. Next-generation biomacromolecule research will aid in the creation of a sustainable global society, advancing fields such as biomanufacturing, agriculture, aquaculture, and other industries.
    DOI:  https://doi.org/10.1021/acs.biomac.4c01621
  49. bioRxiv. 2025 Feb 05. pii: 2025.01.31.635926. [Epub ahead of print]
    Scaling in Biological Systems: A Molecular-Ensemble Duality.
    Julie A Ellsworth, Josh E Baker.
      We have observed in muscle the statistical mechanics of irreversible chemical thermodynamics, revealing the solution to multiple seemingly unrelated paradoxes in science. Analogous to Boltzmann's H theorem, we observe that chemical reaction energy landscapes (ensemble entropic wells) irreversibly evolve over time, pulling reversible chemical reactions forward in time. Loschmidt's paradox assumes that reversible molecular reactions scale up to irreversible changes in an ensemble, and many mathematical constructs have been created to satisfy this assumption (Boltzmann's H-function, chemical activities, the kinetics theory of gases, molecular mechanisms of biological function, etc.). However, using a simple statistical argument, here we show that the irreversible time evolutions of molecular and ensemble states are described by two different non-scalable entropies, creating a molecular-ensemble duality in any system on any scale. This inverts common understandings of mechanistic agency and the arrow of time and disproves all molecular mechanisms of irreversible ensemble processes.
    Significance Statemen: This statistical analysis inverts common understandings of mechanistic agency, entropy, and the arrow of time; it solves several paradoxes in physics; and it disproves molecular mechanisms of irreversible processes.
    DOI:  https://doi.org/10.1101/2025.01.31.635926
This page is being maintained by Thomas Krichel. It was last updated on 2025‒02‒23 at 9:25.