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Threshold Ramsey multiplicity for paths and even cycles
No full textThe Ramsey number r(H) of a graph H is the minimum integer such that any two-coloring of the edges of the complete graph Kₙ contains a monochromatic copy of H. While this definition only asks for a single monochromatic copy of H, it is often the case that every two-edge-coloring of the complete graph on r(H) vertices contains many monochromatic copies of H. The minimum number of such copies over all two-colorings of K_(r(H)) will be referred to as the threshold Ramsey multiplicity of H. Addressing a problem of Harary and Prins, who were the first to systematically study this quantity, we show that there is a positive constant c such that the threshold Ramsey multiplicity of a path or an even cycle on k vertices is at least (ck)ᵏ. This bound is tight up to the constant c. We prove a similar result for odd cycles in a companion paper
Tryptophan-96 in cytochrome P450 BM3 plays a key role in enzyme survival
No full textFlavocytochrome P450 from Bacillus megaterium (P450_(BM3)) is a natural fusion protein containing reductase and hame domains. In the presence of NADPH and dioxygen the enzyme catalyses the hydroxylation of long-chain fatty acids. Analysis of the P450BM3 structure reveals chains of closely spaced tryptophan and tyrosine residues that might serve as pathways for high-potential oxidizing equivalents to escape from the hame active site when substrate oxidation is not possible. Our investigations of the total number of enzyme turnovers before deactivation have revealed that replacement of selected tryptophan and tyrosine residues with redox inactive groups leads to a twofold reduction in enzyme survival time. Tryptophan-96 is critical for prolonging enzyme activity, suggesting a key protective role for this residue
Optical-resolution photoacoustic microscopy with a needle-shaped beam
No full textOptical-resolution photoacoustic microscopy can visualize wavelength-dependent optical absorption at the cellular level. However, this technique suffers from a limited depth of field due to the tight focus of the optical excitation beam, making it challenging to acquire high-resolution images of samples with uneven surfaces or high-quality volumetric images without z scanning. To overcome this limitation, we propose needle-shaped beam photoacoustic microscopy, which can extend the depth of field to around a 28-fold Rayleigh length via customized diffractive optical elements. These diffractive optical elements generate a needle-shaped beam with a well-maintained beam diameter, a uniform axial intensity distribution and negligible sidelobes. The advantage of using needle-shaped beam photoacoustic microscopy is demonstrated via both histology-like imaging of fresh slide-free organs using a 266 nm laser and in vivo mouse-brain vasculature imaging using a 532 nm laser. This approach provides new perspectives for slide-free intraoperative pathological imaging and in vivo organ-level imaging
Topics in Shear Flow (version 2.0)
No full textUnfinished manuscript left by Donald Coles at his death in May of 2013.
From the author's draft preface:
The fundamental premise for the book is that the only reliable information about turbulent flow is experimental information. This varies greatly in quality and completeness, and needs to be carefully screened. Some additional premises will be self-evident in the text. First, it is advisable to understand thoroughly the laminar version of a particular flow, because some conceptual problems are not peculiar to turbulent flow; e.g., the third boundary condition for the mixing layer, or the integral invariant for the wall jet. Second, the most powerful organizing principle so far available for both laminar and turbulent flow is the principle of similarity. Third, the most important phenomenological concept for many turbulent flows is the concept of entrainment. The need of the user is often likely to be for hard numbers and practical insights, rather than for elegance. I have therefore made some use of mixing-length and eddy-viscosity ideas, and even power-law methods, as primitive links between fundamental and technical problems.
Each chapter of the book deals with one of the classical shear flows (mixing layers, jets, plumes, wakes, boundary layers, pipe flow, and so on ) and with its ramifications, or with an important technical problem such as flow management. Wherever possible, the presentation is intended to suggest how various flow problems might be connected analytically and experimentally one to another, using as far as possible a consistent notation and a consistent level of rigor and detail.
Version 2.0 adds a number of missing or newly discovered figures in Chapters 1, 2, 4, 8, and Appendix A. A significant section on similarity laws for turbulent flow, previously missing from Chapter 4, has been recovered and added. A reconstructed list of References Consulted is now available as a separate document
Metasurface‐Enabled Holographic Lithography for Impact‐Absorbing Nano‐Architected Sheets
No full textNano-architected materials represent a class of structural meta-materials that utilze nanoscale features to achieve unconventional material properties such as ultra-low density and high energy absorption. A dearth of fabrication methods capable of producing architected materials with sub-micron resolution over large areas in a scalable manner exists. We present a fabrication technique that employs holographic patterns generated by laser exposure of phase metasurface masks in negative-tone photoresists to produce 30 to 40 micrometer thick nano-architected sheets with 2.1 x 2.4 cm² lateral dimensions and approximately 500 nm wide struts organized in layered 3D brick-and-mortar-like patterns to result in approximately 50 to 70% porosity. Nanoindentation arrays over the entire sample area reveal the out-of-plane elastic modulus to vary between 300 MPa and 4 GPa, with irrecoverable post-elastic material deformation commencing via individual nano-strut buckling, densification within layers, shearing along perturbation perimeter, and tensile cracking. Laser induced particle impact tests (LIPIT) indicate specific inelastic energy dissipation of 0.51-2.61 MJ kg⁻¹, which is comparable to other high-impact energy absorbing composites and nanomaterials, such as Kevlar/polyvinyl butyral (PVB) composite, polystyrene, and pyrolized carbon nanolattices with 23% relative density. These results demonstrate that holographic lithography offers a promising platform for scalable manufacturing of nano-architected materials with impact resistant capabilities
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome
No full text‘Candidatus Methanophagales’ (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus–host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, ‘Candidatus Methanospirareceae’, closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems
Neuromorphic Engineering: In Memory of Misha Mahowald
No full textAbstract
We review the coevolution of hardware and software dedicated to neuromorphic systems. From modest beginnings, these disciplines have become central to the larger field of computation. In the process, their biological foundations become more relevant, and their realizations increasingly overlap. We identify opportunities for significant steps forward in both the near and more distant future
Nanoparticle size and surface chemistry effects on mechanical and physical properties of nano-reinforced polymers: The case of PVDF-Fe₃O₄ nano-composites
No full textIn the present work, PVDF - Fe₃O₄ nanoparticle (NP) nanocomposite films were produced using the electrospinning method. We investigated the effect of NP size on the film's morphology (fiber size), mechanical properties, and physical properties (β-phase percentage). Surprisingly, while nanoparticle size acts as an enhancer for mechanical properties, it appeared to act as an inhibitor in terms of its effects on the crystallization of the β-polymorph. This result seemed in discordance with many previous results. A focus on local interactions between the NP surface chemistry and PVDF chains revealed the influence of grafted ligands at the nanoparticle surface on the crystallization of the piezoelectric phase of PVDF. The results from the molecular dynamics (MD) simulations for systems of PVDF chains with slabs of –OH and oleic acid-grafted magnetite, showed that the probability of beta phase configuration decreases when the nanoparticles are functionalized with oleic acid and becomes more probable for –OH terminated magnetite. These computational results are in accordance with our experimental results. To verify this hypothesis, we prepared films with washed nanoparticles to eliminate the excess oleic acid that acts as a β-polymorph inhibitor. As a result, the amount of β-phase obtained for washed nanoparticles increased and the difference in the amount of β-phase between the different samples decreased. Moreover, when heated, the films of nanocomposite with washed NP developed more β-phase for smaller sizes of nanoparticles. At 140 °C, isomerization occurred, and oleic acid was converted into elaidic acid, reducing the steric hindrance, and promoting the interaction between PVDF chains and the surface of the nanoparticles. This isomerization reaction seems to be an enhancer of the α- to β-phase transition. Our results prove that optimizing multiple properties in nano-reinforced polymers requires consideration of different aspects, such as NP size, surface chemistry, and processing methods.
Our results based on mixed experimental and modeling approach proved the usefulness of simulation in understanding and guiding our experimental results. Our results suggest that for enhancing piezoelectric properties in PVDF magnetite nano-composites, the chemistry and the molecular morphology of the grafted ligands when combined with NP size could lead to multi-properties enhancement simultaneously
Value restructures the organization of free recall
No full textA large body of research illustrates the prioritization of goal-relevant information in memory; however, it is unclear how reward-related memories are organized. Using a rewarded free recall paradigm, we investigated how reward motivation structures the organization of memory around temporal and higher-order contexts. To better understand these processes, we simulated our findings using a reward-modulated variant of the Context Maintenance and Retrieval Model (CMR; Polyn et al., 2009). In the first study, we found that reward did not influence temporal clustering, but instead shifted the organization of memory based on reward category. Further, we showed that a reward-modulated learning rate and source features of CMR most accurately depict reward's enhancement on memory and clustering by value. In a second study, we showed that reward-memory effects can exist in both extended periods of sustained motivation and frequent changes in motivation, by showing equivalent reward effects using mixed- and pure-list motivation manipulations. However, we showed that a reward-modulated learning rate in isolation can support reward's enhancement of memory in pure-list contexts. Overall, we conclude that reward-related memories are adaptively organized by higher-order value information, and contextual binding to value contexts may only be necessary when rewards are intermittent versus sustained
Triage of the Gaia DR3 astrometric orbits – I. A sample of binaries with probable compact companions
No full textIn preparation for the release of the astrometric orbits of Gaia, Shahaf et al. (2019) proposed a triage technique to identify astrometric binaries with compact companions based on their astrometric semimajor axis, parallax, and primary mass. The technique requires the knowledge of the appropriate mass–luminosity relation to rule out single or close-binary main-sequence companions. The recent publication of the Gaia DR3 astrometric orbits used a schematic version of this approach, identifying 735 astrometric binaries that might have compact companions. In this communication, we return to the triage of the DR3 astrometric binaries with more careful analysis, estimating the probability for its astrometric secondary to be a compact object or a main-sequence close binary. We compile a sample of 177 systems with highly probable non-luminous massive companions, which is smaller but cleaner than the sample reported in Gaia DR3. The new sample includes eight candidates to be black-hole systems with compact-object masses larger than 2.4 M_⊙. The orbital–eccentricity–secondary–mass diagram of the other 169 systems suggests a tentative separation between the white-dwarf and the neutron-star binaries. Most white-dwarf binaries are characterized by small eccentricities of about 0.1 and masses of 0.6 M⊙, while the neutron star binaries display typical eccentricities of 0.4 and masses of 1.3 M_⊙